****************************************************************************** From: Tobias Kind Date: 2 Jan 2003 02:42:18 -0800 Subject: Re: HELP: library and structure formula Organization: * Simon wrote in message news:... } I have recently create NIST library from the *.MSP file but now I have a } problem. I would like to insert the structure formula of the compounds in } the database. I have seen that in order to insert a structure in the Salve Simone Cristoni, use the nice LIB2NIST from NIST (Library Conversion Software) http://chemdata.nist.gov/mass-spc/Srch_v1.7/lib2nist.zip http://chemdata.nist.gov/mass-spc/Srch_v1.7/ Follow Readme III Molecular structures located in separate MOLfiles can be associated with the spectra located in a single .MSP file and converted into the user library. To achieve this the MOLfiles should have predefined names and be located in the folder with same name as the name of the input .MSP file and extension MOL. You can also use the alternative approach from David Sparkman. See some real world examples for Lib2Nist at: http://users.chartertn.net/slittle/hplib.html http://www.amdis.net/Chemometrics/Chemometric_examples/chemometric_examples.html Kind regards Tobias Kind www.amdis.net ****************************************************************************** From: Tanya Hoodbhoy Date: 3 Jan 2003 13:28:52 -0800 Subject: iodosobenzoic acid Organization: * Dear Mass Spectrometrists, Do any of you have experience using the chemical iodosobenzoic acid, which cleaves at tryptophan residues, to generate a peptide fragment for MS/MS analysis? If so, I would be interested in the company/product # you purchased the chemical from and a brief protocol on how it was used. Thank you. Tanya Hoodbhoy ****************************************************************************** From: Ramon.M.Barnes Date: Sun, 05 Jan 2003 10:01:51 -0500 Subject: 2004 Winter Conference Call for Papers Organization: * 2004 Winter Conference on Plasma Spectrochemistry Fort Lauderdale, Florida, January 5-10, 2004 Call for Papers The 13th biennial international Winter Conference will be held at the Wyndham Resort and Spa (www.wyndham.com/bonaventure) in Fort Lauderdale, Florida (www.sunny.org). More than 600 scientists are expected, and over 300 papers on modern plasma spectrochemistry will be presented. Symposium Features Elemental speciation, speciation sampling and sample preparation Excitation mechanisms and plasma phenomena Flow injection and flow processing spectrochemical analysis Glow discharge atomic and mass spectrometry Inductively coupled plasma atomic and mass spectrometry Laser ablation and breakdown spectrometry Microwave atomic and mass spectrometry Plasma chromatographic detectors Plasma instrumentation, microplasmas, automation, and software innovations Sample introduction and transport phenomena Sample preparation, treatment, and automation; high-purity materials Spectrochemical chemometrics, expert systems, and software Spectroscopic standards and reference materials, databases Stable isotope analyses and applications Preliminary abstracts (50 words) are solicited on original plasma spectrochemical methods and applications. Abstract deadline is July 3, 2003. Manufacturers of spectroscopic instrumentation and accessories also are invited to exhibit equipment, glassware, publications, and software. Early-bird registrations received before July 3, 2003, will be offered at 2002 Winter Conference rates. Also Continuing Education Short Courses, Friday - Sunday, January 2 - 4 Manufacturer's Seminars, Friday - Sunday, January 2 - 4 5th Annual Golf Tournament, Sunday, January 4 Five Provocative Panel Discussions, Daily Workshop on New Plasma Instrumentation, Tuesday-Thursday, January 6 - 8 For program, registration, hotel, and transportation details, contact Ramon Barnes, ICP Information Newsletter, Inc., P.O. Box 666, Hadley, MA 01003-0666. Phone: 413-256-8942, fax 413-256-3746, e-mail winterconf@chem.umass.edu, http://www-unix.oit.umass.edu/~wc2004. ****************************************************************************** From: Fred Mellon Date: Mon, 6 Jan 2003 09:27:33 -0000 Subject: Re: iodosobenzoic acid Organization: * No personal experience but a colleague (who hasn't used it for years) recommends that you consult http://www.abrf.org/archives/hmail/9924/0038.html for the thread of a discussion on this topic and some recipes. Sigma Aldrich (product no. I8000) and US Alchemy are two of several suppliers. regards, Fred -- Dr Fred A Mellon Institute of Food Research Norwich Research Park Colney Norwich NR4 7UA UK tel +44(0) 1603 255299 fax +44(0) 1603 255038 email: fred.mellon@bbsrc.ac.uk web: www.metabolomics-nrp.org.uk "Tanya Hoodbhoy" wrote in message news:av502r$1de$1@news-int.gatech.edu... } Dear Mass Spectrometrists, } Do any of you have experience using the chemical iodosobenzoic acid, } which cleaves at tryptophan residues, to generate a peptide fragment } for MS/MS analysis? If so, I would be interested in the } company/product # you purchased the chemical from and a brief protocol } on how it was used. } } Thank you. } } Tanya Hoodbhoy ****************************************************************************** From: Marc Engel Date: Mon, 06 Jan 2003 10:09:06 -0500 Subject: voc libraries Organization: * I have been given a project to start a program to analyze vended water samples for VOC's by GCMS. We have an HP/Agilent GCMS with Enhanced ChemStation G1701CA C.00.00 software. We did not purchase any MS libraries for this system. Can someone recommend a library suitable for this analysis either commercial software or free ware. Thanks Marc ****************************************************************************** From: David Sparkman Date: Mon, 06 Jan 2003 17:19:14 GMT Subject: Re: voc libraries Organization: * Marc, You can use either the NIST02 NIST/EPA/NIH Mass Spectral Database, the Wiley7, or the Wiley7N for these compounds. The NIST has a very nice search program and AMDIS which can be valuable in these types of analyses. Another approach would be to build your own library using the ChemStation Library utility. Regards; David -- O. David Sparkman Consultant-At-Large ods@compuserve.com "Marc Engel" wrote in message news:avc6i0$8cv$1@news-int.gatech.edu... } I have been given a project to start a program to analyze vended water } samples for VOC's by GCMS. We have an HP/Agilent GCMS with Enhanced } ChemStation G1701CA C.00.00 software. We did not purchase any MS } libraries for this system. Can someone recommend a library suitable for } this analysis either commercial software or free ware. } Thanks } Marc } } ****************************************************************************** From: Mike Sherrell Date: Mon, 6 Jan 2003 14:45:00 -0800 Subject: LC/Mass specs and MALDIs available Organization: * LC/Mass specs and MALDIs for sale: **LC/MS & MS/MS: Sciex Q-Star: $235,000. Pulsar, not Pulsar I. $16K/factory install. Sciex API 2000: $79,500. NT; decommissioned and AB- certified eligible for svc. contract. Sciex API 150EX: $75,000. Includes HPLC system. Sciex API 150EX: $55,000. Installed. Sciex API 100: $21,000. Installed. Sciex API III+: $25,000. Triple quad: ES, APCI; +$15K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $15,000/installation and 1 year service contract. Sciex API APCI source: $6,000. HP 1100 MSD: $75,000. Model A upgraded to D; ESI and APCI; new optical assembly, new power supply, new analyzer board and new Smartcard. HP 1100 MSD: $39,000. Model A; esi + APCI. Micromass Ultima: $165,000. Quattro; ESI, APCI; new July 2000. Outside US only. MM-certified. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC. Micromass LCZ Pltfrm: $45,000. ESI, APCI; + $5K/install, and 90-day warr. VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Finnigan LCQ Classic: $77,500. API, installed, 1 year warranty, 4000 amu upgrade. LCQ Classic ESI source: $6,000. New/unused ESI source. Finnigan LCQ Deca: $185,000. XP model. 1 year warranty; probes sold separately. Finnigan LCQ Deca: $168,900. 1000 model. Installed w/ 1 year warranty; sources sold separately. Finnigan Navigator: $42,500. Guaranteed good working order. Finnigan TSQ 7000: $60,000. ES, APCI, API 1, Excalibur, good working order. Finnigan TSQ 7000: $75,000. API 2, ES, APCI, Excalibur, installation and warranty included. Finnigan SSQ 7000: $40,000. ES, APCI; Excalibur; API 1 source; install included. Finnigan TSQ 700: $18,000. Electrospray, APCI, Alpha workstn. ~$3K/install. Finnigan SSQ 710: $14,000. Electrospray, APCI. Good working order. Finnigan MAT 900: $40,000. Offers considered. EI, ES, APCI. Finnigan Mat ITS40W. -offers-. With Varian 3400 GC + A200s Auto Sampler. Bruker Esquire LC: $60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract. Xtrell 400 ELQ: $20,000. Or best offer. LC/MS/MS, GC/MS/MS; 10 yrs. old, floor model, well-maintained. 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. VG 7070-EHF. small $s. 1984 model; used for FAB. MM Autospec S: $65,000. European install included; available in US. MM Autospec V: $75,000. European install included; available in US. Kratos Concept. -free-. Except you pay for removal. Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs:. Voyager DE STR: $165,000. New Oct. 2000. Shipping/installation extra. Voyager DE Pro: $145,000. Incl. factory install, certification. Voyager DE: $75,000. 1998 model. Good working order. Voyager DE RP: $50,000. Late '97 model; new detector and laser, rebuilt pump. Micromass Q-Tof 2: $320,000. 2001 model; currently under service contract. Micromass LCT. ~$200,000. API-TOF. Includes HPLC. New July 2000. Bruker Biflex III. ~$50,000. DE; decommissioned by Bruker. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Finnigan LaserMAT 2000: $19,000. Installed w/ 90-day warranty. 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: $5,000. Or best offer. For parts; new laser card and other new boards. **ICP-MS:. Micromass Platform: $69,000. Or best offer. New in box; purchased 7/2001. Install, warr. available. Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. **Other mass specs, NMRs, DNA/protein sequencers & synthesizers available; check the website. All listed items subject to prior sale. Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: "Johnson, Eric M (Coryton)" Date: Mon, 6 Jan 2003 17:14:54 -0000 Subject: Help - How Do I get peak maxima to coincide in SIM Mode Organization: * Can anyone help me resolve my problem :- Have an old HP 5971/5890 System....has never been working so good since I cleaned and fixed virtually every lek on the system....but thats another story. Trying to setup a method to determine PAH's. The problem I have is that I was planning to use three ions to identify each PAH (along with internal standard time windows)and the main ion to quantitate. However I'm finding that I am unable to use three ions because the peak maxima for the individual SIM traces do not exactly have the same retention time. When the RT are all the same to the 2nd decimal place....say 28.27min the the three ions work and can get a posotive ID. However for most of the time I find that at least one of the three ions is 0.01min adrift from the other two and so cannot use the ion ratios for Identification....get a hash sign '#' on the report. Have tried using RTE integration with both centroid and peak top identification....to no avail. Also tried altering the time identification window and again no good. Seems that unless all 3 ions have exactly the same RT then no matter what I do I cannot get the software to identify the peak (HP software...oldish version though !). To solve this, I am thinking of using only two ions to identify the compound and/or changing the number of ions I use for monitoring in each Ion Group. Does the number of ions and dwell time effect the peak tops. For instance if I only monitored 2 ions with same dwell then would you expect peaks to be bang on same RT (obviously for a standard compound which is known to have the ions present). So thinking of experimenting with the ions per window and maybe dwell, but can't see why the software can't accept that a SIM peak could have a time tolerence. Maybe my software has bugs...or is too old to work. The HP help suggests that It should work...but I'm at a loss as what to do next. Is there something in the calibration file parameters which I'm missing....ior a standard way of setting it up to get it to work for multiple ions.....maybe this is a known problem....I've always only used 1 SIM ion in the past for most applications and so not come across this problem before. Any help or comments appreciated. May need to upgrade my software but at what cost ! Thanks Eric M Johnson ****************************************************************************** From: David Sparkman Date: Tue, 07 Jan 2003 15:08:29 GMT Subject: Re: Help - How Do I get peak maxima to coincide in SIM Mode Organization: * Eric, You have one of those damned-if-I-do and damned-if-I-don^Òt situations. You probably have very narrow chromatographic peaks. Therefore, the concentration of the analyte in the ion source is changing very rapidly. This means that you have different concentrations of analyte when you are monitoring different ions. The chromatographic peaks are nothing more that a connection of the dots that represent the ion current for each of your three ions with the highest dot becoming the apex of the chromatographic peak and, thus, the retention time. You can try spending less time on each ion during the SIM analysis. This will result in more points across the chromatographic peak but could result in reduced sensitivity. If you are looking for good quantitation, you will want to have between 15 and 20 points (3-ion spectra) that represent the chromatographic peaks. More than 20 points will not improve your results. You may want to address this question to Dr. ChemUser at http://www.chemuserworld.com. This is a site that specializes in questions about Agilent GC/MS, LC/MS, GC, and LC ChemStations. Regards; David -- O. David Sparkman Consultant-At-Large ods@compuserve.com "Johnson, Eric M (Coryton)" wrote in message news:aveofg$n4p$1@news-int.gatech.edu... } Can anyone help me resolve my problem :- } } Have an old HP 5971/5890 System....has never been working so good since I } cleaned and fixed virtually every lek on the system....but thats another } story. } } Trying to setup a method to determine PAH's. The problem I have is that I } was planning to use three ions to identify each PAH (along with internal } standard time windows)and the main ion to quantitate. However I'm finding } that I am unable to use three ions because the peak maxima for the } individual SIM traces do not exactly have the same retention time. When the } RT are all the same to the 2nd decimal place....say 28.27min the the three } ions work and can get a posotive ID. However for most of the time I find } that at least one of the three ions is 0.01min adrift from the other two and } so cannot use the ion ratios for Identification....get a hash sign '#' on } the report. Have tried using RTE integration with both centroid and peak } top identification....to no avail. Also tried altering the time } identification window and again no good. Seems that unless all 3 ions have } exactly the same RT then no matter what I do I cannot get the software to } identify the peak (HP software...oldish version though !). } } To solve this, I am thinking of using only two ions to identify the compound } and/or changing the number of ions I use for monitoring in each Ion Group. } Does the number of ions and dwell time effect the peak tops. For instance } if I only monitored 2 ions with same dwell then would you expect peaks to be } bang on same RT (obviously for a standard compound which is known to have } the ions present). So thinking of experimenting with the ions per window } and maybe dwell, but can't see why the software can't accept that a SIM peak } could have a time tolerence. Maybe my software has bugs...or is too old to } work. The HP help suggests that It should work...but I'm at a loss as what } to do next. Is there something in the calibration file parameters which I'm } missing....ior a standard way of setting it up to get it to work for } multiple ions.....maybe this is a known problem....I've always only used 1 } SIM ion in the past for most applications and so not come across this } problem before. } } Any help or comments appreciated. May need to upgrade my software but at } what cost ! } } Thanks } Eric M Johnson } } ****************************************************************************** From: gary_bauer Date: Wed, 8 Jan 2003 08:22:56 -0800 Subject: January BAMS meeting Organization: * Wednesday, January 22, 2003 6:00 pm to 10:00 pm Dominic's at Oyster Point 360 Oyster Point Boulevard South San Francisco, CA 94080 (650) 589-1641 For Dinner Reservations: please go to http://www.acteva.com/go/bams. Speaker: Ansgar Brock, Genomics Institute of the Novartis Research Foundation, San Diego, CA Title: "An Integrated Proteomics Platform Based on Multidimensional Chromatography Coupled to High Performance MALDI QFT-ICR MS" Authors: Ansgar Brock, Eric C. Peters, David M. Horn, Christer Ericson, Qui Phung, Scott Ficarro, Art Salomon, Laurence M. Brill Abstract It is now well recognized that the sheer complexity and ever changing nature of the proteome necessitates the development of more powerful, higher-throughput analysis methods. Although throughput can be increased simply by constructing parallel analysis systems, a more elegant approach involves the development of new integrated platforms within which all aspects of the analysis process from sample preparation to data analysis are chosen and optimized with respect to the other components in order to maximize the output of the overall system both in terms of the amount and quality of the data produced. Here we describe a robust, highly automated analysis platform that effectively combines the flexibility and high peak capacity of multi-dimensional liquid chromatography with the high dynamic range and unsurpassed characterization power of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). A matrix-assisted laser desorption/ionization (MALDI) interface is employed to eliminate the experimental limitations imposed by online electrospray coupling. Re-addressable records of thefinal reversed-phase separations are automatically produced using a novel deposition device that simultaneously deposits the effluents of multiple HPLC columns onto surface-patterned MALDI targets through an electrically mediated process. The sample concentration and localization provided by the hydrophobic/hydrophilic targets allow rugged automation of both the separation and the acquisition process. Specifically, the concentration and localization of the deposited samples onto specific locations on the MALDI target plates allows mHPLC methods to be employed rather than the operationally more difficult nano-HPLC without a loss in sensitivity and also obviates the need for "sweet spot" searching during the MALDI process. A unique lysine-specific labeling reagent enables differential quantitation while simultaneously preventing the reported dominance of arginine containing peptides in MALDI MS analyses, thus further increasing the amount of information obtained per analysis. The sample plate is first automatically scanned in the MS mode only, the high dynamic range and exceptional mass accuracy of FT-ICR being maintained by true internal calibration of each spectra using a novel gas phase ion mixing scheme. Data reduction and database searching are performed concomitantly using customized software programs. The resulting monoisotopic masses, integrated intensities, and identifications based on accurate mass measurements and amino acid compositional information are stored in a database. Tandem MS measurements can then automatically be performed as required based on user selected criteria applied to the MS output. Data from the automated analysis of protein digests from both Thermotoga maritima and yeast are used to demonstrate the performance of the overall system. Background: Ansgar Brock received his Diploma in Chemistry from the University of Karlsruhe, Germany and a Ph.D. in Physical Chemistry from Baylor University in 1996. He worked as Postdoctoral associate at Stanford University from 1996-1999 with Professor Richard N. Zare on the development of Hadamard Transform TOF MS. In 1999 Dr. Brock joined the newly founded Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, CA, where he is currently Group Leader of the Protein Profiling Group in the Protein Science Department. His main responsibilities are in the areas of new technology development for proteomics and management of the support for a number of scientific projects at GNF and The Scripps Research Institute in La Jolla. Research interests are in biotechnology, bioanalytical chemistry, separations/mass spectrometry, mass analyzer development, process automation. Meeting Details Date: Wednesday, January 22, 2003 Time: 6:00 pm Social hour and registration 7:00 pm Dinner 8:15 pm Presentation (free) Dinner: Choice of: Grilled Chicken baked with tomatoes, basil & jack cheese Petrale Sole stuffed with dungeness crab & shrimp in butter Stuffed Portabello Mushroom Cost: $25.00 BAMS and SAS members $35.00 Non-members. $15.00 Students only. ALL RESERVATIONS required by noon Friday January 17, 2003 Nothing comes as such a surprise to man as old age Leon Trotsky ****************************************************************************** From: Gr8estgary Date: 08 Jan 2003 04:09:23 GMT Subject: Re: Help - How Do I get peak maxima to coincide in SIM Mode Organization: * You can change a parameter that defines how close in time the 3 ion peaks must be in order to be accepted. Coelution time I think. The # means the target and qualifier ions are not within the time or the quant ratios are outside the acceptable limits. Decreasing the dwell time may help and also the order you enter the ions in the group during aquisition. Better still use an LC with UV & Flouescence detectors and you don't have to worry about crappy GC column separation. ****************************************************************************** From: Hubert Date: Thu, 09 Jan 2003 03:10:12 +0000 Subject: Re: Help - How Do I get peak maxima to coincide in SIM Mode Organization: * Eric, You may try the followings:- In your RTE integrator, select "Extended Area Quant" in your "Subtraction Method". Also, under the "output", lower the "minimum peak area". It may be critical if the area counts of the qualifier ions are too small to be integrated. Hope these help. Hubert "Johnson, Eric M (Coryton)" wrote... } } Can anyone help me resolve my problem :- } Have an old HP 5971/5890 System....has never been working so good since I } cleaned and fixed virtually every lek on the system....but thats another story. } Trying to setup a method to determine PAH's. The problem I have is that I } was planning to use three ions to identify each PAH (along with internal } standard time windows)and the main ion to quantitate. However I'm finding } that I am unable to use three ions because the peak maxima for the } individual SIM traces do not exactly have the same retention time. When the } RT are all the same to the 2nd decimal place....say 28.27min the the three } ions work and can get a posotive ID. However for most of the time I find } that at least one of the three ions is 0.01min adrift from the other two } and so cannot use the ion ratios for Identification....get a hash sign '#' on } the report. Have tried using RTE integration with both centroid and peak } top identification....to no avail. Also tried altering the time } identification window and again no good. Seems that unless all 3 ions } have exactly the same RT then no matter what I do I cannot get the software to } identify the peak (HP software...oldish version though !). } To solve this, I am thinking of using only two ions to identify the } compound and/or changing the number of ions I use for monitoring in each Ion } Group. } Does the number of ions and dwell time effect the peak tops. For instance } if I only monitored 2 ions with same dwell then would you expect peaks to } be bang on same RT (obviously for a standard compound which is known to have } the ions present). So thinking of experimenting with the ions per window } and maybe dwell, but can't see why the software can't accept that a SIM } peak could have a time tolerence. Maybe my software has bugs...or is too old } to work. The HP help suggests that It should work...but I'm at a loss as } what to do next. Is there something in the calibration file parameters which } I'm missing....ior a standard way of setting it up to get it to work for } multiple ions.....maybe this is a known problem....I've always only used } 1 SIM ion in the past for most applications and so not come across this } problem before. } Any help or comments appreciated. May need to upgrade my software but at } what cost ! } Thanks } Eric M Johnson ****************************************************************************** From: Phil Date: Thu, 9 Jan 2003 15:45:57 +0100 Subject: NIST 2.0 Search help Organization: * Hi there, Maybe I am blind or something, but I just can't see how to create a NEW library from within the Librarian tab or elsewhere!! Can anyone help? Thanks Phil ****************************************************************************** From: Jean Francois Borny Date: Thu, 9 Jan 2003 13:51:31 -0600 Subject: Hewlett Packard (now Agilent) GCD Organization: * I'm setting up a GCD. It is currently set up on windows 3.11 (yuk). I have been told that there is no way to upgrade to anything else. Any ideas? Any suggestions? Any upgrades for the GCD software out there? Thanks. ****************************************************************************** From: David Sparkman Date: Fri, 10 Jan 2003 00:04:00 GMT Subject: Re: NIST 2.0 Search help Organization: * Phill, Highlight the spectra in the Librarian Tab Spec List that you want to add to a NEW user library. Click the icon that displays the tool tip "Add to Library". These icons are located just above the spec list and as you drag the Mouse pointer over them, the labels will appear. After Clicking on the Add to Library icon, a dialog box opens. Type the name you want to give your NEW library in the appropriate space at the top of the dialog box. Then put the Mouse pointer on the OK button and click the left Mouse button. You have just created a NEW library. You can then add spectra to it as you want. Regards; David -- O. David Sparkman Consultant-At-Large ods@compuserve.com "Phil" wrote in message news:avka4e$f32$1@news-int.gatech.edu... } Hi there, } } Maybe I am blind or something, but I just can't see how to create a NEW } library from within the Librarian tab or elsewhere!! } } Can anyone help? } } Thanks } } Phil } } } ****************************************************************************** From: Phil Date: Fri, 10 Jan 2003 10:29:59 +0100 Subject: Re: Hewlett Packard (now Agilent) GCD Organization: * Nope... No way...I know for a fact that data reduction will work even under W2K, but as far as acquisition, you can just forget it!! The GCD was meant to be a way to attact "chromatographers" to the world of MS. No further developments were made on it and it died quietly... Bad luck! Phil ****************************************************************************** From: Peter Bradley Date: Fri, 10 Jan 2003 14:52:50 -0500 Subject: Fans for Quattro Organization: * Hi all, I have a colleague who has a triple-quad Quattro LC/MS (1993-94) in which two of the fans in the electronic module have burnt out. These fans are manufactured by Papst (labeled: TYP 3978, 240 V~50/60Hz, 10/9 W). He has tried to contact the manufacturer with no luck. Does anybody know of a supplier for these fans or even if someone has some spare ones they are willing to unload. Thanks for any information. Peter -- Peter Bradley, Chemist PMRA, Health Canada Email: bradleyp@inspection.gc.ca Tel: +1 (613) 759-1285 ****************************************************************************** From: Ricksfbrsc Date: 12 Jan 2003 13:14:27 GMT Subject: Re: Hewlett Packard (now Agilent) GCD Organization: * Agilent has not changed their data format, so that once you have the data you can process it on a current Chemstation system. You'll probably also find that your data on Win 3.11 is not Y2K compliant. I have a MS Engine (5989) and I take the data on an old Win 3.11 PC which is networked to a Win2000 PC with a recent version of ChemStation. I transfer the data over the network to the modern PC and the Y2K issue goes away and all works fine. Also, they make a KVM switch (Global Computer or any other supplier) which allows you to share one keyboard, video display (monitor), and mouse for more than one PC which saves a lot of space since you use 2 PCs to control one instrument. ****************************************************************************** From: Chris Fiot Date: Sun, 12 Jan 2003 15:43:58 GMT Subject: Re: Hewlett Packard (now Agilent) GCD Organization: * Jean Francois Borny wrote in message ... }I'm setting up a GCD. It is currently set up on windows 3.11 (yuk). I have }been told that there is no way to upgrade to anything else. } }Any ideas? Any suggestions? Any upgrades for the GCD software out there? } }Thanks. } Hello Jean Francois, You may want to take a look at MStation, Acquisition Solutions software package. Not only you can use your GCD with a 32 bit Windows version; but you can possibly increase the mass range of the GCD; increase the sensitivity of the GCD by at least a factor 10 (EMeter option); perform multiple Experiment (SIM/Scan within one injection); acquire profile data (raw) over the full mass range. You do not need to upgrade your current ChemStation reduction and sequencing program, because MStation addition is compatible with ChemStation. The basic upgrade, software and hardware (including PC) is sold for $7375. The improved electrometer option (EMeter) is priced $1500. You can find more information on our product at http://home.flash.net/~acqsol/gcd.htm Sincerely, Christian Fiot Acquisition Solutions k " providing the tools to improve your instruments " 7610 Edgeway Dr Houston, Texas 77055 Tel : 713 957 2644 Web : www.flash.net/~acqsol/ ****************************************************************************** From: Karen/Glenn Date: Sun, 12 Jan 2003 11:12:43 -0500 Subject: Atomic Mass Units? Organization: * What is the correct unit to use when referring to a mass range for a mass spectrometer. Do I write" the mass spectrometer was scanned from 50 to 450 amu" or from "50 to 450 u" According to NIST, the correct unit is "u" http://physics.nist.gov/cuu/Units/outside.html What is the correct unit to use in an ACS publication? So if anyone actually knows the answer, let me know. Thanks ****************************************************************************** From: bas Date: 13 Jan 2003 01:00:29 -0800 Subject: Re: Instrument selection (was: Api4000 and Finnigan Quantum) Organization: * Great Tips !!!! tnx for the help, whe are going for the new tsq quantum..... greets bas ****************************************************************************** From: Dr. Dickie Date: Mon, 13 Jan 2003 06:43:48 -0500 Subject: Re: Atomic Mass Units? Organization: * Karen/Glenn wrote: } What is the correct unit to use when referring to a mass range for a mass } spectrometer. Do I write" the mass spectrometer was scanned from 50 to 450 } amu" or from "50 to 450 u" } } According to NIST, the correct unit is "u" } } http://physics.nist.gov/cuu/Units/outside.html } } What is the correct unit to use in an ACS publication? So if anyone } actually knows the answer, let me know. } } Thanks The correct units would be m/z which CAN be expressed as "u" (according to some people--I personally do not like that) or Da (which would be wrong, but I see it done). I would list them as m/z. This is currently still in the battleground area of mass spec. last I heard. Looking in the latest issue of Analytical Chemistry, I see m/z used. The latest JASMS has m/z used (note this is not an ACS publication). Check in the Journal that you want to publish in. -- Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ------------------------------------------------------ "The important thing is not to stop questioning. Curiosity has its own reason for existing." A. Einstein ****************************************************************************** From: "Little, James - Eastman" Date: Mon, 13 Jan 2003 09:46:52 -0500 Subject: Re: NIST 2.0 Search help Organization: * I created a document with pictures that I hope will answer your question.. http://users.chartertn.net/slittle/temp/add.pdf Also, There is a lot of information on my web page under the nist search section "A Little Mass Spectrometry and Sailing": http://users.chartertn.net/slittle particularly at http://users.chartertn.net/slittle/files/documentation.pdf )From: Phil wrote.. ) )Hi there, ) )Maybe I am blind or something, but I just can't see how to create a NEW )library from within the Librarian tab or elsewhere!! ) )Can anyone help? ) )Thanks )Phil James L. Little Bldg 150 Eastman Chemical Company Kingsport, TN 37662-5150 Tel 423-229-8685 FAX 423-229-4558 ****************************************************************************** From: Les Dickson Date: Mon, 13 Jan 2003 09:30:24 -0500 Subject: Guidance on specifying masses for quadrupole MS methods Organization: * I am looking for information, in the form of recommendations or directives from relevant organizations such IUPAC or ASMS, on the appropriate number of decimal points to specifiy for masses in an analytical protocol where a quadrupole MS with unit resolution is used for SIM experiments. Given that an integer mass will likely be out some fraction due to mass defect, can I properly use 1 decimal point, or even 2 to specify a mass under those circumstances? Pointers to relevant documents, and perhaps some personal experience, would be appreciated. Dr. Les Dickson Canadian Food Inspection Agency dicksonl@inspection.gc.ca ****************************************************************************** From: Joerg Hau Date: Mon, 13 Jan 2003 17:47:02 +0100 Subject: Re: Atomic Mass Units? Organization: * Hi Karen/Glenn, } What is the correct unit to use when referring to a mass range for } a mass spectrometer. Do I write "the mass spectrometer was scanned } from 50 to 450 amu" or from "50 to 450 u" A mass spectrometer usually determines only the mass-to-charge ratio, so IMHO it should read "from m/z 50 to m/z 450" (with the "m/z" written in italics). Using "u" or "amu" would imply that you directly measured absolute masses, and I have some difficulties believing that ;-) } What is the correct unit to use in an ACS publication? So if anyone } actually knows the answer, let me know. IIRC we've always used "m/z", and nobody ever complained. When in doubt for a specific journal, look up their Author's Guidelines, the website, or the editor. Cheers + HTH, - Joerg -- joerg.hau(at)swissonline.ch * Lausanne, Switzerland http://www.mysunrise.ch/users/joerg.hau/ "All standard disclaimers apply". ****************************************************************************** From: Chip Cody Date: 13 Jan 2003 10:41:03 -0800 Subject: Re: Atomic Mass Units? Organization: * Mass spectrometers measure mass-to-charge ratio. The symbol for this is "m/z" (printed in italics) which should be used to describe a scan range. Therefore "the mass spectrometer was scanned from m/z 50 to m/z 450". The correct unit for mass is "u" for the unified atomic mass unit. Don't use "amu" which is based on an obsolete standard. There is a detailed discussion of these and other terms in David Sparkman's "Mass Spec Desk Reference" available from lcms.com. Chip Cody Dr. Dickie wrote in message news:... } Karen/Glenn wrote: } } } What is the correct unit to use when referring to a mass range for a mass } } spectrometer. Do I write" the mass spectrometer was scanned from 50 to 450 } } amu" or from "50 to 450 u" } } } } According to NIST, the correct unit is "u" } } } } http://physics.nist.gov/cuu/Units/outside.html } } } } What is the correct unit to use in an ACS publication? So if anyone } } actually knows the answer, let me know. } } } } Thanks } } The correct units would be m/z which CAN be expressed as "u" (according to some } people--I personally do not like that) or Da (which would be wrong, but I see it } done). I would list them as m/z. } This is currently still in the battleground area of mass spec. last I heard. } Looking in the latest issue of Analytical Chemistry, I see m/z used. } The latest JASMS has m/z used (note this is not an ACS publication). } Check in the Journal that you want to publish in. } } } -- } } Dr. Dickie } Skepticult member in good standing #394-00596-438 } Poking kooks with a pointy stick } ------------------------------------------------------ } "The important thing is not to stop questioning. } Curiosity has its own reason for existing." } A. Einstein ****************************************************************************** From: Greg Barton Date: 13 Jan 2003 11:52:01 -0800 Subject: Re: Instrument selection (was: Api4000 and Finnigan Quantum) Organization: * bas wrote in message news:... } Great Tips !!!! } } tnx for the help, whe are going for the new tsq quantum..... } } greets } } bas Bas, could you please share you knowledge, and let us know, what were the reasons for your decision? Greg ****************************************************************************** From: Lee Ferguson Date: 13 Jan 2003 15:19:45 -0800 Subject: Re: Fans for Quattro Organization: * Peter Bradley wrote in message news:... } Hi all, } } I have a colleague who has a triple-quad Quattro LC/MS (1993-94) in which two of the fans in the electronic module have burnt } out. These fans are manufactured by Papst (labeled: TYP 3978, 240 V~50/60Hz, 10/9 W). He has tried to contact the manufacturer } with no luck. Does anybody know of a supplier for these fans or even if someone has some spare ones they are willing to } unload. Thanks for any information. } } Peter Peter, I seem to remember replacing one or two of these fans on an old Quattro I that I used to work on. I believe I found replacements at an Active Electronics (http://www.activestores.com/) store on Long Island, New York. If I remember correctly, the replacements weren't made by Papst. Lee ****************************************************************************** From: J.Rooke Date: 14 Jan 2003 03:23:48 -0800 Subject: Mass Spectral File Formats Organization: * I am trying to write a VB routine which will read the HP Chemstation (.ms) files and enable me to extract the data and plot the chromatogram as a series using either TeeChart or some other graphing package. I've seen a thread from November 2002 which lists the file format of the spectral files, but I'm beginning to think that this is a much older format as part way through the file reading process, the output does not make sense. Does anyone have an idea of how I can extract these data files to a more usable format and pull out the correct values as they are stored? ****************************************************************************** From: Minaz Lakha Date: Tue, 14 Jan 2003 09:53:46 -0800 Subject: C,H,N & S simultaneous anlysis, EA 1108 Organization: * Hi I am using Carlo Erba 1108 instrument and my problem is S analysis I am trying to analyze C,H,N & S simultaneously Parameter about the analysis: Single combustion tube made of Starting from outlet of the tube 1) 4cm quartz wool 2) 8cm of pure reduced Cu 3) 2cm of quartz wool 4) 8cm of Tungstic oxide catalyst 5) 1cm of quartz wool Column 80 mesh porapack column ( prepacked in stainless steel) combustion tube/reduction connected to column by Teflon tubing Flows He flow @ 100 ml/min (85 kpa on instrument regulator) Oxygen @ 50 ml/min ( 75 kpa on " " ) Temp setting Column Temp @ 80 deg C Left oven temp i.e temp of the combustion tube ( with the reduction) @ 1020 deg C Right oven temp ( is empty) @ 500 deg C Sample drop time currently is best at 17 sec. Oxygen injection time for 60 sec. I am not getting a linear calibration curve for S (Calibration based on K factors) I am using sulfanilamide as a standard My C, H & N calibration curve for sulfanilamide is perfect & linear and my values for acetanilide (run as unknown against the sulfanilamide standard) are correct, but my S calibration curve is not linear at all. I can not seem to find a cure for the scattered points for S Does anyone have any suggestions Please if you need more info e me Thank you once again for your help Cheers! Minaz Lakha Dept. of Chemistry University of B.C. ****************************************************************************** From: Ron Orlando Date: Tue, 14 Jan 2003 15:57:29 -0500 Subject: Atlanta/Athens MSDG Meeting 2-10-03 Organization: * The next meeting of the Atlanta/Athens MS discussion group will be held at the CCRC auditorium on Monday, February 10 at 7:00 PM. The speaker for the evening is Professor Neil Kelleher (Department of Department of Chemistry, University of Illinois), who will give us a presentation entitled "Emerging Q-FTMS Instrumentation for MS-Based Enzymology and Top Down Proteomics". I am sure that this will be an interesting talk so please mark your calendars. As always, I need to thank our corporate sponsors. Please let me know if you have any questions regarding the upcoming meeting. We hope everyone will be able to attend. Ron -------------- Corporate Sponsor of AAMSDG Amersham Pharmacia Biotech Inc. Sara FitzGerald 800 Centennial Avenue PO Box 1327 Piscataway, NJ 08855-1327 Telephone: 800-526-3593 x5231 Fax: 770-664-4829 E-mail: sara.fitzgerald@am.apbiotech.com Kratos Analytical, Inc. Brian Stall Shimadzu Biotech/Kratos Analytical 14 Gill Street Woburn MA 01801 Telephone: 603-472-7167 E-mail: bkstall@shimadzu.com Applied Biosystems John A Kearns Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 Telephone: (941) 415-8989 FAX: (941) 415-8979 E-mail: kearnsja@appliedbiosystems.com Thermo Finnigan Corporation Paul A. Steinberg (LC/MS) Southern Region Sales 665 Molly Lane, Suite 140 Woodstock, GA 30189 Telephone: (561) 432-8286 FAX: (561) 432-1658 E-mail: psteinberg@thermofinnigan.com Randy Curles (GC/MS) 665 Molly Lane, Suite 140 Woodstock, GA 30189 Telephone: (770) 516-5589, (770) 457-7577 FAX: (770) 516-6916 E-mail: jcurles@thermofinnigan.com Micromass, Inc. Larry Abbey 4026 Oak Crest Drive Tucker, GA 30084 Telephone: (770) 414-5089 Cell: (404) 625-0727 Fax: (770) 496-0795 E-mail: larry_abby@MSPEOPLE.COM JEOL USA, Inc. Rae Ann Baldwin 11 Dearborn Rd. Peabody, MA 01961-6043 Telephone: (508) 535-5900 FAX: (508) 536-2205 E-mail: baldwin@JEOL.COM Bruker Daltonics Felix Salinas Manning Park Billerica, MA 01821 Tel: (281) 993-1397 Fax: (978) 667-5993 E-mail: felix.salinas@daltonics.bruker.com ----- Directions to the Complex Carbohydrate Research Center from Atlanta 1. Follow I-85 North to Highway 316 (Exit to Lawrenceville/Athens). 2. Follow Highway 316 until it merges with the Epps Bridge Road/Georgia Loop 10 exchange. You will take a right onto the entrance of Georgia Loop 10 (East - this entrance to Georgia Loop 10 is before you cross the bridge that goes over the loop). 3. Follow Georgia Loop 10 to the College Station Road exit. Take this exit. 4. Take a right onto College Station Road. 5. At the first traffic light, take a right onto Riverbend Road. 6. Take a direct right into the parking lot. CCRC will be the second building on your right (the first building is the Riverbend Research Laboratories). ****************************************************************************** From: Dave White Date: Wed, 15 Jan 2003 02:39:47 GMT Subject: Re: Mass Spectral File Formats Organization: * The format hasn't changed, even up to the latest version of ChemStation. When you say the output doesn't make sense, which part of the data file are you extracting, and what are you seeing? The data isn't stored in 'normal' Intel byte order, so you need to reverse the byte ordering of words and longwords before using them. Without using pointers, that's a little tricky (and VB doesn't have pointers). The format is actually fairly straightforward to work with, compared to other mass spec file formats. We have a routine, written in Delphi, which will read file headers, spectra, chromatograms, etc., and the whole routine consists of only 1200 lines, including comments. -- Dave White SpectraChrom Software www.spectrachrom.com dave_white123@spectrachrom.com Remove the numbers from address for valid e-mail "J.Rooke" wrote in message news:b019dv$2jo$1@news-int.gatech.edu... } I am trying to write a VB routine which will read the HP Chemstation } (.ms) files and enable me to extract the data and plot the } chromatogram as a series using either TeeChart or some other graphing } package. I've seen a thread from November 2002 which lists the file } format of the spectral files, but I'm beginning to think that this is } a much older format as part way through the file reading process, the } output does not make sense. Does anyone have an idea of how I can } extract these data files to a more usable format and pull out the } correct values as they are stored? } ****************************************************************************** From: Hubert Date: Wed, 15 Jan 2003 05:20:38 +0000 Subject: Re: Guidance on specifying masses for quadrupole MS methods Organization: * Dr. Dickson, I have done some work on this previously and am glad to share my experience with you. Actually I tried the procedure in setting up the SIM acquisition using the document suggested by HP a few years ago (now Agilent) for MS Chemstation used in HP 597x MSD. In brief, the procedure was to perform a dynamic SIM calibration by setting up a SIM acquisition for several incremental masses around the ion of interest. e.g. if you are looking for the 78 for a fragment of benzene, do a SIM acquisition looking for the 77.8, 77.9, 78.0, 78.1and 78.2 ions. Evaluate the mass spectrum and use the strongest ion in your SIM method. In MS ChemStation, I have tried the so-called "Low" resolution and "High" resolution during acquisition for a drug's derivative which 86 ion was monitored. For "Low" resolution, no significiant difference (~ 10%) if the strongest ion (which was the nominal ion, 86.0) was not picked up for SIM(c.f. 85.8 ion). For "High" resolution, howeve! r, a big drop of sensitivity was seen when the strongest ion (86.1 ion c.f. 85.8 ion) was not used. I think it's a good practice to choose SIM ion in this way to obtain better sensitivity and stability in the SIM method and it won't take too much time on it, 'cos everything nowaday is automated! Just put your standard solution in the autosampler and evaluate the results the other day! Bingo! Hubert Les Dickson wrote.. } }I am looking for information, in the form of recommendations or }directives }from relevant organi! zations such IUPAC or ASMS, on }the appropriate number of decimal points to specifiy for masses in an }analytical protocol where a quadrupole MS with unit }resolution is used for SIM experiments. Given that an integer mass will }likely be out some fraction due to mass defect, can I }properly use 1 decimal point, or even 2 to specify a mass under those }circumstances? Pointers to relevant documents, and }perhaps some personal experience, would be appreciated. } }Dr. Les Dickson }Canadian Food Inspection Agency }dicksonl@inspection.gc.ca ****************************************************************************** From: James Barnett Date: Wed, 15 Jan 2003 16:03:26 -0000 Subject: Re: C,H,N & S simultaneous anlysis, EA 1108 Organization: * "Minaz Lakha" wrote in message news:b01us7$jdk$1@news-int.gatech.edu... } Hi } } I am using Carlo Erba 1108 instrument and my problem is S analysis } I am trying to analyze C,H,N & S simultaneously } } Hi, You might need to make up the combustion tube again, you'll need a whole new quartz tube and fresh packing material. I remember that the tube only lasts for 200 samples before it needs replacement, all that ash gets stuck in the top. And you must use the proper comsumables for microanalysis and not substitutes. That cures most problems, also check out if there are any drying traps that need replacement inside the instrument. Regards, james Barnett aowlthirtythree@dsldotpipexdotcom ****************************************************************************** From: J.Rooke Date: 16 Jan 2003 03:19:09 -0800 Subject: Re: Mass Spectral File Formats Organization: * Dave Thanks for your message. We've managed to read the header information fully and have skipped through the file to find the retention times and abundances, in order to pull out and plot an X/Y series for the TIC. We're unsure what the rest of the data in the file is for. E.g. Mass, Status_word etc. Having been able to plot the TIC, I'm after pulling out the specific ion information (eg. All peaks for m/z 191) which I believe is stored in this .ms file somewhere. Do you have any ideas ? One more question if you don't mind^ÅGC files are typically stored as .ch files, is this the same format for reading as .ms files or do I need to create a new algorithm ? Many thanks for your help James ****************************************************************************** From: Robert Fee Date: 16 Jan 2003 08:01:34 -0800 Subject: Technology News from Scientific Computing & Instrumentation Organization: * Scientific Computing & Instrumentation (SC&I) is your source for the latest news in LIMS, data acquisition, mathematics, statistics, visualization, data analysis, chemistry, pharmaceuticals and more. Every month, we feature articles and product of interest to practicing scientists. These articles are also available for viewing on SC&I's Web site, www.scimag.com. Recently, SCI posted the Top Products of 2002. The choices, as selected by reader interest, are available for viewing here: http://www.scimag.com/scripts/PRheadlines.asp?RELTYPE=TOPF&DISPTYPE=FULLARCH NEW SUBSCRIPTIONS To activate a new FREE email subscription, visit: http://register1.scimag.com/scimag/pc.asp To request your FREE print magazine subscription to Scientific Computing & Instrumentation, visit: http://www.reed4success.com/default.asp?magid=016&promocode=XCA01XX9 ****************************************************************************** From: Fred Mellon Date: Wed, 15 Jan 2003 14:14:40 -0000 Subject: Short courses linked to International Mass Spectrometry Conference, Organization: * Please note that a new feature of the triennial IMSC (Edinburgh, 31 August - 5 September, 2003) is that a number of short courses covering various aspects of mass spectrometry will be held over the weekend immediately preceding the meeting. Details can be found by clicking the 'Short courses' link on the IMSC website: http://www.imsc-edinburgh2003.com regards, Fred -- Dr Fred A Mellon Institute of Food Research Norwich Research Park Colney Norwich NR4 7UA UK tel +44(0) 1603 255299 fax +44(0) 1603 255038 email: fred.mellon@bbsrc.ac.uk web: www.metabolomics-nrp.org.uk ****************************************************************************** From: Joerg Hau Date: Thu, 16 Jan 2003 18:41:49 +0100 Subject: Re: Mass Spectral File Formats Organization: * Hi [ about reading HP MS data files ] Just in case ... eventually, you could also export the data as netCDF (aka "ANDI-MS") files and extract the mass chromatograms from there. Of course that depends on (1) if the HP software supports this export format (I think so), and (2) if the "intermediate" step is acceptable for your application ... reading mass chromatograms from netCDF is rather slow (it requires reading through every MS in the file), but at least I have the routines for reading them at hand ;-): I'm not necessarily a great friend of netCDF, but as long as most MS manufacturers believe their data file format to be a capital secret, it is often the only way to go. Cheers + HTH, - Joerg -- joerg.hau(at)swissonline.ch * Lausanne, Switzerland http://www.mysunrise.ch/users/joerg.hau/ "All standard disclaimers apply". ****************************************************************************** From: Claudia Brackett Date: 16 Jan 2003 10:29:02 -0800 Subject: LC-MS method for nitrates Organization: * Does anyone have an LC-MS method that works for nitrated compounds or works with the EPA method 8330? I am using an Agilent LC-MS system, and I have the LC part working, but need to find the MS conditions. Some of the compounds I am working with are Nitrobenzene, RDX, HMX, 2,4-Dinitrotoluene, 2,4,6-Trinitrotoluene, and 2-Amino-4,6-Dinitrotoluene (EPA mix A). Thanks Claudia Brackett ****************************************************************************** From: Chris Lee Date: Thu, 16 Jan 2003 22:13:31 +0100 Subject: Re: Fans for Quattro Organization: * Fans are fairly industry-standard items. The key specifications are usually written on the label. If the flow-rate isn't mentioned use the power dissipation as a guide. You can find a fan with the same geometry and that blows the same way in the usual big elecronic components catalogues (Farnell and Radiospares in Europe). It isn't worth paying a service call-out for this if you can use a screwdriver & soldering iron. Regards "Lee Ferguson" a écrit dans le message de news: avvofv$qi$1@news-int.gatech.edu... } Peter Bradley wrote in message news:... } } Hi all, } } } } I have a colleague who has a triple-quad Quattro LC/MS (1993-94) in } } which two of the fans in the electronic module have burnt } } out. These fans are manufactured by Papst (labeled: TYP 3978, 240 } } V~50/60Hz, 10/9 W). He has tried to contact the manufacturer } } with no luck. Does anybody know of a supplier for these fans or even if } } someone has some spare ones they are willing to } } unload. Thanks for any information. } } } } Peter } } } Peter, } I seem to remember replacing one or two of these fans on an old } Quattro I that I used to work on. I believe I found replacements at } an Active Electronics (http://www.activestores.com/) store on Long } Island, New York. If I remember correctly, the replacements weren't } made by Papst. } Lee } . ****************************************************************************** From: Pham Tuan Hai Date: Fri, 17 Jan 2003 01:37:06 -0800 (PST) Subject: Re: Mass Spectral File Formats Organization: * Hi, Correct me if I do not understand your intention correctly. Do you want to convert the entire or part of the 3D HP Chemstation LC-MS file into ASCII format? If yes, I have written a macro which can do it in the HP Chemstation itself, even batch processing. It is in fact a modification from the LC-DAD data conversion macro. It is rather slow and has some limitation in mass range/step and elution time range due to memory problem. We received also a Fortran-based program from somebody in the list (I sincerely apologise for not remembering his name and email address because I lost all his mails, but we are surely very grateful). The program is very fast but we had problem in its implementation. If you are interested in the above mentioned macro, just let me know. Cheers Hai __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com ****************************************************************************** From: "Peru,Kerry [NHRC]" Date: Fri, 17 Jan 2003 10:55:02 -0600 Subject: Re: Guidance on specifying masses for quadrupole MS methods Organization: * Les Dickson > wrote.. } I am looking for information, in the form of recommendations or directives } from relevant organizations such IUPAC or ASMS, on the appropriate number of } decimal points to specify for masses in an analytical protocol where a } quadrupole MS with unit resolution is used for SIM experiments. Given that } an integer mass will likely be out some fraction due to mass defect, can I } properly use 1 decimal point, or even 2 to specify a mass under those } circumstances? Pointers to relevant documents, and perhaps some personal } experience, would be appreciated. } } } Dr. Les Dickson } Canadian Food Inspection Agency } dicksonl@inspection.gc.ca Les, In an analytical protocol, since you are not discussing a result obtained from the instrument, but rather an instrument setting or listing the exact masses of specific compounds, I would consider using 1 or 2 decimals just so long as the masses are specified as such. On the other hand, if you are discussing results obtained from your unit mass resolution instrument, the number of significant figures would be important in order not imply that you are mass accurate to the 1st or 2nd decimal on the m/z axis. In this case I would use unit mass only. In other words, if you are discussing m/z (obtained from the instrument) use integer mass, if you are discussing mass (amu), 1 or more decimals should be acceptable. Cheers, Kerry M. Peru Senior Organic MS Research Technologist Environment Canada NWRI - NHRC 11-Innovation Blvd., Saskatoon, SK. S7N 3H5 ph: 306-975-4206 fax:306-975-5143 email: Kerry.Peru@ec.gc.ca ****************************************************************************** From: sales@ietltd.com (usedlabequip) Subject: PE SCIEX API 150, 365, 2000, and 3000 WANTED Date: 17 Jan 2003 11:27:11 -0800 Organization: http://groups.google.com/ Please Contact Ceylan: International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com ph: 847-913-0777 fax: 847-913-0785 sales@ietltd.com ****************************************************************************** From: bas Date: 21 Jan 2003 04:51:20 -0800 Subject: Re: Instrument selection (was: Api4000 and Finnigan Quantum) Organization: * } could you please share you knowledge, and let us know, what were the } reasons for your decision? } } Greg OK no problem: The 2 suppliers invited us to perform an audit on both systems. We found out that the sciex and the Quantum didn`t perform very different, although the sciex was a little more sensitive but thats just for the 2 compounds we used for the tests (cant tell you wich compounds...)So i think it`s unfair to decide what system was more sensitive based on 2 compounds analisis. So we looked at the price and found out the quantum was cheaper. At this moment we`re running 3 old TSQ`s 7000 also from thermo with the same software (excalibur) So based on the software and cheaper price we decided to get the quantum..... BUT, i give you my advice, for a little more cash buy the sciex if you don`t mind having a different software package from all the other systems. The service that comes with the sciex is spendid in contrast with the quantum. The people of thermo finnigan just aren`t good at providing some extra service. ****************************************************************************** From: Jin Ya Date: Tue, 21 Jan 2003 06:24:37 -0800 (PST) Subject: molecular weight measurement of proteins (<40 kDa, Organization: * I got several new spots on SDS-PAGE gel (from 5 kDa-40 kDa, pI 5-7). I already identified them by MALDI and ESI MS/MS, actually they belong to the same protein. I expect they are a set of fragments from the same mother protein and I want to know the exact locations of them in the protein. The peptide sequence maps from MALDI data gave some information, but I think they can be just side proof, right? Now I think maybe direct measurement of their Mw will be helpful, but how to elute them out from gel for MS (MALDI or ESI TOF MS) and get rid of SDS? Negative staining and destaining will be a way? how about CBB stained gel (of course no fixing step)? I couldn't find many useful reference, and wondering isn't it common to measure a protein's exact Mw which was found in SDS-gel? Thank you very much. __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com ****************************************************************************** From: Michael Jordan Date: Wed, 22 Jan 2003 08:38:10 -0500 Subject: Prolab Resources - software for Finnigan Magnum Organization: * We are currently investigating software upgrades for a 10 year old Finnigan Magnum Ion Trap. The current software is the original DOS based program (which is adequate) but we are being pressured by LAN administrators to upgrade to something Windows based. I have entertained the idea of multiple booting of the system between DOS and Windows 2000 but would rather a Windows based package. I have only been able to locate the EnviroLink software offered by ProLab Resources. I would appreciate any comment from the group on this product or if you have knowledge of another Windows based package capable of full control of the Magnum system. Regards, Michael Jordan Mass Spectrometry Technician/ Technicien de spectrométrie de masse Food Safety and Quality/Salubrité et qualité des aliments Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada Telephone/Téléphone: 902-679-5528 Facsimile/Télécopieur: 902-679-2311 32 Main Street/32, Rue Main Kentville, Nova Scotia/Kentville (Nouvelle-Écosse) B4N 1J5 jordanm@agr.gc.ca ****************************************************************************** From: Rene De Boer Date: Thu, 23 Jan 2003 10:29:59 +0100 Subject: mass spectrometry services Organization: * Hi, Does anybody know wether Mass Spectrometry Services (Manchester) is still doing business. I tried to get in contact through e-mail or looked for their site on the internet but both were negative. Do they have a new address? Rene. ****************************************************************************** From: Rene De Boer Date: Thu, 23 Jan 2003 10:37:32 +0100 Subject: MSS software Organization: * We use a recent Mass Spectrometry Services interface coupled with an MS50TC high resolution mass spectrometer for a year now. Last week we tried to install the software on a new PC with a Win 2000 SP3 operating system but without any succes. The initialisation of the USB interface is refused. Does anybody have any experience with this? Your comments please. Rene ****************************************************************************** From: James Barnett Date: Thu, 23 Jan 2003 23:04:51 -0000 Subject: Re: Instrument selection (was: Api4000 and Finnigan Quantum) Organization: * "bas" wrote in message news:b0jp4t$j6f$1@news-int.gatech.edu... } } could you please share you knowledge, and let us know, what were the The service that comes with the sciex is spendid in contrast } with the quantum. The people of thermo finnigan just aren`t good at } providing some extra service. } } Yeah sometimes ThermoFinnigan let themselves down in that department, especially in appilcation software support. Generally they're good, but sometimes they drop the ball. Like it took two weeks for them to come out and replace an HT lead. They did phone an apology, which was nice. A lot of companies suffer from this, so don't let it put you off their products. Regards, James aowlthirtythree@dsl.pipex.net ****************************************************************************** From: P.M. van Galen Date: Fri, 24 Jan 2003 10:59:25 +0100 Subject: Re: mass spectrometry services Organization: * Hello: through direct mail this morning I received the message that MSS-MASPEC was bought by: MasCom, Analysengeraete Service GmbH, Norderoog 1, D-28259 Bremen, Germany T: 0421 572970 F: 0421 571032 info@mascom-ms.de http://www.mascom-ms.de Hope this helps Peter M. van Galen Research Assistant Mass Spectrometry Organic Chemistry Department, Nijmegen University Toernooiveld 1, 6525 ED Nijmegen Netherlands V: +31(0)24 3653269/2095/2362 F: +31(0)24 3652929/3393 mailto:pvang@sci.kun.nl http://oase.uci.kun.nl/~massspec "Rene De Boer" wrote in message news:b0p0b6$d3r$1@news-int.gatech.edu... } Hi, } } Does anybody know wether Mass Spectrometry Services (Manchester) is still } doing business. I tried to get in contact through e-mail or looked for their } site on the internet but both were negative. } Do they have a new address? } } Rene. } } } } ****************************************************************************** From: Jenny Samskog Date: Fri, 24 Jan 2003 11:46:42 +0100 Subject: peak capacity Organization: * Hallo everyone, How is the peak capacity of a mass spectrometer calculated? I have seen several different ways to do it and I would like to know the "correct" way? Regards, Jenny ****************************************************************************** From: Fireguy Date: Fri, 24 Jan 2003 11:33:23 -0500 Subject: Attention Finnigan/Varian ITD 700/800 Users Organization: * The last supported Version of ITDS was 4.1, this version could not be run on a PC newer than something running an old 286 chip. We have a version (installed with over 100 customers) which we were allowed to modify with "Finnigan's approval" which provides the following benefits. 1) Will run on Pentium II/III class machines up to 500MHz, improving performance 2) Will support HD partitions up to 2GB without generating Disk Space calculation errors. 3) Will run under Windows as a DOS application. 4) Supports variable Segment break points 5) Can offer slight sensitivity improvements by allowing more microscans per second. $499 with payment accepted via Credit Cards through Paypal, with immediate e-mail delivery of the install file. For purchase instructions e-mail ktreier@fuse.net Please note Finnigan/Varian do not support or warranty this Version of software. ****************************************************************************** From: Karl Treier Date: Sat, 25 Jan 2003 22:06:04 -0500 Subject: Correction: Attention Finnigan/Perkin Elmer ITD 700/800 Users Organization: * The original posting should have read... The last supported Version of ITDS was 4.1, this version could not be run on a PC newer than something running an old 286 chip. We have a version (installed with over 100 customers) which we were allowed to modify with "Finnigan's approval" which provides the following benefits. 1) Will run on Pentium II/III class machines up to 500MHz, improving performance 2) Will support HD partitions up to 2GB without generating Disk Space calculation errors. 3) Will run under Windows as a DOS application. 4) Supports variable Segment break points 5) Can offer slight sensitivity improvements by allowing more microscans per second. $499 with payment accepted via Credit Cards through Paypal, with immediate e-mail delivery of the install file. For purchase instructions visit http://www.ismywasmy.com/itds_4.htm Please note Finnigan/PE do not support or warranty this Version of software. ****************************************************************************** From: M. Thomson Date: 29 Jan 2003 12:28:46 GMT Subject: GC-MS Spikes Organization: * During development of some GC-MS methods recently I noticed that in one method I was getting a number of sharp peaks throughout the run, the spectra of which indicated that they were due to air (low mass gate was set at 30, and the only major peak was a single signal at m/z 32). I put these down to the ever-present unexplainable leak somewhere, but the pattern was reproducible between all my samples and replicates and I was hoping someone could offer a reasonable explanation as to my this may be happening? Thanks in advance for your help Best Wishes Maranda ****************************************************************************** From: Graeme Robertson Date: Wed, 29 Jan 2003 19:28:51 -0000 Subject: Re: GC-MS Spikes Organization: * You have electrical noise/spikes on your system. Cause--if they occur at exactly the same time every run they must be instrument process related ----- maybe voltage spikes generated by your instrument electronics/detector or if they are occurring during the elution of a compound they may be source pressure ionization effects. Don't be fooled by the spurious "spectra" of the spikes, its just your data system a/d converter trying to make sense of a signal it cant deal with. Air leaks are always present at peak levels that are constant or changing only slowly, not as sudden "peaks" Try running some solvent blank runs to get some baseline data good luck. Graeme. "M. Thomson" wrote in message news:b18lnq$bdn$1@news-int.gatech.edu... } During development of some GC-MS methods recently I noticed that in one } method I was getting a number of sharp peaks throughout the run, the } spectra of which indicated that they were due to air (low mass gate was set } at 30, and the only major peak was a single signal at m/z 32). } } I put these down to the ever-present unexplainable leak somewhere, but the } pattern was reproducible between all my samples and replicates and I was } hoping someone could offer a reasonable explanation as to my this may be } happening? } } Thanks in advance for your help } } Best Wishes } Maranda } ****************************************************************************** From: noone Date: Wed, 29 Jan 2003 19:42:09 -0500 Subject: Re: GC-MS Spikes Organization: * First of all, what mass spectrometer are you using? If you are using an Agilent/HP 5971 or 5972, then I've seen this problem many times in the past. The o-ring seal on top of the diffusion pump will occasionally get coated with diff. pump oil and will lead to 'burping' (I.e. intermittent sucking in of air causing peak widths of only 1 to 2 scans). To correct the problem, vent the instrument and clean the o-ring and sealing surfaces. Clean the o-ring with a lint-free towel. Clean the pump cover and sealing surfaces with a lint-free towel soaked with acetone or other suitable solvent. This has always fixed the problem for me. Unfortunately it will reappear every 6 months or so. As the other poster answered, if the pattern is completely reproducible with respect to retention time, etc, then it may well be an electronic problem. Bill "M. Thomson" wrote in message news:b18lnq$bdn$1@news-int.gatech.edu... } During development of some GC-MS methods recently I noticed that in one } method I was getting a number of sharp peaks throughout the run, the } spectra of which indicated that they were due to air (low mass gate was set } at 30, and the only major peak was a single signal at m/z 32). } } I put these down to the ever-present unexplainable leak somewhere, but the } pattern was reproducible between all my samples and replicates and I was } hoping someone could offer a reasonable explanation as to my this may be } happening? } } Thanks in advance for your help } } Best Wishes } Maranda } ****************************************************************************** From: Tomasz Bienkowski Date: Thu, 30 Jan 2003 08:33:37 +0100 Subject: Help need with HP 5890 II Organization: * Hi Recently in our GC-MS one of the seals broke. We tryed to buy it but is seems that it is imposible in Poland. There is no such seal with number wich we took from manual in data base with replaceable parts. The number is KF25 0100-1597 ( hardware manula page 324 and 325 ). It is between mas spectrometer and GC part. Anyone could tell me were can i get it. Maybe I have wrong part number. Thanks in advance for your help Tomasz Bienkowski -- ----------------------------- mgr Tomasz Bienkowski Instytut Chemii Organicznej PAN ul. Kasprzaka 44/52, 01-224 Warszawa tel. (0-...-22) 6323221 w. 2210, 2211 fax: (0-...-22) 6326681 e-mail: tombi@icho.edu.pl --------------------------- ****************************************************************************** From: Tim Blacker Date: Thu, 30 Jan 2003 16:33:36 -0500 Subject: New auto de novo peptide sequencing software released Organization: * PEAKS 1.2 de novo Peptide Sequencing Software Bioinformatics Solutions Inc. (BSI) is pleased to announce the release of PEAKS 1.2, BSI's automated de novo peptide sequence software. PEAKS accepts MS/MS data input in Micromass (.PKL), Sequest (.DTA) and Mascot Generic Format (.MGF) to provide fast, accurate auto de novo and semi-manual sequencing functionality. The PEAKS de novo approach efficiently searches all possible combinations of amino acids for a given MS/MS spectrum. As PEAKS does not use a database searching methodology, sequence prediction accuracy is not limited by the diversity of any given database - providing great results for unknown peptides. In fact, PEAKS has shown favorable results compared to existing database and de novo software packages. This latest release includes new features to define and search for post-translational modifications (PTMs). The PEAKS Residue List Manager provides a modification library of 26 common PTMs and a facility for defining custom PTMs. Modified and unmodified residues can be grouped into residue lists to provide quick access to frequently used search sets. More information and a demo download version of PEAKS can be found at the BSI website, http://www.bioinformaticssolutions.com/products/peaks.php Should you have any questions or comments, please contact info@bioinformaticssolutions.com Tim Blacker tblacker@bioinformaticssolutions.com 145 Columbia Street West, Suite 2B Waterloo, Ontario, Canada N2L 3L2 T: 519-885-8288 x 18 F: 519-885-9075 ****************************************************************************** From: Dan Date: Thu, 30 Jan 2003 15:55:08 -0600 Subject: Free Incos parts Organization: * I have an old Finnigan Incos 500 MS and many spare parts. Is any one out there in need of boards, complete solid probe, filaments, etc? It is going to be scrapped and if the parts can help someone; let me know. You can have the parts for the cost of shipping. ****************************************************************************** From: Graeme Robertson Date: Thu, 30 Jan 2003 22:44:18 -0000 Subject: Re: Help need with HP 5890 II Organization: * Hi Thomas, Agilent.com [hewlett packard] site lists 0100-1597 as seal, seal-vacuum; NW25 size viton/fluoro. sounds like a standard high vacuum viton seal. O-ring dimensions are as follows Size 360, internal diameter 1.100 inches, O-ring cross section 0.210 inches KF25 nearest metric equivalent, internal diameter 28mm, cross section 5mm. Any high vacuum company Pfeiffer vacuum or Edwards should be able to supply this. Since it is a standard size any commercial industrial o ring company in Poland should be able to supply an O-ring of this size/ material. A bakeout of the o-ring in an oven before use might be prudent, but dont exceed the temperature limits of the material. Cheers Graeme Tomasz Bienkowski" wrote in message news:b1b97q$8k2$1@news-int.gatech.edu... } Hi } } Recently in our GC-MS one of the seals broke. We tryed to buy it but is } seems that it is imposible in Poland. There is no such seal with number wich } we took from manual in data base with replaceable parts. The number is KF25 } 0100-1597 ( hardware manula page 324 and 325 ). It is between mas } spectrometer and GC part. } Anyone could tell me were can i get it. Maybe I have wrong part number. } Thanks in advance for your help } } Tomasz Bienkowski } -- } ----------------------------- } mgr Tomasz Bienkowski } Instytut Chemii Organicznej PAN } ul. Kasprzaka 44/52, 01-224 Warszawa } tel. (0-...-22) 6323221 w. 2210, 2211 } fax: (0-...-22) 6326681 } e-mail: tombi@icho.edu.pl } --------------------------- } } } ****************************************************************************** From: dieter.zimmer.dz@bayer-ag.de Date: Fri, 31 Jan 2003 17:31:45 +0100 Subject: Re: Api4000 and Finnigan Quantum Organization: * bas wrote: }Juergen Kinkeldei wrote in message }news:... } Hi, } we are going to buy a new LC-MS/MS-System and operating yet an api } 365. Which system is more sensitiv and stable for analysis in } serum/blood/urine the api 4000 or the finnigan quantum ? }}Hi there juergen }}We are also planning to buy a new lc/ms/ms for the same aplications }}and we are now busy for 3 months figuring out wich one is the }}best!!!We cant decice between the api 4000 and the quantum (funny we }}have the same issue) }}Perhaps we can help each other?? Greetings, bas Hi Jürgen, Hi Bas there was very recently a paper in RCM on the stability and sensitivity of the TSQ quantum in enhanced resolution mode (which means 0.2 amu FWMH) check it out: M. Jemal, Zh. Ouyang, Rapid Commun. Mass Spectrom, 2003, 17, 24-38 We run two API 4000 since summer 2001 in quantitation in the pharmacokinetics field. They are quite stable and sensitive (but I never did a comparison with the Quantum) . At the beginning there were problems with the ion sources, but the newer generation ion sources seem to be fine. There are some dropouts reported with the turbopumps,which happened to us as well, but this happens with API 3000 too (and I guess with MS of other vendors as well) and is not really critical. regards Dieter Zimmer Bayer AG Dieter.Zimmer.DZ@Bayer-Ag.de ****************************************************************************** From: Robert Date: Fri, 31 Jan 2003 23:12:26 +0100 Subject: Re: molecular weight measurement of proteins (<40 kDa, Organization: * Western blot on PVDF membrane? We do that often (successful)with peptides < 10kDa. Robert Jin Ya wrote: } I got several new spots on SDS-PAGE gel (from 5 kDa-40 } kDa, pI 5-7). I already identified them by MALDI and } ESI MS/MS, actually they belong to the same protein. I } expect they are a set of fragments from the same } mother protein and I want to know the exact locations } of them in the protein. The peptide sequence maps from } MALDI data gave some information, but I think they can } be just side proof, right? Now I think maybe direct } measurement of their Mw will be helpful, but how to } elute them out from gel for MS (MALDI or ESI TOF MS) } and get rid of SDS? Negative staining and destaining } will be a way? how about CBB stained gel (of course no } fixing step)? I couldn't find many useful reference, } and wondering isn't it common to measure a protein's } exact Mw which was found in SDS-gel? } Thank you very much. } } } } __________________________________________________ } Do you Yahoo!? } Yahoo! Mail Plus - Powerful. Affordable. Sign up now. } http://mailplus.yahoo.com } ****************************************************************************** From: carlsons1 Date: Sat, 01 Feb 2003 04:30:54 GMT Subject: Re: Free Incos parts Organization: * Dan, I will take you up on your offer of Incos 500 parts. I may be contacted by E-mail at carlsons@junct.com to work out shipment/ payment details. Russell Carlson ****************************************************************************** From: M. Thomson Date: 3 Feb 2003 16:53:42 GMT Subject: Sample Desalting for small molecules Organization: * I am trying to get some LC-MS data from cleaning swabs that are thought to contain cephalosporins. The problem is that the swab solvent contains 0.05M potassium phosphate buffer (the mobile phase of the validated HPLC method), and the peaks of interest are eluting from the HPLC column in the void section of the RP-HPLC gradient. I cannot find any conditions in which the peaks of interest are retained on the column rather than washing straight out in aqueous conditions. I would like to use our peak trapping set up to get rid of residual salts from the buffer, but I just can't get the peaks I want to stick to the column! I have tried replacing the HPLC mobile phase with ammonium acetate, dilute acids and water, which all work well for peak resolution, and I've also tried a variety of column packing materials (Luna C18, spherisorb, Phenomenex Hydro and Phenomenex polar). I've avoided normal phase as I assumed the salts would just be retained with the peaks of interest in those conditions anyway. I have seen several papers where cephalosporins ionise well by ESI, and am therefore assuming that I cannot get any MS data (even from the standards) because of the presence of the salt. If anyone has any ideas on how I could get rid of the salt (bearing in mind that the species I'm interested in are ~200u), or any little tricks for getting around it when it comes to the MS I would be very grateful. Thanks in advance for your help. Best wishes Maranda ****************************************************************************** From: James Barnett Date: Mon, 3 Feb 2003 20:14:16 -0000 Subject: Re: Sample Desalting for small molecules Organization: * } If anyone has any ideas on how I could get rid of the salt (bearing in mind } that the species I'm interested in are ~200u), or any little tricks for } getting around it when it comes to the MS I would be very grateful. } } Thanks in advance for your help. } } Best wishes } Maranda } You could try www.michrom.com they sell desalting cartridges. I think www.presearch.co.uk are their agents in the UK, I have no connection with either company. Regards, James Barnett ****************************************************************************** From: Kevin McHale Date: 3 Feb 2003 17:05:26 -0800 Subject: Re: Sample Desalting for small molecules Organization: * M. Thomson wrote:... } I am trying to get some LC-MS data from cleaning swabs that are thought to } contain cephalosporins. } } The problem is that the swab solvent contains 0.05M potassium phosphate } buffer (the mobile phase of the validated HPLC method), and the peaks of } interest are eluting from the HPLC column in the void section of the } RP-HPLC gradient. I cannot find any conditions in which the peaks of } interest are retained on the column rather than washing straight out in } aqueous conditions. I would like to use our peak trapping set up to get } rid of residual salts from the buffer, but I just can't get the peaks I } want to stick to the column! I have tried replacing the HPLC mobile phase } with ammonium acetate, dilute acids and water, which all work well for peak } resolution, and I've also tried a variety of column packing materials (Luna } C18, spherisorb, Phenomenex Hydro and Phenomenex polar). I've avoided } normal phase as I assumed the salts would just be retained with the peaks } of interest in those conditions anyway. } } I have seen several papers where cephalosporins ionise well by ESI, and am } therefore assuming that I cannot get any MS data (even from the standards) } because of the presence of the salt. } } If anyone has any ideas on how I could get rid of the salt (bearing in mind } that the species I'm interested in are ~200u), or any little tricks for } getting around it when it comes to the MS I would be very grateful. } } Thanks in advance for your help. } } Best wishes } Maranda Maranda, It is a safe assumption that the high salt concentration is suppressing the analyte ion signal from the ESI source. In order to separate your cephalosporins from the void volume, you may want to try a porous graphite LC column (e.g., Hypercarb from Thermo Hypersil Keystone). These columns demonstrate good retention for highly polar compounds using typical reverse-phase LC solvents across a wide pH range. Best Regards, Kevin McHale Thermo Finnigan ****************************************************************************** From: Ron Orlando Date: Wed, 05 Feb 2003 17:50:15 -0500 Subject: The next meeting of the Atlanta/Athens MS discussion group Organization: * February 5, 2003 To: AAMSDG Members From: Ron Orlando This is a reminder that the next meeting of the Atlanta/Athens MS discussion group will be held at the CCRC auditorium on Monday, February 10 at 7:00 PM. The speaker for the evening is Professor Neil Kelleher (Department of Department of Chemistry, University of Illinois), who will give us a presentation entitled "Emerging Q-FTMS Instrumentation for MS-Based Enzymology and Top Down Proteomics". I am sure that this will be an interesting talk so please mark your calendars. The following meeting has also been tentatively scheduled. Prof. Burnaby Munson will be giving us a talk on Monday March 31 in the CCRC lecture hall. I don't have a title for this talk, but most of you can probably guess what it will be about. Burnaby is a very entertaining speaker and I am sure that you will want to attend this lecture. As always, I need to thank our corporate sponsors. Please let me know if you have any questions regarding the upcoming meeting. We hope everyone will be able to attend. Ron -------------- Corporate Sponsor of AAMSDG Amersham Pharmacia Biotech Inc. Sara FitzGerald 800 Centennial Avenue PO Box 1327 Piscataway, NJ 08855-1327 Telephone: 800-526-3593 x5231 Fax: 770-664-4829 E-mail: sara.fitzgerald@am.apbiotech.com Kratos Analytical, Inc. Brian Stall Shimadzu Biotech/Kratos Analytical 14 Gill Street Woburn MA 01801 Telephone: 603-472-7167 E-mail: bkstall@shimadzu.com Applied Biosystems John A Kearns Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 Telephone: (941) 415-8989 FAX: (941) 415-8979 E-mail: kearnsja@appliedbiosystems.com Thermo Finnigan Corporation Paul A. Steinberg (LC/MS) Southern Region Sales 665 Molly Lane, Suite 140 Woodstock, GA 30189 Telephone: (561) 432-8286 FAX: (561) 432-1658 E-mail: psteinberg@thermofinnigan.com Randy Curles (GC/MS) 665 Molly Lane, Suite 140 Woodstock, GA 30189 Telephone: (770) 516-5589, (770) 457-7577 FAX: (770) 516-6916 E-mail: jcurles@thermofinnigan.com Micromass, Inc. Larry Abbey 4026 Oak Crest Drive Tucker, GA 30084 Telephone: (770) 414-5089 Cell: (404) 625-0727 Fax: (770) 496-0795 E-mail: larry_abby@MSPEOPLE.COM JEOL USA, Inc. Rae Ann Baldwin 11 Dearborn Rd. Peabody, MA 01961-6043 Telephone: (508) 535-5900 FAX: (508) 536-2205 E-mail: baldwin@JEOL.COM Bruker Daltonics Felix Salinas Manning Park Billerica, MA 01821 Tel: (281) 993-1397 Fax: (978) 667-5993 E-mail: felix.salinas@daltonics.bruker.com ----- Directions to the Complex Carbohydrate Research Center from Atlanta 1. Follow I-85 North to Highway 316 (Exit to Lawrenceville/Athens). 2. Follow Highway 316 until it merges with the Epps Bridge Road/Georgia Loop 10 exchange. You will take a right onto the entrance of Georgia Loop 10 (East - this entrance to Georgia Loop 10 is before you cross the bridge that goes over the loop). 3. Follow Georgia Loop 10 to the College Station Road exit. Take this exit. 4. Take a right onto College Station Road. 5. At the first traffic light, take a right onto Riverbend Road. 6. Take a direct right into the parking lot. CCRC will be the second building on your right (the first building is the Riverbend Research Laboratories). ****************************************************************************** From: "marco@chemuserworld.com" Date: Thu, 06 Feb 2003 03:23:28 GMT Subject: Dr. ChemUser Chat Organization: * Sorry for the late notice. There will be a Dr. ChemUser Chat at 10 AM PST tomorrow. The ChemUser Chat will be held weekly. Keep in touch at ChemUserWorld.com for the topic. (http://www.chemuserworld.com) -- marcom@chemuserorld.com ****************************************************************************** From: Fred Mellon Date: Wed, 5 Feb 2003 13:34:28 -0000 Subject: HP5973 communications (?) problem Organization: * We have a 1997 vintage HP5973 GC/MS system running under Windows 95 and MSD Productivity Chemstation Software, A.0301 update. Our problems started after our PC was inadvertently switched off (at the end of a run). Despite several reboot attempts and complete shutdown of the system (GC, MS, autosampler) and re-start, we continue to have the following problem: When we launch Chemstation, the system appears to respond OK (i.e.it loads parameters into the GC, etc.), but then hangs up at the initialisation stage (red box with 'initialising message stays up permanently) and the whole system freezes (cannot select any buttons, programs etc. with the mouse). I'm reluctant to reload the software, but this appears to be our next option, unless anyone can come up with alternative suggestions. Any help much appreciated. regards to all, Fred -- Dr Fred A Mellon Institute of Food Research Norwich Research Park Colney Norwich NR4 7UA UK tel +44(0) 1603 255299 fax +44(0) 1603 255038 email: fred.mellon@bbsrc.ac.uk web: www.metabolomics-nrp.org.uk; www.imss.nl; www.imsc-edinburgh2003.com ****************************************************************************** From: Fred Mellon Date: Thu, 6 Feb 2003 08:40:34 -0000 Subject: HP 5973 Problem solved! Organization: * Before anyone spends time and effort answering my previous post, we managed to solve the Chemstation/MSD 5973 problem I posted earlier. It turned that the default methods file (corrupted?) automatically loaded on launching Chemstation caused the problem. Once we had retrieved a methods file that we knew should work, and renamed this as the default, the system loaded and ran OK. regards, Fred -- Dr Fred A Mellon Institute of Food Research Norwich Research Park Colney Norwich NR4 7UA UK tel +44(0) 1603 255299 fax +44(0) 1603 255038 email: fred.mellon@bbsrc.ac.uk web: www.metabolomics-nrp.org.uk ****************************************************************************** From: Geert Pille Date: 7 Feb 2003 01:39:48 -0800 Subject: polyphenols in ESI- Organization: * Hi, I'm looking for a method to quantify compounds that contain a polyphenol group, right now I can go to 10mM but I have to go to 0.2 mM,in SciFinder I found a few references for the determination but not for the quantification. So far I tried H2O/CH3OH and H2O+0.1%CF3COOH/CH3CN. Any suggestions? ****************************************************************************** From: dieter.zimmer.dz@bayer-ag.de Date: Fri, 7 Feb 2003 16:38:10 +0100 Subject: Re: Sample Desalting for small molecules Organization: * M. Thomson wrote... } I am trying to get some LC-MS data from cleaning swabs that are thought to } contain cephalosporins. } } The problem is that the swab solvent contains 0.05M potassium phosphate } buffer (the mobile phase of the validated HPLC method), and the peaks of } interest are eluting from the HPLC column in the void section of the } RP-HPLC gradient. I cannot find any conditions in which the peaks of } interest are retained on the column rather than washing straight out in } aqueous conditions. I would like to use our peak trapping set up to get } rid of residual salts from the buffer, but I just can't get the peaks I } want to stick to the column! I have tried replacing the HPLC mobile phase } with ammonium acetate, dilute acids and water, which all work well for peak } resolution, and I've also tried a variety of column packing materials (Luna } C18, spherisorb, Phenomenex Hydro and Phenomenex polar). I've avoided } normal phase as I assumed the salts would just be retained with the peaks } of interest in those conditions anyway. } } I have seen several papers where cephalosporins ionise well by ESI, and am } therefore assuming that I cannot get any MS data (even from the standards) } because of the presence of the salt. } } If anyone has any ideas on how I could get rid of the salt (bearing in mind } that the species I'm interested in are ~200u), or any little tricks for } getting around it when it comes to the MS I would be very grateful. } } Thanks in advance for your help. } } Best wishes } Maranda } An ion suppression by phosphate might most probably be your problem, hence you need retention of your analyte. We analyzed in 1996 azlocilline and its polar acid metabolites by direct injection of crude plasma (on-line SPE) using restricted acces columns of the ADS-type (LiChrosphere RP-18 ADS, 25 x 4mm, from Merck), using off-line SPE and other techniques we had also matrix effects (due to salts in the sample and other components, e.g. vehicle). The salts have no retention on these columns they are flushed away while the analytes are retained inside the pores of the material. Another way to do on-line SPE but much faster is Turbulent Flow Chromatography (search the literature if you are not familiar with it, or send me an e-mail). Both methods work for solvents/solutions as well. The Mass Spec we used was an API 300 from AB MDS Sciex. Another possibility, but more time consuming, to achieve more retention would be chemical derivatization of the analyte using standard derivatization reagents. Dieter Zimmer Bayer AG Dieter.Zimmer.DZ@Bayer-Ag.de ****************************************************************************** From: Sean Austin Date: Fri, 07 Feb 2003 17:06:11 +0100 Subject: Re: Sample Desalting for small molecules Organization: * Hi Maranda As already mentioned by someone else the porous graphitised cabon column may solve your problem. We routinely use these to desalt carbohydrates. You may want to try it out as a solid phase extration step prior to RP-HPLC before buying a new HPLC column. The SPE cartridges are available from Alltech. Good luck Sean -- ----------------------------------------------------------------------- Sean Austin | Tel: +31 30 2532860 Dept of Bio-Organic Chemistry | Fax: +31 30 2540980 Bijvoet Centre for Biomolecular Research | University of Utrecht | P.O. Box 80.075 | saustin@boc.chem.uu.nl 3508 TB Utrecht | The Netherlands | http://boc.chem.uu.nl ----------------------------------------------------------------------- ****************************************************************************** From: Dr. Dickie Date: Fri, 07 Feb 2003 12:00:24 -0500 Subject: DNA Organization: * Hello all, I am looking to detect (note, I am not really concerned with accurate mass) ss-DNA in the 200-300 BP region by MALDI. I am currently using a 3-hydroxypicolinic acid/picolinic acid/ diammonium citrate matrix combination (9:1:1), in 25% ACN solution. I have cut some DNA with restriction enzymes where the fragments should be 22 BP, 46 BP, 65 BP, 75 BP, 244 BP, 325 BP, and 396 BP (checked with agarose gel). I detect nothing. Granted, I am not using the most sophisticated MALDI unit (an old Lasermat), no delayed extraction, no reflectron, short flight tube, still; those smaller fragments should be detectable. I would guess the DNA that I am cutting is probably in the 1 ug/ul range. Any suggestions as to tricks to try? Thanks in advance. -- Dr. Dickie Skepticult member in good standing #394-00596-438 Poking kooks with a pointy stick ------------------------------------------------------ "The important thing is not to stop questioning. Curiosity has its own reason for existing." A. Einstein ****************************************************************************** From: Elena Ghetti Date: Sun, 9 Feb 2003 07:41:52 +0000 (UTC) Subject: Cannot understand this paragraph (transmission quadrupole MS) Organization: * hi, I was reading an article on how a transmission quadruple MS works, and I cannot understand this: "They [the poles] can be manufactured as rods with the hyperbolic surface, as round rods, or as a ***single-quartz manual*** having the orthogonally positioned two-hyperbolae cross section with conducting material vapor deposited on the appropriate surfaces" The word that puzzles me is "manual" in the context above, what does it mean? TIA! Elena -- Posted via Mailgate.ORG Server - http://www.Mailgate.ORG ****************************************************************************** From: Graeme Robertson Date: Sun, 9 Feb 2003 18:36:39 -0000 Subject: Re: Cannot understand this paragraph (transmission quadrupole MS) Organization: * Elena.----Try MOLD or MOLDING see the Agilent .com site information on their current benchtop mass spec. A rough description would be a "cylinder "of quartz with its outer wall folded inwards in 4 folds to form a tube with a twin hyperbolic cross section when viewed along the axis of the "cylinder" Graeme "Elena Ghetti" > hi, I was reading an article on how a transmission quadruple MS works, } and I cannot understand this:> } "They [the poles] can be manufactured as rods with the hyperbolic } surface, as round rods, or as a ***single-quartz manual*** having the } orthogonally positioned two-hyperbolae cross section with conducting } material vapor deposited on the appropriate surfaces"> } The word that puzzles me is "manual" in the context above, what does it } mean? } } TIA! } Elena } } } -- } ****************************************************************************** From: Carl Ijames Date: Sun, 09 Feb 2003 22:29:03 GMT Subject: Re: Cannot understand this paragraph (transmission quadrupole MS) Organization: * Perhaps they meant mandrel? -- Regards, Carl Ijames carl.ijames@verizon.net "Elena Ghetti" wrote in message news:b262c7$kqd$1@news-int.gatech.edu... } } hi, I was reading an article on how a transmission quadruple MS works, } and I cannot understand this: } } "They [the poles] can be manufactured as rods with the hyperbolic } surface, as round rods, or as a ***single-quartz manual*** having the } orthogonally positioned two-hyperbolae cross section with conducting } material vapor deposited on the appropriate surfaces" } } The word that puzzles me is "manual" in the context above, what does it } mean? } } TIA! } Elena } } } -- } Posted via Mailgate.ORG Server - http://www.Mailgate.ORG } ****************************************************************************** From: "marco@chemuserworld.com" Date: Sun, 09 Feb 2003 23:42:06 GMT Subject: Re: Cannot understand this paragraph (transmission quadrupole MS) Organization: * Elena, I believe your quotation comes from the article I wrote for Wiley's Base Peak entitled "Mass Spectrometry: A Primer". In this case, the word "manual" should have been "mandrel". This is the device that is the lower of the three in the figure. This is a good example of problems with spell checkers. My spell checker did not show this word misspelled, and I nor the Wiley editors caught it on proofing. Sorry for any inconvenience this may have caused you. Regards; David -- O. David Sparkman Consultant-At-Large ods@compuserve.com "Elena Ghetti" wrote in message news:b262c7$kqd$1@news-int.gatech.edu... } } hi, I was reading an article on how a transmission quadruple MS works, } and I cannot understand this: } } "They [the poles] can be manufactured as rods with the hyperbolic } surface, as round rods, or as a ***single-quartz manual*** having the } orthogonally positioned two-hyperbolae cross section with conducting } material vapor deposited on the appropriate surfaces" } } The word that puzzles me is "manual" in the context above, what does it } mean? } } TIA! } Elena } } } -- } Posted via Mailgate.ORG Server - http://www.Mailgate.ORG } ****************************************************************************** From: Gr8estgary Date: 10 Feb 2003 06:10:00 GMT Subject: Re: Cannot understand this paragraph (transmission quadrupole MS) Organization: * I would guess that it means "mandrel" 4 hyperbolic surfaces are metal coated on the inside of a ceramic insulator/glass. (typical HP spell checker error.) ****************************************************************************** From: Matthew Parson Subject: Doxapram Hydrochloride Enquiry Date: Sun, 9 Feb 2003 16:55:55 +0000 (GMT) Organization: * I am a pharmacy student in England and am emailing regarding a compound called doxapram hydrochloride. I was wondering if you could please help me. I urgently need the proton NMR, carbon-13 NMR, mass spectrum, the UV-visible spectrum and the Infra-red spectrum of this compound and need to analyze what the peaks and values refer to. I have checked many internet sites and have had very little success, and have also checked many books in the library. Please could you refer me to a website/book/other reference where I may be able to find the data or please would you be so kind to send me the spectrums, if possible. I would be most grateful for any help on this matter, many thanks Matthew Parson. ****************************************************************************** From: David Stranz Date: Mon, 10 Feb 2003 10:21:34 -0600 Subject: Re: Doxapram Hydrochloride Enquiry Organization: * Matthew Parson wrote in news:b28hn9$flv$1@news-int.gatech.edu: } I am a pharmacy student in England and am emailing regarding } a compound called doxapram hydrochloride. I was wondering if } you could please help me. I urgently need the proton NMR, } carbon-13 NMR, mass spectrum, the UV-visible spectrum and } the Infra-red spectrum of this compound and need to analyze } what the peaks and values refer to. I have checked many } internet sites and have had very little success, and have } also checked many books in the library. Please could you } refer me to a website/book/other reference where I may be } able to find the data or please would you be so kind to send } me the spectrums, if possible. I would be most grateful for } any help on this matter, many thanks } } Matthew Parson. } } Two minutes on Google using "doxapram NMR" yielded this: Instrumental Data for Drug Analysis : Vol I. Drug Data: Acebutolol - Doxapram Hardback; Book 785 pages Published: September 1992 CRC Press ISBN: 0849395216 ****************************************************************************** From: David Sparkman Date: Mon, 10 Feb 2003 16:33:46 GMT Subject: Re: Doxapram Hydrochloride Enquiry Organization: * Matthew: The proton NMR, UV, IR and mass spectra for this prescription drug are found on page 784 of "Instrumental Data for Drug Analysis", 2nd ED. Volume 1, Terry Mills III and J. Conrad Roberson, CRC Press: Boca Raton, FL, 1993. Regards; David -- O. David Sparkman Consultant-At-Large ods@compuserve.com "Matthew Parson" wrote in message news:b28hn9$flv$1@news-int.gatech.edu... } I am a pharmacy student in England and am emailing regarding } a compound called doxapram hydrochloride. I was wondering if } you could please help me. I urgently need the proton NMR, } carbon-13 NMR, mass spectrum, the UV-visible spectrum and } the Infra-red spectrum of this compound and need to analyze } what the peaks and values refer to. I have checked many } internet sites and have had very little success, and have } also checked many books in the library. Please could you } refer me to a website/book/other reference where I may be } able to find the data or please would you be so kind to send } me the spectrums, if possible. I would be most grateful for } any help on this matter, many thanks } } Matthew Parson. } ****************************************************************************** From: Juergen Kinkeldei Date: 10 Feb 2003 12:17:12 -0800 Subject: Isotopic labeled Steroid hormons Organization: * Hi, i am looking for a company selling isotopic labeled Sterois hormons, like cortisol, testosterone, pregnenolone. I only know CIL, Campro and Radian. Is there any other producer ? Thanks Jürgen Kinkeldei ****************************************************************************** From: Adam Paarlberg Date: 10 Feb 2003 17:24:46 -0800 Subject: tandem mass spectrometry Organization: * I have read extensively about tandem mass spectrometry, and that is the next generation in new-born screening, since it can detect an extremely wide range of compounds resulting from the defective breakdown of fatty and amino acids. Why, then, is it not employed by most hospitals? ****************************************************************************** From: Elena Ghetti Date: Tue, 11 Feb 2003 09:45:30 +0100 Subject: Re: Cannot understand this paragraph (transmission quadrupole MS) Organization: * Thanks to all who answered and cleared all doubts and thank you David, don't worry, it did not cause any inconvenience at all! Greetings from Italy, Elena "Elena Ghetti" ha scritto nel messaggio news:b262c7$kqd$1@news-int.gatech.edu... } } hi, I was reading an article on how a transmission quadruple MS works, } and I cannot understand this: } } "They [the poles] can be manufactured as rods with the hyperbolic } surface, as round rods, or as a ***single-quartz manual*** having the } orthogonally positioned two-hyperbolae cross section with conducting } material vapor deposited on the appropriate surfaces" } } The word that puzzles me is "manual" in the context above, what does it } mean? } } TIA! } Elena } } } -- } Posted via Mailgate.ORG Server - http://www.Mailgate.ORG } ****************************************************************************** From: adolf.muehl Date: Tue, 11 Feb 2003 09:51:31 +0100 Subject: Re: tandem mass spectrometry Organization: * Adam Paarlberg wrote in message ... }I have read extensively about tandem mass spectrometry, and that is }the next generation in new-born screening, since it can detect an }extremely wide range of compounds resulting from the defective }breakdown of fatty and amino acids. Why, then, is it not employed by }most hospitals? Due to economic reasons it would not make sense to do newborn screening in each hospital. Newborn screening is done in specialized labs getting the samples of a whole country/state or region. Yes, TMS is already used by many of those labs and the number of labs introducing TMS is increasing rapidly. Do a net search for "newborn screening tandem mass" and you will get an idea what I am talking about. Adolf Muehl ****************************************************************************** From: Hubert Date: Tue, 11 Feb 2003 04:47:42 +0000 Subject: Re: Sample Desalting for small molecules Organization: * Hi, Dr. Zimmer, Sounds interesting! What is the restricted access column? How is it different from the classical SPE column cleanup? We also occasionally have problem about ion suppression. The polar analyte elute at the void volume. Thanks. Hubert ******************************************************************** An ion suppression by phosphate might most probably be your problem, hence you need retention of your analyte. We analyzed in 1996 azlocilline and its polar acid metabolites by direct injection of crude plasma (on-line SPE) using restricted acces columns of the ADS-type (LiChrosphere RP-18 ADS, 25 x 4mm, from Merck), using off-line SPE and other techniques we had also matrix effects (due to salts in the sample and other components, e.g. vehicle). The salts have no retention on these columns they are flushed away while the analytes are retained inside the pores of the material. Another way to do on-line SPE but much faster is Turbulent Flow Chromatography (search the literature if you are not familiar with it, or send me an e-mail). Both methods work forsolvents/solutions as well. The Mass Spec we used was an API 300 from AB MDS Sciex. Another possibility, but more time consuming, to achieve more retention would be chemical derivatization of the analyte using standard deri! vatization reagents. Dieter Zimmer Bayer AG Dieter.Zimmer.DZ@Bayer-Ag.de ++++++++++++++++++++++++++++++++++ ________________________________________________________________________________ MSN 8 helps ELIMINATE E-MAIL VIRUSES. Get 2 months FREE*. ****************************************************************************** From: Wilson Shou Date: 11 Feb 2003 07:22:32 -0800 Subject: Re: Isotopic labeled Steroid hormons Organization: * CDN Isotopes (http://www.cdniso.com/englishVersion/) sells the deuterated compounds you mentioned in your post. Check their website - I believe that they do have a distributor in Germany. Regards, Wilson Shou Juergen Kinkeldei wrote in message news:... } Hi, } i am looking for a company selling isotopic labeled Sterois hormons, } like cortisol, testosterone, pregnenolone. I only know CIL, Campro and } Radian. Is there any other producer ? } Thanks Jürgen Kinkeldei ****************************************************************************** From: Juergen Gandrass Date: 12 Feb 2003 05:12:13 -0800 Subject: nano LC ESI MS Organization: * Dear all, we are running a QqTOF massspectrometer(QSTAR Pulsar i)from Applied Biosystems /SCIEX equipped with nano ESI sprayer and will buy 2D-nano LC for on-line coupling. My questions are: What are your recommendations concerning the (i) LC Packings system and (ii) Agilent 1100 system or (iii) other manufacturers? Background: The system should: (i) handle on-line enrichment and separation of buffers/salts (e.g. 0.3 mm ID capillary) and separation on an analytical column of 0.075 mm ID; (ii) be compatible (sufficiently inert) with larger proteins in the 30 kDa range. As far as I know the LC Packings system is the only 'inert' system (titanium, fluoroelastomers, sapphire, ruby)and is mostly used by proteomics people in the standard as well as in the inert version. Agilent offers a nano pump based as the capillary version on the traditional 1100 binary gradient pump (same pump units) but optimized for low dead volumes and equipped with an active splitter for column flow. Thanks in advance for any hints and recommendations! Juergen Gandrass ****************************************************************************** From: Martin Steel Date: Wed, 12 Feb 2003 17:32:11 -0500 Subject: Finnigan T-30 Newstar FT/MS for sale Organization: * This is the premier system for multi-client laboratories that require high sample throughput and a variety of ionization and inlet techniques. The Newstar design provides tha capability of ESI, MALDI, EI, CI and ion detection and LC/MS without changing sources. 5-Telsa Magnet option High Performance Chromatography Option Odyssey Satellite Workstation and software option Liquid Chromatograppy system Original list price in 1997 - $1,365,000 Available June 2003 regards Martin Steel ****************************************************************************** From: usedlabequip Date: 13 Feb 2003 09:24:30 -0800 Subject: PE SCIEX API 150, 365, 2000, and 3000 WANTED Organization: * Looking for api 150's, 365's, 2000's, and 3000's. Please Contact Ceylan: International Equipment Trading Ltd. 960 Woodlands Parkway Vernon Hills, IL 60061 http://www.ietltd.com ph: 847-913-0777 fax: 847-913-0785 sales@ietltd.com ****************************************************************************** From: tabooman Date: Fri, 14 Feb 2003 04:14:01 +0000 (GMT) Subject: learning spectroscopy Organization: * Hi all I was wondering if someone could help me out. I am presently taking organic chemistry and we are learning mass spectroscopy, HMNR, CMNR, IR spectroscopy is there any good books out there which give a easy understanding for learning the material or web site tutorials? The one I seem to be having the most trouble with is mass and HMNR but like to review all these techniques. thanks to all who reply ****************************************************************************** From: Mike Sherrell Date: Fri, 14 Feb 2003 12:57:50 -0800 Subject: Mass specs, MALDIs available Organization: * Mass specs, MALDIs available **LC/MS & MS/MS: Sciex Q-Star: $235,000. Pulsar, not Pulsar I. $16K/factory install. Sciex API 2000: $79,500. NT; decommissioned and AB-certified eligible for svc. contract. Sciex API 365: Price not settled; call if interested. Sciex API 150EX: $49,000. Installed. Less $4,000 if you 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; +$15K/intall w/ 1 yr. warr. Sciex API I: $20,000. Single quad; more sensitive than the Sciex 150. + $15,000/installation and 1 year service contract. Sciex API APCI source: $6,000. PE-ABI Mariner: $125,000. New in 1999. Micromass Quattro II: $150-200K. Price depends on whether you want installation, GC and/or HPLC Micromass Quattro: $72,000. ESI, APCI, GC EI/CI; install and 90-day warranty included Micromass LCZ Pltfrm: $45,000. ESI, APCI; + $5K/install, and 90-day warr. VG70E-HF: $20,000. Hi-res mag sector; EI/CI, FAB. Recent refurb. Finnigan Deca XP: $125,000. 30000 model. Includes install and 1 year svc. Finnigan LCQ Classic: $77,500. API, installed, 1 year warranty, 4000 amu upgrade LCQ Classic ESI source: $6,000. New/unused ESI source. Finnigan LCQ Deca: $168,900. 1000 model. Installed w/ 1 year warranty; sources sold separately Finnigan Navigator: $42,500. Guaranteed good working order Finnigan TSQ 7000: $60,000. ES, APCI, API 1, Excalibur, good working order. Finnigan TSQ 7000: $75,000. API 2, ES, APCI, Excalibur, installation and warranty included. Finnigan SSQ 7000: $40,000. ES, APCI; Excalibur; API 1 source; install included Finnigan TSQ 700: $18,000. Electrospray, APCI, Alpha workstn. ~$3K/install Finnigan SSQ 710: $14,000. Electrospray, APCI. Good working order. Finnigan MAT 900: $40,000. Offers considered. EI, ES, APCI. Finnigan Mat ITS40W: offers entertained. With Varian 3400 GC + A200s Auto Sampler. Bruker Esquire LC: $ 60,000. Ion trap. Includes installation, guar. eligible for Bruker svc. contract Xtrell 400 ELQ: $ 20,000. Or best offer. LC/MS/MS, GC/MS/MS; 10 yrs. old, floor model, well-maintained 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. VG 7070-EHF. small $s. 1984 model; used for FAB. MM Autospec S: $65,000. European install included; available in US MM Autospec V: $75,000. European install included; available in US Kratos Concept. Free, except you pay for removal Service and service contracts available for PESciex API 3000, 365 and III+. **MALDI-TOFs: Voyager DE STR: $165,000. New Oct. 2000. Shipping/installation extra. Voyager DE Pro: $145,000. Incl. factory install, certification. Voyager DE: $75,000. 1998 model. Good working order. Voyager DE RP: $50,000. Late '97 model; new detector and laser, rebuilt pump. Micromass Q-Tof 2: $275,000. 2001 model; currently under service contract. Micromass LCT: ~$200,000. API-TOF. Includes HPLC. New July 2000. Bruker Biflex III. ~$50,000. DE; decommissioned by Bruker. LaserTec II: $75,000. By PerSeptive. 5 yrs. old; excellent condition. Thermo-Finnigan Dynamo: $50,000. Linear DE benchtop system; 1 yr. old; pos/neg. Price includes ship, install, 90-day warr. 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: $5,000. Or best offer. For parts; new laser card and other new boards. **ICP-MS: Micromass Platform: $69,000. Or best offer. New in box; purchased 7/2001. Install, warr. available Finnigan MAT SOLA: $50,000. Asking price. 8 yrs. old; incl. GF, hydrides gen. **Other mass specs, NMRs, DNA/protein sequencers & synthesizers available; check the website. All listed items subject to prior sale. Regards, Michael Sherrell Grizzly Analytical (USA) 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com ****************************************************************************** From: Dr. Hartmut Fischer Date: Sun, 16 Feb 2003 11:18:45 +0100 Subject: Contaminants in ESI-MS Organization: * With our API 3000 we have severe problems with contaminants since some weeks, and we do not know where they come from. We observe strong back-ground signals of homologues with differences of 44 (e. g. 419, 463, 507, 551, 595, 639): We think that these are ethoxylated compounds, but we do not know the exact structure. Unfortunately, after each cleaning action the pattern is shifted for some masses, so the spectrum changes from day to day. We cleaned all parts of the HPLC-system and autosampler, and all parts of the ion source, including changing of all parts of the source. The high vaccuum region was cleaned only in its first part around Q0. One strange observation was that if we start with an HPLC-solvent of high aqueous part, wwe get a low base-line. If the acetonitrile content in the eluent is increased, we get a strong rising of the base-line, leading to the signals mentioned above. This is reproducible and thus we thought that this was a proof that the contaminants came from the HPLC-system ore the column. But if we disconnect the eluent-capillary on the API3000, connect it to our API III, and run the same gradient, we get a drop in the baseline when the organic fraction is increased, and we don not see any of our contaminant-masses. Can anyone give me an idea where these contaminats can come from, and what could be the chemical identity of the starting monomere. Hartmut btw: we routinely analyse pharmaceuticals in serum-samples on this machine after plasma-precipitation or liquid-liquid-extraction. ****************************************************************************** From: noone Date: Sun, 16 Feb 2003 13:49:02 -0500 Subject: Re: Contaminants in ESI-MS Organization: * polyethylene glycols most likely "Dr. Hartmut Fischer" wrote in message news:b2odjg$h9f$1@news-int.gatech.edu... } } With our API 3000 we have severe problems with contaminants since some } weeks, and we do not know where they come from. We observe strong } back-ground signals of homologues with differences of 44 (e. g. 419, 463, } 507, 551, 595, 639): We think that these are ethoxylated compounds, but } we do not know the exact structure. Unfortunately, after each cleaning action } the pattern is shifted for some masses, so the spectrum changes from day to } day. } } We cleaned all parts of the HPLC-system and autosampler, and all parts of } the ion source, including changing of all parts of the source. The high } vaccuum region was cleaned only in its first part around Q0. } } One strange observation was that if we start with an HPLC-solvent of high } aqueous part, wwe get a low base-line. If the acetonitrile content in the } eluent is increased, we get a strong rising of the base-line, leading to the } signals mentioned above. This is reproducible and thus we thought that this } was a proof that the contaminants came from the HPLC-system ore the column. } But if we disconnect the eluent-capillary on the API3000, connect it to our } API III, and run the same gradient, we get a drop in the baseline when the } organic fraction is increased, and we don not see any of our } contaminant-masses. } } Can anyone give me an idea where these contaminats can come from, and what } could be the chemical identity of the starting monomere. } } Hartmut } } } btw: we routinely analyse pharmaceuticals in serum-samples on this machine } after plasma-precipitation or liquid-liquid-extraction. } } } ****************************************************************************** From: steve Date: Mon, 17 Feb 2003 11:23:03 +1030 Subject: Re: Contaminants in ESI-MS Organization: * We once had a similar problem and found it to be our HP1090 system. It had a pinhole leak in the high pressure pumps diaphragm which leaked small amounts of oil into the eluant causing high amounts of UV and MS background. Its worth checking if your HPLC is similar ???? Steven Ramsay BSc (Hons) PhD Medical Scientist Chemical Pathology Women's and Children's Hospital 72 King William road, North Adelaide, South Australia, 5006 Dr. Hartmut Fischer wrote } }With our API 3000 we have severe problems with contaminants since some }weeks, and we do not know where they come from. We observe strong }back-ground signals of homologues with differences of 44 (e. g. 419, 463, }507, 551, 595, 639): We think that these are ethoxylated compounds, but we }do not know the exact structure. Unfortunately, after each cleaning action }the pattern is shifted for some masses, so the spectrum changes from day to }day. } }We cleaned all parts of the HPLC-system and autosampler, and all parts of }the ion source, including changing of all parts of the source. The high }vaccuum region was cleaned only in its first part around Q0. } }One strange observation was that if we start with an HPLC-solvent of high }aqueous part, wwe get a low base-line. If the acetonitrile content in the }eluent is increased, we get a strong rising of the base-line, leading to the }signals mentioned above. This is reproducible and thus we thought that this }was a proof that the contaminants came from the HPLC-system ore the column. }But if we disconnect the eluent-capillary on the API3000, connect it to our }API III, and run the same gradient, we get a drop in the baseline when the }organic fraction is increased, and we don not see any of our }contaminant-masses. } }Can anyone give me an idea where these contaminats can come from, and what }could be the chemical identity of the starting monomere. } }Hartmut } } }btw: we routinely analyse pharmaceuticals in serum-samples on this machine }after plasma-precipitation or liquid-liquid-extraction. } } } ****************************************************************************** From: dieter.zimmer.dz@bayer-ag.de Date: Mon, 17 Feb 2003 11:07:11 +0100 Subject: Re: Sample Desalting for small molecules Organization: * Hubert wrote } } Hi, Dr. Zimmer, } } Sounds interesting! What is the restricted access column? How is it } different from the classical SPE column cleanup? We also occasionally } have problem about ion suppression. The polar analyte elute at the void } volume. } } Thanks. } } Hubert } Restricted access means, that large molecules, e.g. proteins, have no access to the pores by simple size exclusion which is controlled by the pore diameter (cut off mostly above 10.000 Da). In the pores is the separation material, e.g. RB C18, which is retaining the "small" molecules inside the pores(those which have access to the pores)meanwhile the proteins (or other large molecules which are restricted from access to the pores) are washed away.The outer surface of the particles is modified in such a way, that no unwanted retention and/or degradation of proteins (plugging) occurs.Please search the literature and/or Merck website for Merck Licrosphere ADS or similar materials and you will find all relevant information. Give me a call for more discussion. (+49-202-364173) best regards Dieter Zimmer ****************************************************************************** From: Lee Ferguson Date: 17 Feb 2003 11:54:21 -0800 Subject: Re: Contaminants in ESI-MS Organization: * Harmut, You have sodiated nonylphenol ethoxylates. These are ubiquitous contaminants of plastic and are present in lots of cleaning materials, emulsifiers, etc. I should know: I analyzed these compounds in environmental samples for several years. Blanks are a horrendous problem. A problem is that these are extremely electrospray-active. Even trace quantities will produce lots of signal. My advice: just clean everything again and watch exposure of your samples to plastics and surfaces. Lee ****************************************************************************** From: "Marcom@ChemUserWorld.com" Date: Tue, 18 Feb 2003 01:59:55 GMT Subject: Dr. ChemUser Chat Organization: * There will be a Dr. ChemUser Chat at 10 AM PST this week on Thursday February 20, 2003. The ChemUser Chat will be held weekly. Keep in touch at ChemUserWorld.com for the topic. (http://www.chemuserworld.com) At 10 AM PT on February 27, 2003 there will be a ChemUserWorld Chat featuring Dr. Ross Willoughby and Dr. Ed Sheehan, two of the autors of "A Global View of LC/MS" 2nd. "A Global View of LC/MS is list as one of the widely sold mass spectromter books by Amzon.com. This Chat will help you with you specific questions about electrospray (ES) and atmospheric pressure chemical ionization (APCI). Be sure to drop in with your LC/MS questions. This is a unique opportunity to get and share some good information. -- marcom@chemuserorld.com ****************************************************************************** From: Francesc Carrera Date: Tue, 18 Feb 2003 09:15:46 +0100 Subject: Plasticizer in PVC Organization: * Hello MS people, I am trying to identify extractables and leachables in a PVC blister. With a simple extraction with any organic solvent I detect by GC-MS two main products: - 2-ethyl-1-hexanol - an unidentified product (Wiley library) with the following MS profile (electron impact, 70eV): m/e %abundance m/e %abundance 41