MassSpec research
This will hold the stuff for my mass spec research with Carl Ebeling as my advisor.
Papers from John Keane
he safest and quickest route to get started is probably to accelerate the "search" process (like the Toronto team did), based on the popular open-source algorithm in the "X!Tandem" program. Here are a few links to how it works:
X! Tandem flow chart Craig R, Cortens JP, Beavis RC. <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15595733&query_hl=7&itool=pubmed_docsum> Related Articles, <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15595733> <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15595733&itool=iconabstr&query_hl=7&itool=pubmed_docsum> Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004 Nov-Dec;3(6):1234-42. Craig R, Beavis RC. <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14976030&query_hl=7&itool=pubmed_docsum> Related Articles, <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=14976030> <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14976030&itool=iconfft&query_hl=7&itool=pubmed_docsum> TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004 Jun 12;20(9):1466-7. Epub 2004 Feb 19.
http: //www.eecg.toronto.edu/~jayar/pubs/alex/RCM_HAPI_.pdf http: //falsepositives.blogspot.com/2005/03/mass-spectrometry-analysis-with-field.html
Research Article Hardware-accelerated protein identification for mass spectrometry Anish T. Alex 1 2, Michel Dumontier 2, Jonathan S. Rose 1, Christopher W. V. Hogue 2 * 1Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario, M5S 3G4 Canada 2Blueprint Initiative, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 522 University Avenue, Suite 900, Toronto, Ontario, M5G 1W7 Canada email: Christopher W. V. Hogue (chogue@blueprint.org)
- Correspondence to Christopher W. V. Hogue, Blueprint Initiative, Samuel
Lunenfeld Research Institute, Mount Sinai Hospital, 522 University Avenue, Suite 900, Toronto, Ontario, M5G 1W7 Canada.
Other pages
http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2003/75/i04/abs/ac0258709.html
