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- Main Page (6445 bytes)
23: ...rceforge.net/ Comet], as well as spectral library searching with [[SpectraST]], and cross-linking data with [...
68: searching are subsequently processed through the Trans Prot... - Debugging:Understanding XSL-Generating Code in Perl (1339 bytes)
10: ...s a variable defined previously in the XSL file. Searching for this definition, we find - Software:PeptideProphet (1728 bytes)
8: ... by tandem mass spectrometry (MS/MS) and database searching. By employing database search scores, number of t... - Software:TPP (8915 bytes)
82: ===Spectral Library Building and Searching=== - TPP:X!Tandem and the TPP (5454 bytes)
14: ...butes, important for the quantitation tools, when searching mzXML files directly: - Software:Tandem2XML (1413 bytes)
24: When searching mzXML files directly, note that the following Tan... - Software:SpectraST (70083 bytes)
1: ...th "contrast") is a spectral library building and searching tool designed primarily for shotgun proteomics ap...
5: ...= Introduction to Shotgun Proteomics and Spectral Searching ==
9: ...and accuracy. Unfortunately, traditional sequence searching is a challenging, error-prone, and computationall...
11: ...thod in complementing, if not replacing, sequence searching in many proteomics applications.
13: === Advantages of Spectral Searching === - Spectrast create.params (4398 bytes)
87: # (e.g. for sequence-searching them) - TPP Tutorial v1 (43187 bytes)
224: ... can be hundreds of times faster than traditional searching, with comparable or better accuracy. Clicking on... - Software:da2tpp (2167 bytes)
30: ...dentical precursors and attributes scan number by searching - Expert search and TPP usage (12929 bytes)
1: This is a guide to searching and running the TPP on MS/MS data from within ISB...
48: ...d the second pass with generous criteria but only searching those proteins that were matched in the first pas... - Terry's compbio links (11123 bytes)
139: [[Expert search and TPP usage | Notes on searching and TPP usage from the Unix command line at ISB]] - Terry's blog (18394 bytes)
50: ... the future''' (according to Stein): 1. SpectraST searching 2. Search against library of spectra that were u...
51: * Minimum size library for spectral searching is 20,000, else too many FP. If library too small...
53: * Can find more proteins by '''searching DNA databases'''. Alexei searches ESTs. - Building Peptide Atlas (26978 bytes)
14: ...d patients. The pepXML files should be created by searching the spectra with a database search engine such as...
16: ...ecoys are available for SpectraST searching. When searching with SpectraST, set the database to the biosequen... - Software:Mayu (3991 bytes)
16: ...iscriminant score is compatible with target decoy searching - Alt NxST search strategy (1763 bytes)
1: The instructions below are for searching MS/MS data from glycocapture experiments. It is ... - Processing glycopeptide data (6720 bytes)
19: The basic method entails searching against a modified db with all NXS/T replaced by ... - TPP Tutorial v2 (15736 bytes)
51: ...09\tandem'' directory as input files for database searching.
77: ...h you will need to create). Now we can move on to searching these data: - PeptideAtlas software (2240 bytes)
10: ...lding PeptideAtlas -- converting file formats and searching -- but some of it is useful during the build proc... - TPP:4.3.0 Release Notes (13496 bytes)
190: ... and possible_charge when searching; refine decoy searching - consider 2nd annotation
208: * Fix seg fault when searching mzXMLs with possibleCharge (e.g. with charge pred...
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