****************************************************************************** From: Paul Morrison Date: Fri, 24 Apr 1998 14:37:53 -0400 Subject: MALDI trypsin map against a database Organization: Dana-Farber Cancer Institute We are using a MALDI/TOF to create accurate mass maps of tryptic digests. This works great. Even from an acrylamide gel from an old notebook this technique works. We have been using MS-Fit/Protein Prospector at UCSF and ProFound at Rockefeller to search databases with these mass fingerprints. The Question: What other tools are there? I'll give an example of a problem which isn't quite covered by these programs. Virus A is cracked and run on a gel. 25 bands are excised and digested by trypsin, reduced and alkylated. Mass fingerprints are produced by MALDI from the 25 samples. Now since the samples are real life some of the samples have more than one band, or the signal is shaky etc. so we want to optimize the search. Since the 88 protein ORFS that make up this virus are known the database for searching can be made quite small. This way the multiple bands in a sample might be deconvoluted. Is there a program that will take the 88 ORFS, computer digest and allow me to compare my mass numbers to this sample set? Another problem which would be solved with the same solution is the MS-Fit top three hits. Now I want to compare just to those three while adding a little more data. PAWS doesn't quite make it. Any suggestions? thanks, Paul Paul Morrison D830 Molecular Biology Core Facilities Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115 p_morrison@dfci.harvard.edu http://mbcf.dfci.harvard.edu phone 617-632-3082 fax 617-632-4814 ****************************************************************************** From: dave@nospam.com Date: Mon, 27 Apr 1998 19:31:03 GMT Subject: Re: MALDI trypsin map against a database Organization: dave's not here a program called ProComp, developed by Phil Andrews at the Univ. of Michigan Med. School, generates full and/or partial digests of an input sequence. i don't know it he is still releasing/supporting the software, but i found it useful for generating digests, as it does full digests and gives all possible enzymatic peptides. i don't recall if there is an option in this software to do a comparison to more that one sequence at a time, but the output for each theoretical digest could be piped into some form of database which could be searched with the experimental digest masses. }Another problem which would be solved with the same solution is the }MS-Fit top three hits. Now I want to compare just to those three while }adding a little more data. PAWS doesn't quite make it. what additional data do you want to add? more (weaker intensity?) digest peaks? you could do this one at a time with PAWS. this also sounds like making your own local database of the three top hits to search with your data would be the way to go. -dave _____________________________________________ spam might be good with cheese, but i already had lunch. i can be reached at ddogruel@trailx.comx by removing the x in both places.