****************************************************************************** From: Olivier Plaut Date: Mon, 05 Jan 2004 12:51:40 +0100 Subject: Re: Agilent filaments Organization: * I was told by an Agilent tech that they received bad batches... The tech told me to put new filaments in methanol and to sonicate them before mounting. Olivier Gun Blomkvist a écrit : } We have been using an Agilent 5973 instrument for about two years, } mainly for analysis of organohalogens with NCI/methane. Earlier this } year we began experiencing problems with the filaments; shortly after } installation of a new filament, sensitivity started to decrease } rapidly and we found that the filament was bent. As this has been } repeated several times, it seems that Agilent's production methods } have changed somehow. } Two questions: } 1) Has anybody else had the same problem? } 2) We have found that older batches of filaments, part no. } G.1099-80053, batch no beginning with 0, work well. Does anybody have } one or more of these and is willing to part with them? } } Regards, } Gun ****************************************************************************** From: Thomas Frenzel Date: 5 Jan 2004 05:15:30 -0800 Subject: handbook on high resolution mass spectrometry Organization: * Does anybody know a comprehensive textbook covering theory and application of high resolution mass spectrometry by means of magnetic sector field instruments? Thank you for your help. Thomas ****************************************************************************** From: John M Roman Date: 5 Jan 2004 10:32:23 -0800 Subject: Re: gcms methods Organization: * Becky: Try this reference for glucose analysis by gc/ms: MG Kienle, et al, Journal of Chrom.,Biomedia Applications, 573(1992)127-131, "Determination of plasma[6,6-2H2) glucose by GC/MS" I've been quantitating glucose in plasma and serum by gc/ms since 1998. I'm measuring deuterated(2-H2) to non-deuterated (0-H2)ratios. In this paper they measure m/z187 and 189. I'm using m/z 217 and 219. I receive my samples as methanolic/water solutions. Transfer the samples to glass vials, evaporate under N2, add ~1-2mg hydroxylamine HCl + 100uL pyridine; cap, vortex, heat 30mins @ 90 deg C; uncap, add ~100uL actic anhydride, cap, vortex, heat 30mins @ 90 deg C; uncap, quantitative transfer to autosmpler vial with acetonitrile; adjust to final volume, gc/ms. John M.Roman MS Lab SAIC-Frederick NCI-Frederick PO Box B Frederick, MD 21702 ****************************************************************************** From: David Sparkman Date: Mon, 5 Jan 2004 11:20:02 -0800 Subject: Re: handbook on high resolution mass spectrometry Organization: * Thomas, I assume you mean double-focusing mass spectrometers. I never likes that sector field terminology. both the electric sector and the magnetic field are fields and sectors. JEOL (http://www.jeol.com) has some good information under the Essays/Tutorial section. The book by John Roboz written in the 1968 is a very good source. This book has been reprinted by ASMS. Regards; David "Thomas Frenzel" wrote in message news:btbsnc$qqs$1@news-int2.gatech.edu... } } Does anybody know a comprehensive textbook covering theory and } application of high resolution mass spectrometry by means of magnetic } sector field instruments? } } Thank you for your help. } } Thomas } ****************************************************************************** From: Kjell Mortier Date: Tue, 6 Jan 2004 17:42:29 +0100 Subject: zero air or nitrogen in LC-MS ionization Organization: * A question concerning installation of LC-MS/MS API4000. We have to choose between using zero grade air and nitrogen as nebulizer and auxillary gas for an API (applied biosystems) instrument with the turbo V source. Does anyone has some experience if this can effect the ionization of your compound (electrospray or APCI). Does the oxygen has an effect on the ionization? Why would you prefer the one or the other gas, aside from costs? According to the pre-installation guide, both gases work fine, but the people from AB would advize zero grade air. This would be an additional cost for us, so we prefer nitrogen (very pure grade). thanks for any comments ****************************************************************************** From: Michael Sherrell Date: Mon, 12 Jan 2004 21:23:12 -0800 Subject: Seqs, synths, mass specs/MALDIs, liquid handlers available Organization: * Grizzly Analytical: Sequencers, synthesizers, mass specs, MALDIs, liquid handlers, cytometers etc. for sale New engineering development, service and retail facility: 377 Oyster Pt Blvd #11, South San Francisco CA 94080 **Oligosynthesizers: ABI 3900: $75,000. 90-day parts & labor warranty. (3900 parts: independent sources; savings over list prices.) Expedite 8909: $14,500. Includes M.O.S.S, rebuilt w/ new ABI valves, 90-day warranty. + $3,500/trityl. ABI 394: $14,200. Rebuilt; 90-day warranty. ABI 394: $19,900. Trityl, MAC, rebuilt: about as good as the new 3400. ABI 392: $12,200. Rebuilt; 90-day warranty. ABI 3948: $25,000. Rebuilt/installed w/ 90-day warranty. ABI 390Z: $11,000. Rebuilt/warranteed. (Oligosynthesis reagents, ~75% off list: Oxidizer, Cap A, Cap B, Activator, Deblock, amadites, + 8909 columns) Beckman 1000M: $11,000. Excellent condition; guaranteed. CyClone: $7,500. New-in-box; 90 day parts warranty. Similar to ABI 392. Biosearch 8700: $10,000. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. BioSearch 8750: $10,500. Rebuilt; Phoenix upgrade (>35% efficiency gain), 90-day warr. Biosearch 8700: $8,000. Rebuilt; 90-day warr. + $2K/Windows. BioSearch 8750. ~$4,000. Have 5; cheaper & faster than 394s. Cruachem PS250. <=$2,500. 6 available. *High throughput synthesizers: BLP 192: $125,000. 2 plates, 8 min. cycle time. New; incl. install + 1 yr. warr. Polygen 10. Call if interested. Polyplex Gene Machine: $89,000. Installed/warranteed. **Oligosequencers: ABI 3100: $90,000. Includes factory install, software license. ABI 310: $28,000. Mac. Includes factory install; guar. eligible for service. ABI 310: $31,000. PC. Includes factory install; guar. eligible for service. ABI 3700: $75,000. Includes factory install; guar. eligible for service. ABI 3700: $19,000. From major genome center; beautifully maintained. MegaBace 4000: Offers considered. Have three; currently under mfr. svc contract. MegaBace 1000: $22,000. Incl. installation by manufacturer. ABI 377: $15,500. 96-lane; install factory incl., eligible for service. (Also suitable for tiling.). Genescan: $5,000. Licensed software for the 377, 310 or 373. ABI 373 stretch: $9,000. Big Dye upgrade. Pharmacia ALF Express: $14,000, incl. 90-day parts & labor warr. Visible Genetics: $20,000. Unused. Have 3. LiCor 4200: $25,000. Incl. Global Upgrade; guaranteed installable. LiCor 4000LS <: $20,000. 1994 model; can have Global Upgrade. Genomyx LR: $2,500. Boots; many accessories. MJ Basestation 51. Call for pricing. No robotic loading, 2 years old, under service contract. MJ Research BaseStation: $105,000. 2 yrs old; still under svc. contract. MJ Research BaseStation: $125,000. 6 mos. old; still under svc. contract. **Real-time PCR: ABI 7700: $34,000. Installed/warranteed. BioRad iCycler: $32,000. 90-day warranty. **Peptide synthesizers: ABI 433: $33,000. Original, ABI-supportible 433. These come and go; call/email to reserve. 90-day warr. ABI 433: $24,000. Upgraded from 431. We support. Rebuilt, 90-day warr. ABI 431: $16,000. Rebuilt, 90-day warr. ABI 430: $10,500. Rebuilt, 90-day warranty. ABI 432: $15,000. Rebuilt, 90-day warranty. Capriccio 1: $65,000. New instrument. Benchtop, large scale; faster and more efficient than ACT 400. Incl. install, 1 yr svc. PerSeptive 9500: $12,750. Rebuilt w/ 90-day warranty. PerSeptive 9050: $16,000. Rebuilt w/ 90-day warranty. CS Bio 336. ~$27,000. 6 mos old; lease default. 3 peps simultaneous; .05-.25 mmol. ACT LabTech III: $15,000. 30-day warranty. Pioneer: $40,000. Includes factory install, eligible for svc. contract MPS unit for the Pioneer peptide synthesizer: $5,000. New and unused; price = 25% of new cost. ACT 396 MPS: $42,000. Factory refurb; includes 120-day warranty. PerSeptive 9600: $13,750. Rebuilt, warranteed. ACT Vantage: $79,000. Excellent condition. ACT 357-MPS. Call for pricing. ACT 90: $16,250. Only used twice. Incl. install; guar. eligible for svc. Argonaut Quest 205: $27,000. ASW model. Argonaut Quest 210: $19,000. ASW model. **Peptide sequencers: ABI 494 HT: $55,000. Installed, guaranteed ok for service contract. ABI 494 cLc. Offers considered. ABI 492: $20,000 installed, eligible for service contract. Beckman 6300. Various prices. Have several; can rebuild or sell for parts. ABI 421: $10,000. Offers considered. ABI 477/120: $1,500. Good working order or right of return. ABI 477. Service, parts available. ABI 473/476: $15,000. Good working order; install/service available. ABI 470A: $2,000. For parts. Many extra parts. *[Note: various other ABI, HP, Millipore, Biosearch, Beckman, etc. sequencers, synthesizers etc. available; please inquire.] **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Sciex API 3000 upgrade: $35,000. HSID interface: higher sensitivity and s/n at high flow rates; comparable to API 4000. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 365: $49,000. Sciex upgraded from original 300. Incl. turboionspray, installation, guaranteed eligible for service contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex APCI source: $7,900. For API 150 or 300 or Q-Star Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $165,000. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $30,000. ES, API 1, Alpha station, good working order. +$20K/current Xcalibur, installation and 30-day warranty. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. MM Autospec M: $115,000. Mag Sector; orthogonal TOF MS/MS; 4 sources, FPD and TOF included; currently working well. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE STR. $129,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $45,000. Extensively refurbished. Voyager DE: $76,000. Incl. install. 2002 model. ABI 4700: Must sell; all offers considered. TOF/TOF MS/MS Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $275,000. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$200,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $50,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. HP G2025A LD-TOF: free for parts, you pay shipping. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. **Liquid handlers: Biomek FX (core system): $450,000 good working order. Includes 3 meter Orca, fluorometer, incubator, more. Biomek FX: $60,000. Single arm. Biomek 2000, no side loader, $49,000. Beckman Multimek, $34,000. Zymark Sciclone: 1.5 years old; $43K. Zymark Staccato system: $250,000 and up, depending on accessories, install, warranty. XP-arm based Zymarks: $10,000 and $20,000, depending on accessories. Tecan RSP-200/8 ID Robot Sample Processor, fully equipped: call/email if interested. Hamilton MicroLab AT2 Plus robot, $38,000 Packard Multiprobe 20400 and CP20400, Packard refurbed, $16,500 for either Transgenomic WAVE system, $22,000 incl. installation, eligible for svc. Quantity discounts for up to 20 units. Tecan Genesis RSP 150, no Roma, $52,000 delivered w/ 90-day warranty. Tecan Genesis RSP 100, $41,000 delivered w/ 90-day warranty. LC Packings UltiMate NanoLC system w/ FAMOS autosampler, $37,300 Scitec robotic liquid handling system, 3-meter rail, $60,000 guaranteed working Tom-Tec Quadras, various configurations, refurbished and warrantied. Hamilton Microlab 2200: call for pricing. Gilson 215: call for price. ABI 877 Catalyst Turbo: $12,000 or best offer Bio-Dot sub-microliter 8-channel aspirate/dispense system (typically 96-well microplate source, glass slide, microwell plate or membrane target), ~ 5 years old. **Other expensive hi-tech items: *NMRs: Bruker Avance 700 NMR, shielded, 2 yrs old, $1.26M new, $850K installed + ship; excl. $15K site license. Varian Inova 600 NMR: $275,000 guaranteed installable; +$25K/install. FX90Q NMR w/ Tek-Mag, $19,500. Others available; inquire if interested. *Flow cytometers: COULTER® EPICS XL-MCL^Ù: $45,000. 4 color with Multi Carousel Loader includes rebuilt, installation and one-year warranty. Coulter Epics Elite: 9 years old but never used. Call/email if interested. COULTER® EPICS XL^ÙFlow Cytometer: $45,000.00 Currently in operation. Includes XL2, EXPO and Data Mate Software, APC UPS Back-up, factory installation, and other options. FACS Vantage SE with the DIVA option: $160,500. (2 lasers: 488nm and UV tunable). Bought in June '02 and never used. BD FACSCalibur w/ FACSLoader: $84,000. 4 color. 2001; excellent condition. BD FACScan; offers considered. 3 color w/ argon laser, FITC, PE & 7 AAD BD FACSort Cell Sorter, $39,000. 3 color, MAC G3, Cellquest, install included MoFlo Analyzer with MoSkeeto System: $99,750.00. 6-channel / 5-color detector, Carvo MSP - 9000 Auto sampler, Summit 3.1 Software, Laser. Scanning Cytometer: Microscope-based. Two-laser system. $85,000 guaranteed installable. Others available; inquire if interested. *Arrayers/spotters/readers: HP/Affymetrix GeneArray G2500A system, $117,500. Complete system, factory install, guar. eligible for factory service contract. New list: $199K. Affymetrix GeneChip system: $120,000. 2003; unused. HP GeneArray G2500A reader w/ laser, $22,000, including new data system but no fluidics station. Affymetrix 417 Arrayer/spotter: seller considering rather low offers; call if interested. Affymetrix 417 Arrayer/spotter: $34,500 reconditioned with 1 year warranty HP/Affymetrix GeneArray Scanner Model G2500A, unused, $49,000. CELLOMICS ScanArray HCS: 2003 model. Factory install, license discount available; offers considered. Packard ScanArray 4000: $35,950. 2000 instrument. Incl. factory install; eligible for service contract. Packard ScanArray 3000: $17,250. Incl. factory install; eligible for service contract. Genomic Solutions GeneTAC microarray Hybridization Station: $27,000. (for details see www.genomicsolutions.com/products/bio/hyb.html) Amersham Lucidea SLIDE PRO Hybridization Station: $18,500. Ciphergen ProteinChip Reader PBS II: $65,000. Current upgrades; includes factory install, 30-day warranty. *Spot pickers: Genetix QPix2 benchtop: $79,570 installed. Incl. 96-well picking head, gridding option, etc; Q-Fill optional. Genetix QBot picker/arrayer. Call/email if interested. BioRobotics BioPick automatic colony picker. Excellent condition. ~$60,000 Genomic Solutions Flexys; much less than new price; call/email if interested. *Microscopes: ZEISS Axioskop Trinocular Microscope, $24,650 For phase contrast, DIC and Epi-Flourscence Cambridge Stereoscope S90B SEM w/ Kevex EDX: $25,000. Incl. secondary and backscattering detectors, Polaroid system, some options, factory installation. Working now. Optional one year service sontracts available. Meridian ACAS 570C LSCM. Other Laser Scanning Confocal microscopes available, call or email for list. Leica Confocal TCS-4D: $51,000. NT upgrades, 2 or 3 laser w/ DMRBE microscope bought new in 1997. Includes factory installation. Various (SEM) Scanning Electron Microscopes, $9,500-$375,000. Call or email for list. Various (TEM) Transmission Electron Microscopes, call or email for list. Various surgical, neuro surgical microscopes, call or email for list. Various optical microscopes, call or email for list. *Truly miscellaneous: Molecular Devices/LJL Biosystems Criterion Analyst HT System: $35,000. Amersham Typhoon 9410 scanner: Accepting offers. 2003 system, top condition. The first large-format gel , blot and microarray imager; also optimized for protein research. Perkin Elmer 1010M Micro Densitometer: was $325,000 new. Now in Japan. Call if interested. Amersham FARCyte/Tecan Ultra fluorescence plate reader, new in box, $50,000. List: $80K. Accutag Radio Frequency Reader/10k Automated Microreactor Sorting System, $80,000 Genevac's Mega 1200 ultra high throughput solvent evaporation system, 1.5 yrs old but unused, $200,000 or best offer. New Brunswick Bioflo 3000 bioreactor: $18,900. 10 liter; new probes; 90-day warr. Process Engineers 29 liter mammalian cell bioreactor, new/unused, ~$35,000 or best offer. *(other bioreactors/fermenters available; inquire if interested.) Cambridge Stereoscope S90B SEM w/ Kevex EDX: $10,000. Incl. secondary and backscattering detectors, Polaroid system, some options. Working now. **Too hard to classify: Li-Cor Odyssey: $25,000 ($40K new). Guaranteed good working order. See for specs. BioCAD 20s and 60s w/ 90-day warr. available for $10-15,000, depending on details. 700E also avail. ABI VISION Workstation (souped-up BioCAD; see AB website for details): offers considered. Luminex LX100 (simultaneous assay of multiple analytes): $29,000. Glycoprep 1000 automated hydrazinolysis machine: $9,000; good working order Packard Topcount 12-detector 96 well microplate scintillation counter, $35,000 Jasco FP6500 Fluorescence Spectrometer. Excellent condition. $11,500. ABI 120 HPLC, $1,500 ABI 877: have several; different configs, prices, none very expensive; call PE 9600 thermalcyclers: $3,750 w/ 90-day warranty PE 9700 96-well thermalcyclers: $5,300 w/ 90-day warranty PE 9700 384-well thermalcyclers: $5,450 w/ 1 yr. warranty PE 2400 thermalcyclers: $2,450 w/ 90-day warranty PE 480 thermalcyclers: $3,000 guaranteed working; have several Beckman P/ACE MDQ: $24,000 Beckman P/ACE 5510: $19,500. Refurbed, warranteed. MD PhosphorImager Storm 860, $30,000. MD FSI FluorImager, $15,000 MD Personal Densitometer SI -- call to discuss price MD Cytosensor, $8,750. 4 channel; virtually unused. **Service: We rebuild valve blocks for ABI 430, 431 and 39x @ $65/port, 90-day warranty Service and contracts on ABI 39n and PerSeptive 8909/8905s available. Service contracts on Hewlett Packard HPLCs, GCs and MSs available at a savings over HP rates **Also available: Agilent 1100 HPLCs, virtually all configurations/detectors. HPLCs, ICs, CEs, FPLCs: microbore to prep scale. A variety of other lab instruments. Call or check the website: www. grizzlyanalytical. com. Please call or email for more information or if you have items to sell. Michael Sherrell Grizzly Analytical (USA) www.grizzlyanalytical.com 707 887 2919/fax 707 887 9834 [All the items are subject to prior sale.] [If you do not wish to receive my emails, please return this with "Stop" in the subject line, and accept my apologies for the inconvenience.] ****************************************************************************** From: "Skorich, Steven" Subject: Library Search Glitch Date: Mon, 12 Jan 2004 18:11:53 -0600 Organization: * I am running ThermoQuest Mass Lab 1.33 nder Windows 95, with an old VG Trio-1 and HP5890. Quite suddenly, my library search function has ceased to operate. If I attempt to search a library with a query spectrum, the library function locks up the computer, and I have to reboot. I have reloaded the NIST library from CD-ROM without apparent effect on the problem. The data acquisition and instrument control functions work, the instrument calibrates. It is only the library search that causes this error. Can anyone give me some pointers on what files to look for (and where to look) to determine if files that should be there are missing? I'm reluctant to reinstall the whole system unless I absolutely must. Any help that anyone can give me will be appreciated greatly. Thanks! Steven R. Skorich Medtronic Energy and Component Center Analytical Chemistry laboratory ****************************************************************************** From: "Little, James - Eastman" Date: Sun, 18 Jan 2004 11:23:00 -0500 Subject: Interpretation of CID Spectra Organization: * We are interested in gaining expertise in the interpretation of CID spectra of relative small organic molecules (100-1000, not peptides). I am trying to justify with my management having a course taught at our laboratory. I noticed three different courses on the internet. 1. Advanced LC/MS III, Interpretation of CID Mass Spectra, Jack Henion, Cornell University 2. Advanced Interpretation of CID Mass Spectra from LC/MS,Developing a systematic methodology for Special Interpretation, Robert D. Voyksner, Ph. D., LCMS Limited 3. Interpretation of MS-MS Mass Spectra, Hyphen MassSpec Consultancy Has anyone taken any of these classes? Was the information useful in the identification of unknowns in your work? James Little Tel. No. 423-229-8685 office Tel. No. 423-229-8022 lab "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle Sailing Club (Intranet) Web Page: http://eastmanweb/fp39/ ****************************************************************************** From: Jenny Date: 21 Jan 2004 23:17:55 -0800 Subject: Contaminant peaks Organization: * I am presently trying to set up a mass spectrometer with an electrospray source to be able to run protein non-covalent complexes regularly. This requires aqueous solvents. Unfortunatly when I run water based solvents I am always seeing the following masses in my spectra. 214.09, 257.24, 315.25, 391.28, 419.28, 447.34, (Phthalates) 519.12, 593.15, 667.17, 741.20 (A series increasing in increments of 74 (C3H6O2). I think these peaks are the sodium adducts of the series, meaning the M+H masses are 497, 571, 645, 719) These peaks also have a tendency to stay in the instrument, and I need to clean the source thoroughly to get rid of them. They also charge more readily than my samples, leading to signal suppression. Can anyone identify these peaks with possible suggestions as to where they are coming from? Thanks, Jenny Mitchell PS. Is there a reference list of masses of common contaminants anywhere? ****************************************************************************** From: Tony Bristow Date: Thu, 22 Jan 2004 17:41:12 +0000 Subject: Re: Contaminant peaks Organization: * Hi Jenny With regards to a reference list of masses of common contaminants, see JASMS, 1999, 10, 1174-1187. Also, see the University of Southampton MS website at http://www.soton.ac.uk/~msweb/help.htm. Best Wishes Tony Bristow ******************************************************************* This email and any attachments are confidential. Any use, copying or disclosure other than by the intended recipient is unauthorised. If you have received this message in error, please notify the sender immediately via +44(0)20 8943 7000 or notify postmaster@lgc.co.uk and delete this message and any copies from your computer and network. LGC Limited. Registered in England 2991879. Registered office: Queens Road, Teddington, Middlesex, TW11 0LY, UK ****************************************************************************** From: David Stranz Date: Thu, 22 Jan 2004 09:33:11 -0600 Subject: Re: Contaminant peaks Organization: * Jenny wrote in news:buonhp$pjq$1@news-int.gatech.edu: } I am presently trying to set up a mass spectrometer with an } electrospray source to be able to run protein non-covalent } complexes regularly. This requires aqueous solvents. } Unfortunatly when I run water based solvents I am always seeing } the following masses in my spectra. } } 214.09, 257.24, 315.25, } } 391.28, 419.28, 447.34, } (Phthalates) } } 519.12, 593.15, 667.17, 741.20 } (A series increasing in increments of 74 (C3H6O2). I think } these peaks are the sodium adducts of the series, meaning the } M+H masses are 497, 571, 645, 719) } } These peaks also have a tendency to stay in the instrument, and } I need to clean the source thoroughly to get rid of them. They } also charge more readily than my samples, leading to signal } suppression. Can anyone identify these peaks with possible } suggestions as to where they are coming from? } } Thanks, } } Jenny Mitchell } } PS. Is there a reference list of masses of common contaminants } anywhere? } } Some links to identification of contaminants in MS spectra: http://www.iscpubs.com/articles/al/a9911kum.pdf (phthalates) http://www.proteinworks.com/contamin.htm http://prowl.rockefeller.edu/contam/contents.htm Detergents are known to cause severe signal suppression in ESI, and could also be responsible for dissolving the phthalates you're seeing. If your protein complexes are membrane-bound and you are using detergents in their isolation, that might be a source of the sodiated series you see. It might also be membrane lipids themselves. An email to Carol Robinson's group at Cambridge might get some advice on sample handling. Regards, David ****************************************************************************** From: Chip Cody Date: 23 Jan 2004 03:36:27 -0800 Subject: Re: Contaminant peaks Organization: * The m/z 214.09 is most likely to be N-butylbenzenesulfonamide (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and a contaminant that I have often seen in LC/MS and FTICR. I do not know the origin of this contamination, but I am quite certain of the identification because we have used exact mass, MS/MS, isotope ratios, etc. to identify it. Chip Cody David Stranz wrote in message news:... } Jenny wrote in } news:buonhp$pjq$1@news-int.gatech.edu: } } } I am presently trying to set up a mass spectrometer with an } } electrospray source to be able to run protein non-covalent } } complexes regularly. This requires aqueous solvents. } } Unfortunatly when I run water based solvents I am always seeing } } the following masses in my spectra. } } } } 214.09, 257.24, 315.25, } } } } ...remainder of message deleted.. ****************************************************************************** From: Eppendorf Date: Fri, 23 Jan 2004 16:59:59 GMT Subject: ICP-MS problems with Vanadium Organization: * Has anyone else seen problems with measuring V by ICP-MS? Specifically, the numbers tend to start out fine (cal verifications and QC checks) but the numbers tend to rise consistently as the run goes on. By the end of a standard ~20 sample run the numbers are way outside of QC limits. We measure V at 50.944. To make matters worse, the problem is somewhat intermittent. Sometimes (once in maybe 10 runs) it'll work just fine. I would greatly appreciate any input on this. Thanks in advance. ****************************************************************************** From: Kajjo Date: 24 Jan 2004 09:06:38 -0800 Subject: Old manuals? Varian SMS data file format for GC/MS? Organization: * Hi everyone! Does anyone know details of the SMS Varian data file format. As far as we know, old manuals contained a appendix or section describing the binary format (header, byte order etc) of the SMS files. Unfortunately, the new device came without any such description and we would like to write a program to automatically process our GC/MS data files. Any help much appreciated! Kajjo Please answer also by email to kajjo@gmx.de Thanks! ****************************************************************************** From: Giganews Date: Sat, 24 Jan 2004 15:36:42 -0600 Subject: Re: Contaminant peaks Organization: * Chip; We salso ee this ion fairly frequently. NBBS is a plasticizer used in production of some polyamides. It's reportedly neurotoxic. ....Dave Hachey "Chip Cody" wrote in message news:burbph$3c6$1@news-int.gatech.edu... } } The m/z 214.09 is most likely to be N-butylbenzenesulfonamide } (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and } a contaminant that I have often seen in LC/MS and FTICR. I do not } know the origin of this contamination, but I am quite certain of the } identification because we have used exact mass, MS/MS, isotope ratios, } etc. to identify it. } } Chip Cody } } } David Stranz wrote in message news:... } } Jenny wrote in } } news:buonhp$pjq$1@news-int.gatech.edu: } } } } } I am presently trying to set up a mass spectrometer with an } } } electrospray source to be able to run protein non-covalent } } } complexes regularly. This requires aqueous solvents. } } } Unfortunatly when I run water based solvents I am always seeing } } } the following masses in my spectra. } } } } } } 214.09, 257.24, 315.25, } } } } } } } ...remainder of message deleted.. } ****************************************************************************** From: Chip Cody Date: 26 Jan 2004 04:49:50 -0800 Subject: Re: Contaminant peaks Organization: * Thanks for the information, Dave. I have been trying to find where this could come from. We don't presently see it in our AccuTOF, but it has been a problem in the past on other machines that I have worked with. NBBS has been detected in plastic used for food wrapping -- a Google search will show you a paper from SIS about short-path thermal desorption used to detect this compound. It is frustrating to have a contamination problem that eventually goes away and we never find out where it came from. If we knew the origin (tubing, solvent containers, seals, or?), it would be easier to solve the problem. NBBS is particularly annoying because it has a high proton affinity and it can give strong signals even at low levels. In some old Nicolet FTMS systems, m/z 214 would be the only peak remaining if we trapped ions for very long times. Everything else transferred a proton to the NBBS. Chip Giganews wrote in message news:... } Chip; } } We salso ee this ion fairly frequently. NBBS is a plasticizer used in } production of some polyamides. It's reportedly neurotoxic. } } ....Dave Hachey } } } "Chip Cody" wrote in message } news:burbph$3c6$1@news-int.gatech.edu... } } } } The m/z 214.09 is most likely to be N-butylbenzenesulfonamide } } (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and } } a contaminant that I have often seen in LC/MS and FTICR. I do not } } know the origin of this contamination, but I am quite certain of the } } identification because we have used exact mass, MS/MS, isotope ratios, } } etc. to identify it. } } } } Chip Cody } } } } } } David Stranz wrote in } message news:... } } } Jenny wrote in } } } news:buonhp$pjq$1@news-int.gatech.edu: } } } } } } } I am presently trying to set up a mass spectrometer with an } } } } electrospray source to be able to run protein non-covalent } } } } complexes regularly. This requires aqueous solvents. } } } } Unfortunatly when I run water based solvents I am always seeing } } } } the following masses in my spectra. } } } } } } } } 214.09, 257.24, 315.25, } } } } } } } } } } ...remainder of message deleted.. } } ****************************************************************************** From: Giganews Date: Tue, 27 Jan 2004 04:20:57 -0600 Subject: Re: Contaminant peaks Organization: * Chip; Thanks for the comments on NBBS. It's not a major problem in our lab, we tend to see more PEG and PPG related polymers from detergents and cosmetics as frequent contaminants. We have also seen a lot of silicone polymers from silastic tubing and seals. The current generation of LC/MS instruments is so sensitive that contaminants are showing up everywhere. ....Dave Hachey "Chip Cody" wrote in message news:bv3720$20f$1@news-int.gatech.edu... } } Thanks for the information, Dave. I have been trying to find where } this could come from. We don't presently see it in our AccuTOF, but } it has been a problem in the past on other machines that I have worked } with. NBBS has been detected in plastic used for food wrapping -- a } Google search will show you a paper from SIS about short-path thermal } desorption used to detect this compound. } } It is frustrating to have a contamination problem that eventually goes } away and we never find out where it came from. If we knew the origin } (tubing, solvent containers, seals, or?), it would be easier to solve } the problem. NBBS is particularly annoying because it has a high } proton affinity and it can give strong signals even at low levels. In } some old Nicolet FTMS systems, m/z 214 would be the only peak } remaining if we trapped ions for very long times. Everything else } transferred a proton to the NBBS. } } Chip } } Giganews wrote in message news:... } } Chip; } } } } We salso ee this ion fairly frequently. NBBS is a plasticizer used in } } production of some polyamides. It's reportedly neurotoxic. } } } } ....Dave Hachey } } } } } } "Chip Cody" wrote in message } } news:burbph$3c6$1@news-int.gatech.edu... } } } } } } The m/z 214.09 is most likely to be N-butylbenzenesulfonamide } } } (C10H15NO2S, [M+H]+ m/z 214.09015, CAS# 3622-84-2), a plasticizer and } } } a contaminant that I have often seen in LC/MS and FTICR. I do not } } } know the origin of this contamination, but I am quite certain of the } } } identification because we have used exact mass, MS/MS, isotope ratios, } } } etc. to identify it. } } } } } } Chip Cody } } } } } } } } } David Stranz wrote in } } message news:... } } } } Jenny wrote in } } } } news:buonhp$pjq$1@news-int.gatech.edu: } } } } } } } } } I am presently trying to set up a mass spectrometer with an } } } } } electrospray source to be able to run protein non-covalent } } } } } complexes regularly. This requires aqueous solvents. } } } } } Unfortunatly when I run water based solvents I am always seeing } } } } } the following masses in my spectra. } } } } } } } } } } 214.09, 257.24, 315.25, } } } } } } } } } } } } } ...remainder of message deleted.. } } } } ****************************************************************************** From: usedlabequip Date: 30 Jan 2004 11:56:17 -0800 Subject: ABI SCIEX Q TRAP LC/MS/MS AVAILABLE Organization: * Applied Biosystems Q-TRAP LC/MS/MS with HTLCHPLC Cohesive system model 2300 turboflow available. The system is 1 year old. Please contact for further details. International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 ****************************************************************************** From: Marc Rosen Date: Fri, 30 Jan 2004 23:00:15 -0500 Subject: Advice on MS/MS of a compound Organization: * I have a compound that we synthesized (a prodrug made from a natural product, modified by attaching a peptide ) The MW is 1648, verified by MALDI. When I analyze by electrospray I see very little M+1 but the doubly charged and triply charge species (m/z = 825.3 and 550.8, respectively) provide a significant signal. I'm using -a triple quad- an API3000, direct infusion dissolved in 50% CH3CN with 0.1% formic acid. (Should I switch to methanol?) Do you think I could do a product ion scan on the double charged and triple charged ions and arrive at the same fragments? Also, my guess is that I could produce fragments with an m/z greater than the two values I listed above. I'm still very new to MS (my other work pulls me away too much) and I won't get to try these experiments until late next week, so if anyone can offer some predictions I would appreciate it. Read you later, Marc ****************************************************************************** From: James Barnett Date: Sat, 31 Jan 2004 19:32:22 +0000 Subject: Re: Advice on MS/MS of a compound Organization: * Marc Rosen wrote: } I have a compound that we synthesized (a prodrug made from a natural } product, modified by attaching a peptide ) The MW is 1648, verified by } MALDI. When I analyze by electrospray I see very little M+1 but the doubly } charged and triply charge species (m/z = 825.3 and 550.8, respectively) increasing the source voltage can redue multi charge states, ut in creases fagmentation. } provide a significant signal. I'm using -a triple quad- an API3000, direct } infusion dissolved in 50% CH3CN with 0.1% formic acid. (Should I switch to } methanol?) Yup MeCN reduces the charge on the droplet as the droplet desolvates. MeOH and isopropyl alcohol don't leak as much charge away from the droplet as it desolvates, hence larger signal. } Do you think I could do a product ion scan on the double charged and triple } charged ions and arrive at the same fragments? Also, my guess is that I } could produce fragments with an m/z greater than the two values I listed } above. your fragments will also have multiple charge states as well, the amino acid fragment for sure. } I'm still very new to MS (my other work pulls me away too much) and I won't } get to try these experiments until late next week, so if anyone can offer } some predictions I would appreciate it. } Read you later, } Marc Regards, James } } } ****************************************************************************** From: Freddy Smith Date: Sun, 01 Feb 2004 00:51:32 -0600 Subject: LC-MS (ion trap) Organization: * Just wondering if anyone had any feedback to give on the Finnigan LCQ Classic ion-traps ??? We are interested in possibly buying an instrument but have not had much experience with LC-MS-MS (only GC-MS). All comments welcomed ?? Freddy ****************************************************************************** From: ad@news1.news.xs4all.nl Date: Mon, 2 Feb 2004 19:40:51 +0100 Subject: Re: LC-MS (ion trap) Organization: * if you want any usefull info tell wat you want to do with the instrument. ad "Freddy Smith" wrote in message news:bvjric$gpl$1@news-int.gatech.edu... } Just wondering if anyone had any feedback to give on the Finnigan LCQ } Classic ion-traps ??? } } We are interested in possibly buying an instrument but have not had much } experience with LC-MS-MS (only GC-MS). } } All comments welcomed ?? } } Freddy } } ****************************************************************************** From: Mike Sherrell Date: Mon, 2 Feb 2004 12:47:17 -0800 Subject: LC/Mass specs and MALDIs for sale Organization: * Grizzly Analytical LC/Mass specs and MALDIs for sale. **LC/MS & MS/MS: Q-Star Pulsar i: price not yet set. XL; 2002 system. Call/email if interested. Q-Star Pulsar: $170,000. Not the "i". Recently pmd. + $16K/factory installation. Q-Trap: $125,000 installed, eligible for service. Sciex API 3000 upgrade: $35,000. HSID interface: higher sensitivity and s/n at high flow rates; comparable to API 4000. Sciex API 2000 upgrade: $25,000. 4x sensitivity increase to appx API 3000 specs. Incl. install, warr. Sciex API 300: $49,000. NT; has 365 interface. ES only. Install included; guar. eligible for svc contract. Sciex 365 w/ EP10+: $139,000. Custom upgrade; more sensitive than API 3000. Sciex API 365 upgrade: $105,000. 10x+ sensitivity upgrade; near-equal to 4000. Sciex API 150EX: $59,000. NT. Install included. Sciex API 150EX: $44,000. MCA upgraded to EX; identical performance. MAC; NT + $10,000. Incl. install. Sciex NT workstation: $2,500. Use to upgrade Macs on 150, 365, 2000, 3000. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$24K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $20,000/installation and 1 year service contract. Sciex APCI source: $7,900. For API 150 or 300 or Q-Star Sciex MicroIon spray source: $7,900. For API 150, 300 or Q-Star. Very low flow. PE-ABI Mariner: $55,000. Price includes factory install. Agilent 1100 MSD Trap. Call to discuss price. 2001 model. Agilent 1100 MSD: $various. All Models (A - D) with varying sources (ESI, APCI, APPI). Most any configuration. Can include install, 90-day warranty and training. Finnigan Deca XP+: $165,000. 2002; pristine; installed and calibrated but never used. Includes factory install, guar. eligible for svc. Finnigan Deca XP: $135,000. 30000 model. Includes install and 1 year svc. Factory upgrade to XP + for addt'l $14,000. LCQ DECA: $104,750. ESI, nanosprayNT, Xcalibur 1.2, installation. Finnigan LCQ DUO: $75,000 installed. Finnigan LCQ Classic: $58,500. ESI, installation, 90-day warr. LCQ Classic ESI source: $7,500. New/unused ESI source. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $30,000. ES, API 1, Alpha station, good working order. +$20K/current Xcalibur, installation and 30-day warranty. Finnigan SSQ 7000: $45,000. ES, APCI; Excalibur 1.0; API 1 source; install incl. Finnigan TSQ 700: $30,000. Electrospray, APCI. Install included. Finnigan SSQ 710: $25,000. Electrospray, APCI, API 1, Alpha workstation, install included. Finnigan Mat ITS40W. Call to discuss price. With Varian 3400 GC + A200s Auto Sampler. Micromass LCT API-oaTOF MS: $160,000. Sold new for $260,000 in July 2000. Includes Waters HPLC. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass Q-Tof II: $185,000. Hybrid Quadrupole. Installed, eligible for service contract. Waters (MM) ZMD 2000: $29,500. ESI, APCI; guaranteed good working order. Does not include software license. Micromass ZABSpec Ultima OA TOF: $89,000. 1997 model. Good working order. Micromass Autospec M: $179,000. TOF MS/MS. Incl. FPD, 5 sources, guar. eligible for svc. ($700K new). VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Fisons VG 2000. <$100,000. Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890 included. Install, license & 90-day warr. + $14,500. HP 5989: $21,500. Electrospray, APCI; 2000 amu. VG Trio 2: $7,500. Electrospray; complete; parts or fixer-upper unit. Nermag R10c. <$10,000. Like new; make offer. MM Autospec M: $115,000. Mag Sector; orthogonal TOF MS/MS; 4 sources, FPD and TOF included; currently working well. MM Autospec S: $78,500. European install included; available in US. MM Autospec V: $90,000. European install included; available in US. *Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE: Voyager DE: $69,500. 2000 instrument. Installed, guaranteed. Voyager DE STR. $136,000. Installed, guaranteed. Voyager DE Pro: $109,000. Incl. factory install, certification. Voyager DE RP: $78,900. Extensively refurbished. ABI 4700: Must sell; all offers considered. TOF/TOF MS/MS Mariner ESI-TOF: $55,000. Installed/guar. ok for factory service. Micromass Reflectron: $110,000. Incl. MassPrep enclosed robotic sampler system. + $30,500/install. Micromass Q-Tof 2: $140,750. 2001 model; currently under service contract. Micromass Q-Tof 1: $155,000. + $41K/install and license. Incl. CapLC, many upgrades and extras. Micromass Q-Tof 1: $42,500. Z Spray ESI probe, MassLynx ver 3.4. Guaranteed installble; +$27K/installation. Micromass LCT. ~$155,000. API-TOF. Includes HPLC. New July 2000. Sequenom System: $215,000. 2001 model. Bruker BiFlex III, Oracle software, SpectroCheck, Reader and Jet. Installation incl. Bruker Reflex IV: $207,500. 2001 model; list $300K. Incl. ion source, TOF analyzer, detector, two NT processing stations. Bruker Reflex III: $130,000. 1999 model; includes chiller, standalone AS-90. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $55,000. Linear DE benchtop system; 2 yrs. old; pos/neg. Price includes ship, install, train, 90-day warr. Finnigan LaserMAT 2000: $25,000. Includes ship, install, 90-day parts warr. Kratos Kompact III: offers considered; call or email if interested. SRI custom design: $100,000. Ideal for SNP determination. Asking price. 384 samples/20 min. Can be tested. Finnigan MAT Vision 2000: $80,000. Reflectron. Includes install, 1 year warranty. VG Tof-Spec: $6,000. Or best offer. For parts; new laser card and other new boards. *Also available: service/contracts on Voyager DE, DE RP and PRO. **Other MS: Agilent 5973N MS with 6890N GC: Offers considered. New in box; autosampler, software, 1 yr. parts warranty. Have two. PE Elan 6000: $50,000. ICP-MS. + $2,500/install. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. Finnigan T-30 Newstar. Call to discuss price. FT-MS. Was $1.4M in 1997. Price negotiable. JOEL HX 110. Call to discuss price. Tandem Mass spec. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com **Other mass specs, NMRs, DNA/protein sequencers & synthesizers available; check the website. All listed items subject to prior sale. ****************************************************************************** From: Jenny Date: 2 Feb 2004 17:44:46 -0800 Subject: Air compressors Organization: * Thought I'd send this out to see if anyone has any advice. In order to generate Nitrogen gas for electrospray nebulisation we have recently installed Nitrogen generators which are powered by oil-free air compressors. We use this system on both an FTMS and a triple quad instrument. This works well, except that we seem to be overworking the air compressors and they keep breaking down. The company that supplied the air compressors have been brilliant and they are very good and keep replacing the compressors, but we've been through three in five months - and this cannot go on for ever. We are using the air compressors within their operating specifics - though perhaps they do not like our 30 degree plus climate, and tropical storms. Anyone had similar difficulties - and more importantly found any solutions? Jenny ****************************************************************************** From: Freddy Smith Date: Tue, 03 Feb 2004 17:41:26 -0600 Subject: Re: LC-MS (ion trap) Organization: * We would like to be able to analyze low level impurities (100-500 ppm) in relatively dirty matrices to clean matrices (alot of other non-GC-able cmps). Would like to use for identification purposes in a lab where the MS would every now and then be plubed to an 1100 LC system (non-routine kinda stuff for plant support group). Thanking you ad@news1.news.xs4all.nl wrote: } if you want any usefull info tell wat you want to do with the instrument. } } ad } } "Freddy Smith" wrote in message } news:bvjric$gpl$1@news-int.gatech.edu... } } Just wondering if anyone had any feedback to give on the Finnigan LCQ } } Classic ion-traps ??? } } } } We are interested in possibly buying an instrument but have not had much } } experience with LC-MS-MS (only GC-MS). } } } } All comments welcomed ?? } } } } Freddy } } } } ****************************************************************************** From: Marc Rosen Date: Tue, 3 Feb 2004 21:36:37 -0500 Subject: Re: Air compressors Organization: * Hello Jenny, We purchased a suitable compressor to provide air for four N2 generators after discovering that our house compressor was not capable of servicing even one N2. Due to space constraints and noise level, the compressor resides in what was a darkroom that was fitted with additional ductwork to keep it at a tolerable 26-30 C. The compressor runs constantly and there have been no failures (yet). I will try to get more information tomorrow when i go into work. Marc "Jenny" wrote in message news:bvoagq$hth$1@news-int.gatech.edu... } } Thought I'd send this out to see if anyone has any advice. } } In order to generate Nitrogen gas for electrospray nebulisation we } have recently installed Nitrogen generators which are powered by } oil-free air compressors. We use this system on both an FTMS and a } triple quad instrument. This works well, except that we seem to be } overworking the air compressors and they keep breaking down. The } company that supplied the air compressors have been brilliant and they } are very good and keep replacing the compressors, but we've been } through three in five months - and this cannot go on for ever. We are } using the air compressors within their operating specifics - though } perhaps they do not like our 30 degree plus climate, and tropical } storms. Anyone had similar difficulties - and more importantly found } any solutions? } } Jenny } ****************************************************************************** From: Ilham Sanhaji Date: Wed, 4 Feb 2004 11:58:44 -0500 Subject: proteins in liquid matrices/ Maldi-Tof Organization: * Hi everybody First of all I ask you to excuse my English because i'm francophone I have few problems with Maldi -TOf i want to analyse proteins using liquid matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi don't succeed to have signal of proteins, large and small ones.but i can have signal of matrices. Another issue is that a vaccum in ionisation source take 4hours to be reached.so does someone have suggestions for solving these problems. thank you. ****************************************************************************** From: grober Date: Wed, 4 Feb 2004 20:15:50 -0000 Subject: Re: Air compressors Organization: * Hi Jenny, manufacturers do tend to be a bit optimistic when quoting "performance" figures for their units. I think that many rely on a "recovery period" i.e. the compressor unit recovering/cooling while the reservoir/tank supplies the output. If the compressor runs continuously it may not cope. The other possibility is that your voltage supply is marginal with respect to the voltage/current rating of the electric motor driving the compressor causing the motor to overheat/burn out. I have always found JUNAIR Compressors to be reliable units when rated correctly for the load demanded. "Jenny" wrote in message news:bvoagq$hth$1@news-int.gatech.edu... } } Thought I'd send this out to see if anyone has any advice. } } In order to generate Nitrogen gas for electrospray nebulisation we } have recently installed Nitrogen generators which are powered by } oil-free air compressors. We use this system on both an FTMS and a } triple quad instrument. This works well, except that we seem to be } overworking the air compressors and they keep breaking down. The } company that supplied the air compressors have been brilliant and they } are very good and keep replacing the compressors, but we've been } through three in five months - and this cannot go on for ever. We are } using the air compressors within their operating specifics - though } perhaps they do not like our 30 degree plus climate, and tropical } storms. Anyone had similar difficulties - and more importantly found } any solutions? } } Jenny } ****************************************************************************** From: motmot Date: Wed, 04 Feb 2004 22:25:20 -0500 Subject: check valve in nitrogen line Organization: * Does anyone know if installation of a check valve in the nitrogen line that supplies our mass specs might cause a contamination issue? We supply nitrogen to 2 triples, a QTOF and an LCQ from a dedicated nitrogen generator and the system works fabulously (and has been installed for over 2 years). I want to do some plumbing changes that would involve installing a check valve just after the nitrogen generator. When I look at catalogs that describe check valves, I see scary descriptions of the check valve components like "silicone base lubricant" or "molybdenum disulfide base lubricant" and things like Viton or fluorocarbon o-rings. I don't want to contaminate my nitrogen supply, but I want a check valve, but they all seem to have these components. Anyone have any experience with this? Thanks, Sue Hill Praecis Pharmaceuticals Waltham, Massachusetts susan.hill@praecis.com ****************************************************************************** From: Cory Date: 4 Feb 2004 21:52:18 -0800 Subject: LC/MS contaminants - your help appreciated Organization: * Hi, Having a hard time chasing a contaminant and hoping some one might be able to shed some light on the situation. This series of ions is very strong under electrospray conditions and appears in what should be clean water with 0.1% formic acid. 429, 445, 503, 519, 536, 593, 610 The most abundant peak at 445 is fragmented to give rise to the following species 429, 359, 341, 147, 73 - 341 is the base peak The issue is that this contamination has been completly intractible. It appears despite numerous bottles of water and acid and significant changes in composition and different spray setups. Another observation is that at low curtain gas levels the ions are strong and they can be significantly depressed with increased curtain gas. I'm at my wits end and hope that someone could help me with this - unfortunately I'm not well versed in small molecule mass spec so interpreting the ms/ms spectra will take me some time without a helping hand. I'm sure that someone will recognize this - my hunch is that this is a Si contaning compound - how it is showing up in our solvent I don't know yet... Thanks much, Cory ****************************************************************************** From: Dr. Dickie Date: Thu, 05 Feb 2004 17:54:06 -0500 Subject: Re: proteins in liquid matrices/ Maldi-Tof Organization: * On Wed, 4 Feb 2004 11:58:44 -0500, Ilham Sanhaji wrote: }Hi everybody } First of all I ask you to excuse my English because i'm francophone }I have few problems with Maldi -TOf i want to analyse proteins using liquid }matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with }Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi }don't succeed to have signal of proteins, large and small ones.but i can have }signal of matrices. Another issue is that a vaccum in ionisation source take }4hours to be reached.so does someone have suggestions for solving these }problems. thank you. If I could ask: why do you want to use those matrices? Why not use DHB or HCCA, or sinapinic for very high molecular weight proteins. Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ==================================== "Let be be finale of seem. The only emperor is the emperor of ice-cream" Wallace Stevens-1923 ===================================== ****************************************************************************** From: Simon Grist Date: Fri, 06 Feb 2004 14:18:41 +0000 Subject: Re: proteins in liquid matrices/ Maldi-Tof Organization: * Hi, from experience, glycerol is definately not compatable with MALDI techniques. Even a concentration as low as 0.5% v/v will interfere with protein crystallisation and ionisation. How big are the proteins you are looking at? Have you tried the following matrices - DHB or alpha-cyano for proteins smaller than 10KDa, or sinapinic acid for anything over 10KDa? For any of the above matrices, try 10mg/ml dissolved in 50:50 0.1%TFA/acetonitrile. Sime Ilham Sanhaji wrote: } Hi everybody } First of all I ask you to excuse my English because i'm francophone } I have few problems with Maldi -TOf i want to analyse proteins using liquid } matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with } Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi } don't succeed to have signal of proteins, large and small ones.but i can have } signal of matrices. Another issue is that a vaccum in ionisation source take } 4hours to be reached.so does someone have suggestions for solving these } problems. thank you. ****************************************************************************** From: Chip Cody Date: 6 Feb 2004 08:11:43 -0800 Subject: Re: LC/MS contaminants - your help appreciated Organization: * Are you suspecting silicon because of the m/z 73 peak? I don't recognize the contaminants, but if silicon is present, the M+2 isotope should be distinctive. As you probably know, the masses and relative isotopic of Si isotopes are: 27.976927 100.0000 28.976495 5.0778 29.973770 3.3473 So the M+2 isotope peak abundances will be quite distinctive for species containing multiple silicons. Good luck! Chip Cody JEOL USA, Inc. Cory wrote in message news:... } Hi, } } Having a hard time chasing a contaminant and hoping some one might be } able to shed some light on the situation. This series of ions is very } strong under electrospray conditions and appears in what should be } clean water with 0.1% formic acid. } } 429, 445, 503, 519, 536, 593, 610 } } The most abundant peak at 445 is fragmented to give rise to the } following species } } 429, 359, 341, 147, 73 - 341 is the base peak } } The issue is that this contamination has been completly intractible. } It appears despite numerous bottles of water and acid and significant } changes in composition and different spray setups. Another } observation is that at low curtain gas levels the ions are strong and } they can be significantly depressed with increased curtain gas. } } I'm at my wits end and hope that someone could help me with this - } unfortunately I'm not well versed in small molecule mass spec so } interpreting the ms/ms spectra will take me some time without a } helping hand. I'm sure that someone will recognize this - my hunch is } that this is a Si contaning compound - how it is showing up in our } solvent I don't know yet... } } Thanks much, } } Cory ****************************************************************************** From: "rainer [iso-8859-2] lörwald" Date: Sun, 08 Feb 2004 00:07:55 +0100 Subject: Re: LC/MS contaminants - your help appreciated Organization: * Hi Cory, these masses are very common in ESI, especially at low flow rates. We suggest them to originate from the fused silica tubing very often used in these systems. Try using FS tubing that is not deactivated. Your observation that a higher curtain gas level suppresses these ions might be caused by a general decrease of ion transmission. Best Regards Rainer Cory schrieb: } } Hi, } } Having a hard time chasing a contaminant and hoping some one might be } able to shed some light on the situation. This series of ions is very } strong under electrospray conditions and appears in what should be } clean water with 0.1% formic acid. } } 429, 445, 503, 519, 536, 593, 610 } } The most abundant peak at 445 is fragmented to give rise to the } following species } } 429, 359, 341, 147, 73 - 341 is the base peak } } The issue is that this contamination has been completly intractible. } It appears despite numerous bottles of water and acid and significant } changes in composition and different spray setups. Another } observation is that at low curtain gas levels the ions are strong and } they can be significantly depressed with increased curtain gas. } } I'm at my wits end and hope that someone could help me with this - } unfortunately I'm not well versed in small molecule mass spec so } interpreting the ms/ms spectra will take me some time without a } helping hand. I'm sure that someone will recognize this - my hunch is } that this is a Si contaning compound - how it is showing up in our } solvent I don't know yet... } } Thanks much, } } Cory ****************************************************************************** From: Bertram.Frank@epamail.epa.gov Date: Mon, 09 Feb 2004 11:31:45 -0500 Subject: Re: Air Compressors Organization: * Jenny: 1) I am not aware of any air compressors that are designed to run constantly. They all have a duty cycle in their specifications as far as I know, and to exceed that is asking for breakdown. Duty cycle is how long they can run and how long they have to rest to cool down before running again. They get very hot when they are running, and the compressor section will burn up eventually. 2) You didn't say what kind of failures you were experiencing. If they are on the electric motor side, then it could be your storms, where you can have spikes in the line voltage, and you can get protection on the line for that. Also, have the line voltage checked. If it is wrong, that can burn up a motor, especially if it is too low. (A low voltage causes more current draw and they get too hot.) 3) We have many zero air generators all over the building, plan to add N2 generators with the new mass specs, and we NOW feed them from a BIG compressor upstairs. We had problems galore in the past. We also had two cheap compressors that were a bad design ($300) and they were removed from the market. The piston rod disintegrated. If you have trouble keeping up with the N2 generators, you need more than one compressor for them, OR go to a bigger tank capacity with higher pressure (say 175 psi) so it doesn't have to run so often to refill the tank. 4) The compressor we now have is an oil-less, cast iron, 2-cylinder, 10 HP, 230 VAC, 3-phase, with 120 gallon receiving tank at 155 psi, and a refrigerated dryer on the output. It cost about $12,000, but it feeds the whole building, which is extensive. Ultimately, it is cheaper than all the problems we had before and all the down time. It also cured the wet air lines on the old building air. Before they would sometimes have water running out of them like a faucet because the coalescing filters overloaded and building maintenance couldn't seem to do anything about it. I am no expert but I have been through a bit of this, so if you have more questions, feel free. Frank ****************************************************************************** From: "Little, James - Eastman" Date: Tue, 10 Feb 2004 09:16:02 -0500 Subject: MW Calculator for Excel Organization: * Anyone got a copy of mm.xla an Excel Add-in written by Christain Hauck and described in Citation: Hauck, Christian. An Excel 4.0 Add-in Function to Calculate Molecular Mass J. Chem. Educ. 1996 73 431? I want something to calculate nominal MW in an Excel spreadsheet and possibly average and accurate. James Little Tel. No. 423-229-8685 office Tel. No. 423-229-8022 lab "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle Sailing Club (Intranet) Web Page: http://eastmanweb/fp39/ "Twenty years from now you will be more disappointed by the things you didn't do than by the ones you did. So throw off the bowlines, sail away from the safe harbor. Catch the trade winds in your sails. Explore. Dream. Discover." ****************************************************************************** From: max Date: 10 Feb 2004 08:06:11 -0800 Subject: super basic mass spec tutorial Organization: * Hi, I'm working with a group that is using mass spec methods frequently and I don't have the technical background to get more than 30% of what they're saying. Can anyone recommend books or websites to get my feet wet? I only have a basic college chemistry background, so it would need to fairly low level. Thanks in advance for your help, Max ****************************************************************************** From: Chip Cody Date: 10 Feb 2004 10:17:37 -0800 Subject: Re: proteins in liquid matrices/ Maldi-Tof Organization: * Liquid-matrix MALDI is less common than solid-matrix MALDI, but it is an active area of research. Various matrix mixtures have been developed for lasers with different wavelegths. Take a look at the notes on the following web sites: http://www.chemistry.wustl.edu/~msf/damon/samp_prep_liquid.html www.chemistry.wustl.edu/~msf/ ASMS2002/Ying_Li_Poster.pdf The notes in the first site listed point out some potential problems, such as larger sample amounts required (1-10 pmol) than for solid-matrix MALDI, and limitations on mass range (25 kDa) and resolving power (a few hundred). Several reference articles on liquid-matrix MALDI are cited. If your ion source is not equipped for analysis of materials with higher vapor pressures, this may be difficult. We had good luck in using MALDI on a magnetic sector MS with the liquid matrix developed by Kolli and Orlando: V.S.K. Kolli, R. Orlando. 1996. A new matrix for MALDI on magnetic sector instruments with point detectors. Rapid Commun. Mass Spectrom. 10: 923-926. Another alternative is to use AP/MALDI, where vacuum problems are eliminated. Chip Cody JEOL USA, Inc. Ilham Sanhaji wrote in message news:... } Hi everybody } First of all I ask you to excuse my English because i'm francophone } I have few problems with Maldi -TOf i want to analyse proteins using liquid } matrices like glycerol with Rhodamine 6G or Nitro benzyl Alcohol(NBA) with } Diphenyl Butadiene. Glycerol and NBA are the absorbing liquids. Unfortunatlyi } don't succeed to have signal of proteins, large and small ones.but i can have } signal of matrices. Another issue is that a vaccum in ionisation source take } 4hours to be reached.so does someone have suggestions for solving these } problems. thank you. ****************************************************************************** From: Kendall Powell Date: 11 Feb 2004 06:12:29 -0800 Subject: Re: LC/MS contaminants - your help appreciated Organization: * Cory- An excellent paper detailing many of the common contaminants in ESI and APCI mass spec is: J. Am. Soc. Mass Spectrom 1999, 10, 1174-1187 In their table 3 they list the series of ions 355, 429, 503, 593, 667, 741, and 815 as coming from silicone rubber polymer - you also observed several of these ions. Hope that helps. -Kendall Cory wrote in message news:... } Hi, } } Having a hard time chasing a contaminant and hoping some one might be } able to shed some light on the situation. This series of ions is very } strong under electrospray conditions and appears in what should be } clean water with 0.1% formic acid. } } 429, 445, 503, 519, 536, 593, 610 } } The most abundant peak at 445 is fragmented to give rise to the } following species } } 429, 359, 341, 147, 73 - 341 is the base peak } } The issue is that this contamination has been completly intractible. } It appears despite numerous bottles of water and acid and significant } changes in composition and different spray setups. Another } observation is that at low curtain gas levels the ions are strong and } they can be significantly depressed with increased curtain gas. } } I'm at my wits end and hope that someone could help me with this - } unfortunately I'm not well versed in small molecule mass spec so } interpreting the ms/ms spectra will take me some time without a } helping hand. I'm sure that someone will recognize this - my hunch is } that this is a Si contaning compound - how it is showing up in our } solvent I don't know yet... } } Thanks much, } } Cory ****************************************************************************** From: Mudbunny Date: 11 Feb 2004 12:10:14 -0800 Subject: Question on HRMS Organization: * OK, this may be a silly question, but I can't seem to find the answer. I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One of the parameters which is open to change is sec/decade. I know that this has to do with the scan rate, but I can't find, anywhere, a definition of what this is. I am used to seeing it in terms of scans/second. Thanks Marcel ****************************************************************************** From: David Stranz Date: Thu, 12 Feb 2004 11:08:19 -0600 Subject: Re: Question on HRMS Organization: * Mudbunny wrote in news:c0e2mt$qad$1@news-int2.gatech.edu: } OK, this may be a silly question, but I can't seem to find the } answer. } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One } of the parameters which is open to change is sec/decade. I know } that this has to do with the scan rate, but I can't find, } anywhere, a definition of what this is. I am used to seeing it } in terms of scans/second. } } Thanks } } Marcel } } Try the Mass Spec Desk Reference by O. David Sparkman (ISBN0-9660813- 2-3). For magnetic sector instruments, a "decade" is an order of magnitude change in the m/z range, e.g. m/z 100 - 1000. sec/decade is therefore the rate at which the accelerating voltage is changed (assuming fixed magnetic field strength) in order to scan that m/z range. See page 49 of the Desk Reference for a more complete description; it is too lengthy to type here. David ****************************************************************************** From: Chip Cody Date: 12 Feb 2004 10:06:08 -0800 Subject: Re: Question on HRMS Organization: * Seconds per decade means the time it takes to scan an m/z range of M to 10M, i.e. the starting mass and the ending mass differ by a factor of 10. For example, 1 second per decade would allow you to scan from m/z 35 to m/z 350 in one second, or from m/z 500 to m/z 1000 in one second. The reason for this is the following: Traditional magnetic sector mass spectrometers scan the magnet exponentially. The scan law is: m(t) = m(o)e^kt Where e is 2.718281828..., m(t) is mass at time t, m(0) is the starting mass, k is a constant related to the scan speed and t is time. The exponential magnet scan provides a constant peak width independent of m/z. If you want to express the scan law in linear form (y=ax+b), you have to use logarithms. It is convenient to use base 10 logs, hence the use of the "decade". (If you used natural logs, you would have to express a scan range of M to 2.303M, not a very intuitive value!). Chip Cody (JEOL) Mudbunny wrote in message news:... } OK, this may be a silly question, but I can't seem to find the answer. } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One of } the parameters which is open to change is sec/decade. I know that this } has to do with the scan rate, but I can't find, anywhere, a definition } of what this is. I am used to seeing it in terms of scans/second. } } Thanks } } Marcel ****************************************************************************** From: Rod Buchanan Date: Thu, 12 Feb 2004 19:54:02 -0000 Subject: Re: Question on HRMS Organization: * "Mudbunny" wrote in message news:c0e2mt$qad$1@news-int2.gatech.edu... } OK, this may be a silly question, but I can't seem to find the answer. } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One of } the parameters which is open to change is sec/decade. I know that this } has to do with the scan rate, but I can't find, anywhere, a definition } of what this is. I am used to seeing it in terms of scans/second. } } Thanks } } Marcel } Brief answer: It is the time during scanning for the focussed mass to be reduced to one-tenth (i.e. by one decade of mass) such as from m/z 1000 to m/z 100. Thus the larger the number, the slower the scan. Explanation: On a magnetic sector instrument, such as the Concept, now manufactured and supported by MSI (Altrincham, England) the magnet is usually scanned with an exponential decay scan law. Traditionally this was achieved by allowing the magnetic current to decay through an R/C circuit, but is now frequently achieved by a programmed scan on a high resolution DAC. In terms of AMU per second the scan slows down the lower in mass that is scanned. The resolution of a sector instrument is usually defined in terms of the ratio of masses that may be resolved at a 10% valley. Thus on a Concept operating at 10,000 resolution, masses differing by 1 part in 10,000 are resolved, so it is possible to separate ion species at m/z 250.000 and 250.025. The resolution, as defined above, is approximately constant over the whole mass range so if an exponential scan law is used, the time that is needed to scan over a peak remains approximately constant. [The maths is a bit long for inclusion here] Data is collected at a fixed rate during the scan, thus the number of data points collected will be similar for every peak. This has considerable advantages in calculating peak centroids and peak areas. Please feel free to email me off group if you want more information. See below for the address. MACH 3x tip: You can get help on many of the parameters and buttons by placing the mouse over the item concerned an pressing the "Help" button on the keyboard. For the SunView version of MACH 3, help is obtained by clicking the middle mouse button on the item concerned. Rod Buchanan, MACH 3 programmer, Mass Spectrometry International, Altrincham, England rod (at) massint http://www massint.co.uk ****************************************************************************** From: Reinhard Stroh Date: Fri, 13 Feb 2004 11:12:32 +0100 Subject: Re: Air compressors Organization: * Jenny wrote: } Thought I'd send this out to see if anyone has any advice. } } In order to generate Nitrogen gas for electrospray nebulisation we } have recently installed Nitrogen generators which are powered by } oil-free air compressors. We use this system on both an FTMS and a } triple quad instrument. This works well, except that we seem to be } overworking the air compressors and they keep breaking down. The } company that supplied the air compressors have been brilliant and they } are very good and keep replacing the compressors, but we've been } through three in five months - and this cannot go on for ever. We are } using the air compressors within their operating specifics - though } perhaps they do not like our 30 degree plus climate, and tropical } storms. Anyone had similar difficulties - and more importantly found } any solutions? } } Jenny } Hi, Jenny, we evaluated compressors for use with nitrogen generators. We were told not to use oil-free compressors because they are not so robust. Instead, we use normal compressors, a cold-trap (2 degrees C) and a couple of spray- and dust filters as well as an activated coal filter. This works excellent since 4 years or so. We never had problems with the N2 quality so far. Of course, the filters have to be replaced in time. Our company is located in Austria, so you´ll have different suppliers. We use "MARK" Compressors (a subsidiary of Atlas Copco). In the US you may find "GARDNER" Compressors (Denver). regards Reinhard ****************************************************************************** From: Phil Date: Thu, 12 Feb 2004 00:01:10 +0100 Subject: Re: MW Calculator for Excel Organization: * [Moderator's note - Three files were attached to this, but the posting program does not handle attachments well. The files may be found at http://www.chemistry.gatech.edu/stms/Module1.bas http://www.chemistry.gatech.edu/stms/CalcForm.frx and http://www.chemistry.gatech.edu/stms/CalcForm.frm DB] Hi there James, Found your message tonight. I don't have any mm.xla addin but did quickly make this macro for you.. Maybe this can help. If not, feel free to modify and spread it around. I started off a Javascript I found on the net. Just fire up Excel and VBA, import these 2 files under the PERSONAL.XLS workbook and save it, then run it. This one is interactive, but could easily be modified to return the value as a function. If you don't see a PERSONAL.XLS workbook on the top left pane of the VBA environment, just start Tools/Macros/Record New macro. This will open a window asking you where you want to store the macros. Select Personal.xls. A small toolbar with a record button will show up. Just close this toolbar and your personal.xls file will be created. It is not fully tested and only expects that you type formulas exactly as they should be, that is, lower and upper cases. If I have a minute one day, I'll fix this. Hope this helps. Let me know Rgds from Paris, France Phil "Little, James - Eastman" a écrit dans le message de news:c0arhe$3r2$1@news-int.gatech.edu... } } Anyone got a copy of mm.xla an Excel Add-in written by Christain Hauck and described in Citation: Hauck, Christian. An Excel } 4.0 Add-in Function to Calculate Molecular Mass J. Chem. Educ. 1996 73 431? } } I want something to calculate nominal MW in an Excel spreadsheet and possibly average and accurate. } } } } } James Little } Tel. No. 423-229-8685 office } Tel. No. 423-229-8022 lab } "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle } Sailing Club (Intranet) Web Page: http://eastmanweb/fp39/ } } "Twenty years from now you will be more disappointed by the things you didn't do than by the ones you did. So throw off the } bowlines, sail away from the safe harbor. Catch the trade winds in your sails. Explore. Dream. Discover." } } ****************************************************************************** From: usedlabequip Date: 13 Feb 2004 10:13:30 -0800 Subject: Refurbished Analytical Equipment Available Organization: * !!!!FOR SALE!!!! 1. Applied BioSystems Prism 7900HT Real Time PCR 2. PerSeptive-ABI Mariner (ESI-TOF) Biospectrometry Workstation 3.) Cohesive Technologies model turboflow 2300 HTLC/HPLC system complete with HP 1100 # G1322A Degasser, # G1311A Quat. Pump, & # G1312 Binary Pump 4.) Perspective BioSystems VOYAGER-DE STR MALDI-TOF. 5.) Applied BioSystems Q-TRAP, LC/MS/MS 6.) Micromass Q-TOF II 7.) Thermo Finnigan TSQ 7000 with API II LC/MS/MS 8.) Thermo Finnigan LCQ Classic LC/MS/MS 9.) Micromass ZMD 2000 LC/MS 10.) Micromass Quattro Ultima LC/MS/MS 11.) Varian Unity Inova 300 MHz NMR 12.) Varian Mercury MVX 300 MHz NMR 13.) Bruker AC300 MHz Plus NMR 14.) Varian Unity Plus 400 MHz NMR 15.) Varian Unity 500 MHz NMR 16.) Bruker Avance 500 MHz LC/NMR 17.) Varian Inova 600 MHz LC/NMR 18.) Bruker Avance 700 MHz NMR 19.) Genomics Solutions GeneTAC Hybstation *Please call for further details. International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com Ph: 847.913.0777 Fax: 847.913.0785 ****************************************************************************** From: Elijah Bailey Date: 14 Feb 2004 10:15:55 -0800 Subject: NewBie: Help Organization: * I got some mass spec data of blood samples (for cancer patients) to analyze and it is distributed in 4 directories. NormalControl, Benign, Malignant, Reference I understand Benign and Malignant stand for cancer. What might be NormalControl and Reference? I dont know any biology, just trying my luck here if someone could help. Thanks in Advance for your help/comments, --Elijah ****************************************************************************** From: Joerg Hau Date: Sun, 15 Feb 2004 10:49:43 +0100 Subject: Re: Question on HRMS Organization: * Hi David } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. One } } of the parameters which is open to change is sec/decade. I know } } that this has to do with the scan rate, but I can't find, } } anywhere, a definition of what this is. I am used to seeing it } } in terms of scans/second. } } For magnetic sector instruments, a "decade" is an order of magnitude } change in the m/z range, e.g. m/z 100 - 1000. sec/decade is } therefore the rate at which the accelerating voltage is changed } (assuming fixed magnetic field strength) in order to scan that m/z } range. In theory I agree, but in practice may obtain rather bad mass spectra if you vary the accelerating voltage over such a large range (e.g. from 3000 to 300 V!). On a sector field instrument, voltage scanning is usually used only for very narrow mass ranges (e.g. ion source tuning), linked scans, or fast monitoring of multiple mass traces. Generally not more than 10% sweep of the full voltage. Common practice instead to keep the accelerating voltage constant and to scan the magnetic field. As Chip Cody and Rod Buchanan pointed out, peak width will be constant in time if you scan with an exponential scan law. Again, all this applies to sector field MS only ... ah, those good ol' sector machines ... Cheers + HTH, - Joerg -- joerg dot hau at swissonline dot ch * Lausanne, Switzerland http://homepage.sunrise.ch/mysunrise/joerg.hau/ "All standard disclaimers apply". remove "nospam." from my address to reply (this became necessary due to increasing SPAM) ****************************************************************************** From: Maxell Date: 15 Feb 2004 04:06:49 -0800 Subject: Databases Organization: * Hi! Where can I find a good database that is searchable on molecular weight. It should preferably be free of charge. ****************************************************************************** From: David Stranz Date: Mon, 16 Feb 2004 08:29:57 -0600 Subject: Re: Question on HRMS Organization: * Joerg Hau wrote in news:c0ostl$67i$1@news-int.gatech.edu: } Hi David } } } } I am using a Kratos Concept HRMS, on MACH3x (v5.2) software. } One } } of the parameters which is open to change is sec/decade. } I know } } that this has to do with the scan rate, but I can't } find, } } anywhere, a definition of what this is. I am used to } seeing it } } in terms of scans/second. } } } } For magnetic sector instruments, a "decade" is an order of } magnitude } change in the m/z range, e.g. m/z 100 - 1000. } sec/decade is } therefore the rate at which the accelerating } voltage is changed } (assuming fixed magnetic field strength) in } order to scan that m/z } range. } } In theory I agree, but in practice may obtain rather bad mass } spectra if you vary the accelerating voltage over such a large } range (e.g. from 3000 to 300 V!). On a sector field instrument, } voltage scanning is usually used only for very narrow mass } ranges (e.g. ion source tuning), linked scans, or fast } monitoring of multiple mass traces. Generally not more than 10% } sweep of the full voltage. } } Common practice instead to keep the accelerating voltage } constant and to scan the magnetic field. As Chip Cody and Rod } Buchanan pointed out, peak width will be constant in time if you } scan with an exponential scan law. } } Again, all this applies to sector field MS only ... ah, those } good ol' sector machines ... } } Cheers + HTH, } } - Joerg } } My comments were paraphrased from David Sparkman's MS Desk Reference, so I think your complaint is with him! I traded MS hardware for PC hardware a long time ago... I'm wary of magnetic fields now. Cheers, David ****************************************************************************** From: Darryl Date: 16 Feb 2004 11:50:52 -0800 Subject: HP5989 HELP Organization: * Hi, I have a 5989. I've spent 2500$ on having the HP engineer come out to repair but he and the people who designed it could not fix it. SOOOOOOOOO. The problem seems to be in the feedback portion of the mass filter electronics. Symptoms are 0 abundance. We swapped the RFPA board and controller board plus they soaked me for some consumables like HED and ceramic blocks. any advice please email me if you think you can help this is real pain to figure out thanks ****************************************************************************** From: Chip Cody Date: 19 Feb 2004 05:44:43 -0800 Subject: Re: Question on HRMS Organization: * As Joerg pointed out, the most common scan mode for a magnetic sector is to set the accelerating voltage and electrostatic sector analyzer (ESA) to pass ions of a set kinetic energy and then to scan the magnetic field. The advantage of this scan mode is that one can scan over the full m/z range of the spectrometer with (essentially) a constant sensitivity as a function of m/z. The disadvantage is that magnet hysteresis leads to small (ppm-level) variations from scan to scan that require an internal standard with lots of peaks if one wishes to measure exact masses. Exact calibration of a magnet scan requires four reference points to bracket each measured m/z. Voltage scanning is an alternative. In this scan mode, you "park" the magnet at a fixed value and scan the accelerating voltage and ESA. Magnet hysteresis is not a problem, but the response decreases as voltage decreases (and m/z increases) during the scan. If our mass spectrometers are adjusted correctly, we can scan the voltage from M to 2M (50% of the acclerating voltage range), but the signal at 2M will be decreased. Lock masses from known reference standards are used to correct slow ppm-level drift in the magnetic field due to temperature fluctuations. Electric field scans are linear, so calibration only requires two reference points. Scanning from M to 2M is more-or-less the maximum possible range for a voltage scan. Scanning over a decade would produce no signal for the high-m/z ions. The same comments apply to selected ion monitoring (SIM) measurements. Magnet switching is used for low-resolution SIM, and voltage switching is used for high-resolution SIM. There are exceptions to everything. We have performed magnet-switching HRSIM experiments, but they are uncommon. Magnetic sectos scans are discussed on our web page at: http://www.jeol.com/ms/docs/ms_analyzers.html Other scan modes involve scanning both the magnet and ESA together. Linked-scan MS/MS is discussed at: http://www.jeol.com/ms/docs/ms-ms.pdf Chip Cody (JEOL) ------------------------------------------------------- Joerg Hau wrote in message ... } } } } For magnetic sector instruments, a "decade" is an order of magnitude } } change in the m/z range, e.g. m/z 100 - 1000. sec/decade is } } therefore the rate at which the accelerating voltage is changed } } (assuming fixed magnetic field strength) in order to scan that m/z } } range. } } In theory I agree, but in practice may obtain rather bad mass spectra } if you vary the accelerating voltage over such a large range (e.g. } from 3000 to 300 V!). On a sector field instrument, voltage scanning } is usually used only for very narrow mass ranges (e.g. ion source } tuning), linked scans, or fast monitoring of multiple mass traces. } Generally not more than 10% sweep of the full voltage. } ****************************************************************************** From: Mudbunny Date: 19 Feb 2004 13:34:57 -0800 Subject: Re: Question on HRMS Organization: * Chip Cody wrote in message news:... } Seconds per decade means the time it takes to scan an m/z range of M } to 10M, i.e. the starting mass and the ending mass differ by a factor } of 10. For example, 1 second per decade would allow you to scan from } m/z 35 to m/z 350 in one second, or from m/z 500 to m/z 1000 in one } second. I am just trying to understand, so forgive the question. Shouln't the last example be from m/z 500(M) to m/z 5000(10M)?? ****************************************************************************** From: Mudbunny Date: 19 Feb 2004 13:42:13 -0800 Subject: Re: Question on HRMS Organization: * } In theory I agree, but in practice may obtain rather bad mass spectra } if you vary the accelerating voltage over such a large range (e.g. } from 3000 to 300 V!). On a sector field instrument, voltage scanning } is usually used only for very narrow mass ranges (e.g. ion source } tuning), linked scans, or fast monitoring of multiple mass traces. } Generally not more than 10% sweep of the full voltage. So then I can tell my bosses, who want me to use the Concept to do quantitation of pesticides by GC-MS (m/z range of about 60 to 450) that it is not really going to be useful? From what I understand from all of the response so far (thank you!! thank you!! thank you!!!) I will get decent response at the low masses, but as I get higher, the response is going to suck, thus making it very difficult to do quantitative analysis of compounds in the ppb concentration range. This then will lead them to the next question that I would like to confirm. They are then going to ask me to do SIM analysis of the pesticides. How can I go from a basic MS dataset to the exact masses required for a SIM experiment. I have a direct probe, so is it as simple as putting a sample of the pesticide on the end of the probe, sticking it in, and then using the scope to manually look for peaks?? Thanks again for all of your help. Marcel ****************************************************************************** From: Mudbunny Date: 19 Feb 2004 13:47:06 -0800 Subject: Re: Question on HRMS Organization: * } Voltage scanning is an alternative. In this scan mode, you "park" the } magnet at a fixed value and scan the accelerating voltage and ESA. } Magnet hysteresis is not a problem, but the response decreases as } voltage decreases (and m/z increases) during the scan. } } If our mass spectrometers are adjusted correctly, we can scan the } voltage from M to 2M (50% of the acclerating voltage range), but the } signal at 2M will be decreased. Lock masses from known reference } standards are used to correct slow ppm-level drift in the magnetic } field due to temperature fluctuations. Electric field scans are } linear, so calibration only requires two reference points. Scanning } from M to 2M is more-or-less the maximum possible range for a voltage } scan. Scanning over a decade would produce no signal for the high-m/z } ions. Ahhh. That'll teach me to reply before reading the whole thread. Thanks!! } The same comments apply to selected ion monitoring (SIM) measurements. } Magnet switching is used for low-resolution SIM, and voltage } switching is used for high-resolution SIM. There are exceptions to } everything. We have performed magnet-switching HRSIM experiments, but } they are uncommon. Ahhh. Interesting. I will, in the very near future, be using the instrument to do the quantitative high res SIM of various nitrosamines, with pfk as the reference. So what are the advantages and disadvantages of using the instrument in Field stabilisation mode vs. Current stabilisation mode? In this case, sensitivity is a must, as we will be looking at concentrations in ppt (parts per trillion) levels. Marcel ****************************************************************************** From: "Horler, R" Date: Fri, 20 Feb 2004 09:35:00 +0000 Subject: Tryptic digests Organization: * Hello To set the scene I am currently involved in a creating a new E coli database and part of what we plan to put in this database is a large collection of experimental data from published work. One problem I am having at the moment is a number of proteomic experiments show a predicted number of tryptic fragments but the actual numbers vary hugely between different published work. My understanding, as a geneticist, is that trypsin cuts like a restriction enzyme after arginine or lysine residues and therefore I would have thought that the number of fragments would be easy to predict. The numbers for specific proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. Could you tell me if my understanding of the specificity of trypsin digest is correct and if not what it is? If so why would the predicted number of fragemtns vary so much in the two examples? Regards Richard ****************************************************************************** From: Freddy Smith Date: Fri, 20 Feb 2004 07:07:16 -0600 Subject: Re: Question on HRMS Organization: * Mudbunny wrote: } } In theory I agree, but in practice may obtain rather bad mass spectra } } if you vary the accelerating voltage over such a large range (e.g. } } from 3000 to 300 V!). On a sector field instrument, voltage scanning } } is usually used only for very narrow mass ranges (e.g. ion source } } tuning), linked scans, or fast monitoring of multiple mass traces. } } Generally not more than 10% sweep of the full voltage. } } So then I can tell my bosses, who want me to use the Concept to do } quantitation of pesticides by GC-MS (m/z range of about 60 to 450) } that it is not really going to be useful? From what I understand from } all of the response so far (thank you!! thank you!! thank you!!!) I } will get decent response at the low masses, but as I get higher, the } response is going to suck, thus making it very difficult to do } quantitative analysis of compounds in the ppb concentration range. } } This then will lead them to the next question that I would like to } confirm. They are then going to ask me to do SIM analysis of the } pesticides. How can I go from a basic MS dataset to the exact masses } required for a SIM experiment. I have a direct probe, so is it as } simple as putting a sample of the pesticide on the end of the probe, } sticking it in, and then using the scope to manually look for peaks?? } I am new to the MS field but am of the thought that it will be very difficult to detect ppb components in a mix with the direct probe method. I would have imagined that one would require pre separation with a GC column. Even with SIM you would not be able to quantify your levels as you would not know which species are generating those ions, with the added problem that some of these ions might be secondary ions ?? More experienced users might be able to comment further and correct me on this if I am wrong ??? } } Thanks again for all of your help. } } Marcel ****************************************************************************** From: Freddy Smith Date: Fri, 20 Feb 2004 07:09:51 -0600 Subject: Ion traps Organization: * Just wondering if anyone had any feedback to give on the Finnigan LCQ Classic ion-traps ??? We are interested in possibly buying an instrument but have not had much experience with LC-MS-MS (only GC-MS). All comments welcomed ?? We would like to be able to analyze low level impurities (100-500 ppm) in relatively dirty matrices to clean matrices (alot of other non-GC-able cmps). Would like to use for identification purposes in a lab where the MS would every now and then be plubed to an 1100 LC system (non-routine kinda stuff for plant support group). Freddy ****************************************************************************** From: Eric van der Horst Date: 20 Feb 2004 05:45:50 -0800 Subject: sensitivity in LC-MS(/MS) dependend on guad column Organization: * During method development in our laboratory we sometimes come across a peculiar problem: The sensitivity of the Mass spectrometer (Peak heigth and total area under the chromatogram) can be dependent on whether or not we use a guard column or a fritt filter. Sensitivity has been seen to increase and decrease, depending on the compound. Not only for processed samples from a biological matrix, but also in test solutions (compound dissolved a water/organic solvent mixture)this effect occurs. The ionisation technique we use is turbo-ionspray. From ionisation theory I cannot understand what would cause the change in sensitiviy. Could someone hazard a guess for me? Thanking you in advance, Eric van der Horst ****************************************************************************** From: Chip Cody Date: 20 Feb 2004 08:00:21 -0800 Subject: Re: Question on HRMS Organization: * There are several questions pending. Here are some answers: 1. This is where that art of analytical method development comes into play. The method development for HRSIM requires careful choice of the target m/z set for each analyte. Because of the M to 2 M (or less...) limitation, you cannot always chose the most abundant peaks as you might for LRSIM. It is sometimes better to chose a closely spaced set of peaks at higher m/z, even if they are not the most abundant. For example, one might monitor M+. and [M-Cl]+, or M+. and isotope peaks for a polychlorinated species. There are established protocols (e.g. EPA protocols) for HRSIM for many compound classes. 2. Yes, I made a mistake. I intended to say that a decade is 500 to 5000. I was thinking about the M to 2M range for voltage scans. 3. I don't know about the stabilization modes on the Concept. On our machines, the Hall probe field regulation can be turned off, but this is only sometimes done at a resolving power of 30,000 or more when noise from the regulation circuit can become significant. If you do not use field stabilization, you may have cleaner peaks at very high resolution, but you must rely on the lock mass correction and temperature stability in the lab and cooling water is critical. I do not turn off field stabilization for any routine measurements that I make. Chip Cody Mudbunny wrote in message news:... } } Voltage scanning is an alternative. In this scan mode, you "park" the } } magnet at a fixed value and scan the accelerating voltage and ESA. } } Magnet hysteresis is not a problem, but the response decreases as } } voltage decreases (and m/z increases) during the scan. } } } } If our mass spectrometers are adjusted correctly, we can scan the } } voltage from M to 2M (50% of the acclerating voltage range), but the } } signal at 2M will be decreased. Lock masses from known reference } } standards are used to correct slow ppm-level drift in the magnetic } } field due to temperature fluctuations. Electric field scans are } } linear, so calibration only requires two reference points. Scanning } } from M to 2M is more-or-less the maximum possible range for a voltage } } scan. Scanning over a decade would produce no signal for the high-m/z } } ions. } } Ahhh. That'll teach me to reply before reading the whole thread. } Thanks!! } } } The same comments apply to selected ion monitoring (SIM) measurements. } } Magnet switching is used for low-resolution SIM, and voltage } } switching is used for high-resolution SIM. There are exceptions to } } everything. We have performed magnet-switching HRSIM experiments, but } } they are uncommon. } } Ahhh. Interesting. I will, in the very near future, be using the } instrument to do the quantitative high res SIM of various } nitrosamines, with pfk as the reference. So what are the advantages } and disadvantages of using the instrument in Field stabilisation mode } vs. Current stabilisation mode? In this case, sensitivity is a must, } as we will be looking at concentrations in ppt (parts per trillion) } levels. } } Marcel ****************************************************************************** From: Mudbunny Date: 20 Feb 2004 10:11:24 -0800 Subject: Re: Question on HRMS Organization: * Freddy Smith wrote in message news:... } Mudbunny wrote: } } } } So then I can tell my bosses, who want me to use the Concept to do } } quantitation of pesticides by GC-MS (m/z range of about 60 to 450) } } that it is not really going to be useful? From what I understand from } } all of the response so far (thank you!! thank you!! thank you!!!) I } } will get decent response at the low masses, but as I get higher, the } } response is going to suck, thus making it very difficult to do } } quantitative analysis of compounds in the ppb concentration range. } } } } This then will lead them to the next question that I would like to } } confirm. They are then going to ask me to do SIM analysis of the } } pesticides. How can I go from a basic MS dataset to the exact masses } } required for a SIM experiment. I have a direct probe, so is it as } } simple as putting a sample of the pesticide on the end of the probe, } } sticking it in, and then using the scope to manually look for peaks?? } } } } I am new to the MS field but am of the thought that it will be very } difficult to detect ppb components in a mix with the direct probe method. } I would have imagined that one would require pre separation with a GC } column. Even with SIM you would not be able to quantify your levels as you } would not know which species are generating those ions, with the added } problem that some of these ions might be secondary ions ?? More } experienced users might be able to comment further and correct me on this } if I am wrong ??? I think I was pretty unclear on the above. (I was typing it after a long day at work and my mind was focussed on going home and watching Survivor and CSI). Anyways, I should have said to (1)use the probe on the neat compounds to determine the exact masses (2) inject single component mixes into the GC to determine the retention time and (3) then use those determined masses/RTs in a SIM experiment to do the quantitation. Marcel ****************************************************************************** From: Mudbunny Date: 20 Feb 2004 10:14:36 -0800 Subject: Re: NewBie: Help Organization: * Elijah Bailey wrote in message news:... } I got some mass spec data of blood samples (for cancer patients) } to analyze and it is distributed in 4 directories. } } NormalControl, Benign, Malignant, Reference } } I understand Benign and Malignant stand for cancer. What might be } NormalControl and Reference? I dont know any biology, just trying } my luck here if someone could help. I am not in Biology either, but Here is what I think. NormalControl indicates, to me, that you might be doing analyses of patients undergoing some sort of therapy. The NormalControl would be bloodsamples of patients who are not undergoing the treatment, or they may be of the patient before the treatment. To establish a baseline of sorts. Reference would be reference compounds or spectra. Of the chemo drug, normal blood components and the like. Keep in mind I am not experienced at all with blood chemistry or any biology at all. Good luck. Marcel ****************************************************************************** From: phil harris Date: 20 Feb 2004 12:03:35 -0800 Subject: frac pattern and background gas Organization: * I was working with a process mass spec (quadrupole) and observed what I saw as unusual results. Any advice on explaining these. To do our quantititative work, we need to determing the fractionation pattern of the gases of interest. In general, they are similar to the NIST library but each mass spec is a bit different. To determine our methane fractionation patter, we initially used a methane balance argon cylinder. However, when we ran a mixture that had both 50 % hydrogen and 20 % CO2 in it (along with argon and methane), we got significantly different fractionation patterns (ie ion current at masses 15, 14 and 13 were several percent different than they were for the methane/argon cylinder). I am not concerned that the absolute currents were different, but rather that their ratio was different as this indicates a change in the fractionation pattern. I can understand that as I change the gas composition, I can get different amounts of gas getting through the capillary leak, but I am not sure why the fractionation pattern changed. Is this due to ion molecule reactions, and the H2+ ions reaction with neutral species from the methane ? I would have thought that about 1 - 10 microtorr, these sort of reactions would be inconsequential. Any advice or suggestions ? Regards Phil ****************************************************************************** From: TObject Date: Sun, 22 Feb 2004 20:59:28 GMT Subject: Re: Databases Organization: * On peptide-catalog.com you can search for peptides by molecular weight. http://www.peptide-catalog.com/PC/Peptides Try google, it pulls out a number of such web sites. "Maxell" wrote in message news:c0osu6$4ut$1@news-int2.gatech.edu... } } Hi! } Where can I find a good database that is searchable on molecular } weight. It should preferably be free of charge. } ****************************************************************************** From: Kendall Date: Mon, 23 Feb 2004 03:01:06 GMT Subject: Re: Tryptic digests Organization: * } To set the scene I am currently involved in a creating a new E coli } database and part of what we plan to put in this database is a large } collection of experimental data from published work. } } One problem I am having at the moment is a number of proteomic } experiments show a predicted number of tryptic fragments but the actual } numbers vary hugely between different published work. My understanding, } as a geneticist, is that trypsin cuts like a restriction enzyme after } arginine or lysine residues and therefore I would have thought that the } number of fragments would be easy to predict. The numbers for specific } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } Could you tell me if my understanding of the specificity of trypsin } digest is correct and if not what it is? If so why would the predicted } number of fragemtns vary so much in the two examples? } } Regards } } Richard Richard- While I'm not entirely clear on what your stated numbers mean, let me take a stab at your questions anyway. First off, your understanding of the specificity of Trypsin is correct, though, depending on the specific amino acid sequence, there can be additional "rules". A brief explanation of these special cases of Trypsin behavior can be found at: http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html#Tryps I must admit, however, that I do not understand what your stated numbers for each of the two protein examples means (i.e., 19 or 27 for fep A). Do you mean that one source predicts 19 peptides and another predicts 27 peptides? Or do you mean that one source reports the *detection* of 19 peptides and another reports the detection of 27? If the numbers are theoretical numbers of peptides, I cannot answer your question. However, if the numbers are from two different sets of experimental results, there are several possibilities: 1. Trypsin digestion may not go to completion if the experimental conditions are not chosen properly. For instance, some proteins, under physiological conditions, are highly resistant to protease digestion (i.e., Ribonuclease A). However, under slightly destabilizing conditions, with the addition of some heat or a chemical denaturant, the folded protein structure "breaks down" allowing digestion to proceed to completion. 2. If all of the peptides are analyzed at the same time, i.e. a MALDI experiment or an electrospray (ESI) experiment without chromatographic separation, the ionization of some peptides will suppress the ionization of other peptides present in the mixture. This ionization suppression effect is widely observed when analyzing mixtures of peptides, and for this reason many times a chromatographic separation is coupled to a mass spec. in order to lower the number of peptides that are introduced to the mass spec at the same time. 3. MALDI and ESI experiments performed on the same peptide digest will often produce non-identical, but complimentary, results. Often MALDI can "see" some peptides that are not seen by ESI, and vice versa. Hope I understood your question and some of my ramblings were helpful; if not, let me know! -Kendall ****************************************************************************** From: David Stranz Date: Mon, 23 Feb 2004 13:58:09 -0600 Subject: Re: Tryptic digests Organization: * Kendall wrote in news:c1cud3$jbp$1@news-int2.gatech.edu: } } To set the scene I am currently involved in a creating a new E } coli } database and part of what we plan to put in this database } is a large } collection of experimental data from published } work. } } } One problem I am having at the moment is a number of proteomic } } experiments show a predicted number of tryptic fragments but } the actual } numbers vary hugely between different published } work. My understanding, } as a geneticist, is that trypsin cuts } like a restriction enzyme after } arginine or lysine residues } and therefore I would have thought that the } number of } fragments would be easy to predict. The numbers for specific } } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } } Could you tell me if my understanding of the specificity of } trypsin } digest is correct and if not what it is? If so why } would the predicted } number of fragemtns vary so much in the } two examples? } } } Regards } } } } Richard } } } Richard- } } While I'm not entirely clear on what your stated numbers mean, } let me take a stab at your questions anyway. First off, your } understanding of the specificity of Trypsin is correct, though, } depending on the specific amino acid sequence, there can be } additional "rules". A brief explanation of these special cases } of Trypsin behavior can be found at: } } http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.h } tml#Tryps } } I must admit, however, that I do not understand what your stated } numbers for each of the two protein examples means (i.e., 19 or } 27 for fep A). Do you mean that one source predicts 19 peptides } and another predicts 27 peptides? Or do you mean that one source } reports the *detection* of 19 peptides and another reports the } detection of 27? } } If the numbers are theoretical numbers of peptides, I cannot } answer your question. } } However, if the numbers are from two different sets of } experimental results, there are several possibilities: } 1. Trypsin digestion may not go to completion if the } experimental conditions are not chosen properly. For instance, } some proteins, under physiological conditions, are highly } resistant to protease digestion (i.e., Ribonuclease A). } However, under slightly destabilizing conditions, with the } addition of some heat or a chemical denaturant, the folded } protein structure "breaks down" allowing digestion to proceed to } completion. 2. If all of the peptides are analyzed at the same } time, i.e. a MALDI experiment or an electrospray (ESI) } experiment without chromatographic separation, the ionization of } some peptides will suppress the ionization of other peptides } present in the mixture. This ionization suppression effect is } widely observed when analyzing mixtures of peptides, and for } this reason many times a chromatographic separation is coupled } to a mass spec. in order to lower the number of peptides that } are introduced to the mass spec at the same time. } 3. MALDI and ESI experiments performed on the same peptide } digest will often produce non-identical, but complimentary, } results. Often MALDI can "see" some peptides that are not seen } by ESI, and vice versa. } } Hope I understood your question and some of my ramblings were } helpful; if not, let me know! } } -Kendall } } } An additional complication to the above is that in many cases "identification" of a peptide is made via a database search, using one of the many software programs and databases available. Failure to "identify" a peptide could mean that a) the peptide wasn't observed experimentally (due to reasons described above), b) the selection criteria for deciding which experimental m/z values to submit for the search excluded one or more of the observed peptides (signal too weak, too many peptides already on the list, whatever), c) the database has sequence errors, resulting in calculation of an incorrect theoretical mass for the peptide and therefore a failure to match numerically, d) the database doesn't contain information about post- translational modifications, and the experimental peptide is modified (thus again, a mismatch between observed and theoretical mass based on sequence), e) in ESI in particular, the charge state on the observed peptide wasn't correctly deduced from the data, and therefore the mass presented to the search is incorrect, f) the observed peptide has an adduct (such as sodium or potassium) that isn't accounted for by the search software (which might assume everything is protonated), g) the database doesn't contain the protein from which the peptide was derived, and therefore the protein reported as the "hit" is just plain wrong, or h) any one of a number of other ways things could go awry. Hope this "helps" :-) David ****************************************************************************** From: "Horler, R" Date: Tue, 24 Feb 2004 11:34:44 +0000 Subject: Re: Tryptic digests Organization: * Kendell Many thanks for your response. It has expanded my knowledge of MS although unfortunately the numbers are the predicted number of tryptic peptides. Other data i.e. detected number, understandably are also different but that was to be expected at least now i understand why a bit better. Many thanks Richard Kendall wrote: } } To set the scene I am currently involved in a creating a new E coli } } database and part of what we plan to put in this database is a large } } collection of experimental data from published work. } } } } One problem I am having at the moment is a number of proteomic } } experiments show a predicted number of tryptic fragments but the actual } } numbers vary hugely between different published work. My understanding, } } as a geneticist, is that trypsin cuts like a restriction enzyme after } } arginine or lysine residues and therefore I would have thought that the } } number of fragments would be easy to predict. The numbers for specific } } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } } } Could you tell me if my understanding of the specificity of trypsin } } digest is correct and if not what it is? If so why would the predicted } } number of fragemtns vary so much in the two examples? } } } } Regards } } } } Richard } } Richard- } } While I'm not entirely clear on what your stated numbers mean, let me take a } stab at your questions anyway. First off, your understanding of the } specificity of Trypsin is correct, though, depending on the specific amino } acid sequence, there can be additional "rules". A brief explanation of } these special cases of Trypsin behavior can be found at: } } http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html#Tryps } } I must admit, however, that I do not understand what your stated numbers for } each of the two protein examples means (i.e., 19 or 27 for fep A). Do you } mean that one source predicts 19 peptides and another predicts 27 peptides? } Or do you mean that one source reports the *detection* of 19 peptides and } another reports the detection of 27? } } If the numbers are theoretical numbers of peptides, I cannot answer your } question. } } However, if the numbers are from two different sets of experimental results, } there are several possibilities: } 1. Trypsin digestion may not go to completion if the experimental conditions } are not chosen properly. For instance, some proteins, under physiological } conditions, are highly resistant to protease digestion (i.e., Ribonuclease } A). However, under slightly destabilizing conditions, with the addition of } some heat or a chemical denaturant, the folded protein structure "breaks } down" allowing digestion to proceed to completion. } 2. If all of the peptides are analyzed at the same time, i.e. a MALDI } experiment or an electrospray (ESI) experiment without chromatographic } separation, the ionization of some peptides will suppress the ionization of } other peptides present in the mixture. This ionization suppression effect } is widely observed when analyzing mixtures of peptides, and for this reason } many times a chromatographic separation is coupled to a mass spec. in order } to lower the number of peptides that are introduced to the mass spec at the } same time. } 3. MALDI and ESI experiments performed on the same peptide digest will often } produce non-identical, but complimentary, results. Often MALDI can "see" } some peptides that are not seen by ESI, and vice versa. } } Hope I understood your question and some of my ramblings were helpful; if } not, let me know! } } -Kendall ****************************************************************************** From: bizzwire Date: Wed, 25 Feb 2004 01:23:07 GMT Subject: Re: Tryptic digests Organization: * One reason for the discrepency *could be* that several cleavage sites could result in the same tryptic fragment. for example, for example, say the sequence -X-R-R-X (where X is any non-arg/non-lys amino acid, R=Arginine) appears twice in the primary structure. Complete digestion will result in two monopeptide arginine fragments. Do you count this as one or two fragments? Besides simply relying on the output of a computer program, you might find it instructive to take a paper and pencil, and try determining the theoretical number of peptides based on some pretty straightforward cleavage rules. } From: "Horler, R" } Organization: * } Newsgroups: sci.techniques.mass-spec } Date: Fri, 20 Feb 2004 09:35:00 +0000 } Subject: Tryptic digests } } Hello } } To set the scene I am currently involved in a creating a new E coli } database and part of what we plan to put in this database is a large } collection of experimental data from published work. } } One problem I am having at the moment is a number of proteomic } experiments show a predicted number of tryptic fragments but the actual } numbers vary hugely between different published work. My understanding, } as a geneticist, is that trypsin cuts like a restriction enzyme after } arginine or lysine residues and therefore I would have thought that the } number of fragments would be easy to predict. The numbers for specific } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } Could you tell me if my understanding of the specificity of trypsin } digest is correct and if not what it is? If so why would the predicted } number of fragemtns vary so much in the two examples? } } Regards } } Richard } } } } } ****************************************************************************** From: David Stranz Date: Mon, 23 Feb 2004 13:58:09 -0600 Subject: Re: Tryptic digests Organization: * Kendall wrote in news:c1cud3$jbp$1@news-int2.gatech.edu: } } To set the scene I am currently involved in a creating a new E } coli } database and part of what we plan to put in this database } is a large } collection of experimental data from published } work. } } } One problem I am having at the moment is a number of proteomic } } experiments show a predicted number of tryptic fragments but } the actual } numbers vary hugely between different published } work. My understanding, } as a geneticist, is that trypsin cuts } like a restriction enzyme after } arginine or lysine residues } and therefore I would have thought that the } number of } fragments would be easy to predict. The numbers for specific } } proteins are 19 or 27(fepA) , 19 or 38(fhuA) for example. } } } Could you tell me if my understanding of the specificity of } trypsin } digest is correct and if not what it is? If so why } would the predicted } number of fragemtns vary so much in the } two examples? } } } Regards } } } } Richard } } } Richard- } } While I'm not entirely clear on what your stated numbers mean, } let me take a stab at your questions anyway. First off, your } understanding of the specificity of Trypsin is correct, though, } depending on the specific amino acid sequence, there can be } additional "rules". A brief explanation of these special cases } of Trypsin behavior can be found at: } } http://www.expasy.org/tools/peptidecutter/peptidecutter_enzymes.h } tml#Tryps } } I must admit, however, that I do not understand what your stated } numbers for each of the two protein examples means (i.e., 19 or } 27 for fep A). Do you mean that one source predicts 19 peptides } and another predicts 27 peptides? Or do you mean that one source } reports the *detection* of 19 peptides and another reports the } detection of 27? } } If the numbers are theoretical numbers of peptides, I cannot } answer your question. } } However, if the numbers are from two different sets of } experimental results, there are several possibilities: } 1. Trypsin digestion may not go to completion if the } experimental conditions are not chosen properly. For instance, } some proteins, under physiological conditions, are highly } resistant to protease digestion (i.e., Ribonuclease A). } However, under slightly destabilizing conditions, with the } addition of some heat or a chemical denaturant, the folded } protein structure "breaks down" allowing digestion to proceed to } completion. 2. If all of the peptides are analyzed at the same } time, i.e. a MALDI experiment or an electrospray (ESI) } experiment without chromatographic separation, the ionization of } some peptides will suppress the ionization of other peptides } present in the mixture. This ionization suppression effect is } widely observed when analyzing mixtures of peptides, and for } this reason many times a chromatographic separation is coupled } to a mass spec. in order to lower the number of peptides that } are introduced to the mass spec at the same time. } 3. MALDI and ESI experiments performed on the same peptide } digest will often produce non-identical, but complimentary, } results. Often MALDI can "see" some peptides that are not seen } by ESI, and vice versa. } } Hope I understood your question and some of my ramblings were } helpful; if not, let me know! } } -Kendall } } } An additional complication to the above is that in many cases "identification" of a peptide is made via a database search, using one of the many software programs and databases available. Failure to "identify" a peptide could mean that a) the peptide wasn't observed experimentally (due to reasons described above), b) the selection criteria for deciding which experimental m/z values to submit for the search excluded one or more of the observed peptides (signal too weak, too many peptides already on the list, whatever), c) the database has sequence errors, resulting in calculation of an incorrect theoretical mass for the peptide and therefore a failure to match numerically, d) the database doesn't contain information about post- translational modifications, and the experimental peptide is modified (thus again, a mismatch between observed and theoretical mass based on sequence), e) in ESI in particular, the charge state on the observed peptide wasn't correctly deduced from the data, and therefore the mass presented to the search is incorrect, f) the observed peptide has an adduct (such as sodium or potassium) that isn't accounted for by the search software (which might assume everything is protonated), g