Difference between revisions of "MassSpec research"
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This will hold the stuff for my mass spec research with Carl Ebeling as my advisor. | This will hold the stuff for my mass spec research with Carl Ebeling as my advisor. | ||
| + | '''2/15/06''' | ||
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| + | So now its downloading XTandem, figuring out what's going on there and waiting for some example data from John. Though I should have plenty to do in figuring out XTandem without the data . .. . | ||
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| + | Meeting with Carl and John 2:00 on Friday. Don't forget. | ||
==Papers from John Keane== | ==Papers from John Keane== | ||
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to how it works: | to how it works: | ||
| − | [http://www.proteome.ca/x-bang/tandem/docs/scoring-state-final.htm X! Tandem flow chart | + | [http://www.proteome.ca/x-bang/tandem/docs/scoring-state-final.htm X! Tandem flow chart (Not yet useful)] |
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| − | http: //www. | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15595733&query_hl=7&itool=pubmed_docsum Open source system for analyzing, validating, and storing protein identification data. (Useful soon I think)] |
| − | http: // | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15595733 Related papers.] |
| − | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14976030&query_hl=7&itool=pubmed_docsum TANDEM: matching proteins with tandem mass spectra. (Not yet useful)] | |
| − | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=14976030 Related papers.] | |
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| − | + | [http://www.eecg.toronto.edu/~jayar/pubs/alex/RCM_HAPI_.pdf Hardware-accelerated protein identification for mass spectrometry (Useful)] | |
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| − | + | [http://falsepositives.blogspot.com/2005/03/mass-spectrometry-analysis-with-field.html Short analysis of the Toronto work on some blog (Not useful yet)] | |
==Other pages== | ==Other pages== | ||
| − | http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2003/75/i04/abs/ac0258709.html | + | [http://www.thegpm.org/ The Global Proteome Machine Organization (Tons of open-source code to validate designs and such)] |
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| + | [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2003/75/i04/abs/ac0258709.html A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes (Sounds useful)] | ||
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| + | [http://www.thegpm.org/GPM/references.html Literature References for The GPM Project (literary references are always good)] | ||
| − | http://www. | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14512343&query_hl=6&itool=pubmed_docsum Designing hardware for protein sequence analysis (sounds related)] |
Latest revision as of 04:43, 16 February 2006
This will hold the stuff for my mass spec research with Carl Ebeling as my advisor.
2/15/06
So now its downloading XTandem, figuring out what's going on there and waiting for some example data from John. Though I should have plenty to do in figuring out XTandem without the data . .. .
Meeting with Carl and John 2:00 on Friday. Don't forget.
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 (Not yet useful)
Open source system for analyzing, validating, and storing protein identification data. (Useful soon I think) Related papers.
TANDEM: matching proteins with tandem mass spectra. (Not yet useful) Related papers.
Hardware-accelerated protein identification for mass spectrometry (Useful)
Short analysis of the Toronto work on some blog (Not useful yet)
Other pages
The Global Proteome Machine Organization (Tons of open-source code to validate designs and such)
Literature References for The GPM Project (literary references are always good)
Designing hardware for protein sequence analysis (sounds related)
