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- Recipe for generating proteotypic peptides for example database (10354 bytes)
2: to include changes needed to show (almost) all peptides. Updated based on 2009-08
45: ...eve_20080530/peptideSieve_080527/peptideSieve/bin/PeptideSieve .
46: ...eotypic/bin/PepSieve_20080530/peptideSieve_080527/peptideSieve/properties.txt .
59: ...ith ENS entries first for mapping, since the same peptides from proteins without mapping can then borrow the...
135: peptides (req)
Page text matches
- Main Page (6445 bytes)
39: ...rs by detecting differentially expressed features/peptides using a MS1 based processing pipeline. Corra has ...
63: ...multi-organism, publicly accessible compendium of peptides - TPP:V5Feedback (11460 bytes)
51: ...nk in the comet pepxml view of the top 5 matching peptides results in a bad url error</s>
99: ... in pepxmlviewer when a peptide is clicked on (no peptides shown in view)</s> - Software:Prequips:Inclusion List Builder (3897 bytes)
3: ...lusion lists and subsequent mapping of identified peptides to features.
51: ...p-peptides-to-master-table.mov How map identified peptides back to the master table.] - TPP:Developer Documentation (23931 bytes)
204: ...-format file called 'summary.xml', containing the peptides identified by the search engine.
234: ...retrieve all proteins corresponding to identified peptides
291: ... to find all proteins corresponding to identified peptides and overwrites results to interact.xml
367: ...PS: write output tab delim xls file including all peptides
393: ... run get all proteins corresponding to degenerate peptides from database - Software:Overview (3074 bytes)
56: ...PeptideSieve]]: A tool for predicting proteotypic peptides - Software:msBID (1414 bytes)
11: * Map identified peptides from MS2 to the features detected from MS1.
14: ...array] for selecting the differentially expressed peptides. - TPP:7.0.0 Release Notes (6884 bytes)
90: * VMC Model checkbox on "Analyze Peptides" page
110: * Support 10x more peptides PER protein than previously (now 1e6!) - Software:PeptideProphet (1728 bytes)
8: ...o distinguish correctly from incorrectly assigned peptides in the data set and computes for each peptide ass... - Software:ProteinProphet (6941 bytes)
8: ...e developed a model that has as input the list of peptides assigned to MS/MS spectra and corresponding proba...
32: ...PS: write output tab delim xls file including all peptides
38: ...obabilities of the peptides: a protein with three peptides of probabilities 0.9, 0.6, and 0.4 would have NSP...
48: ...le, (e.g. ProteinProphet at least 0.9, at least 3 peptides, each observed more than once at PeptideProphet P...
52: ...roup is needed to explain the presence of all the peptides in the group. Applying [http://en.wikipedia.org/w... - Software:ASAPRatio (1791 bytes)
1: [[Image:ASAPRatio_GUI.jpg|right]]
9: ... byproduct of the software is to identify outlier peptides which may be misidentified or, more interestingly... - Software:Libra (1189 bytes)
5: ... spectra that have isobaric multi-reagent labeled peptides. More specifically, at ISB we use Libra on MS/MS ... - Software:TPP (8915 bytes)
5: [[image:TPP.jpg|1200px]]
7: image:TPP.jpg|
69: ...S|XPRESS]]: Calculation of relative abundances of peptides and proteins from isotopically labeled MS/MS samp... - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
2: |[[Image:alert.jpg|middle|left]]
222: [TPP Tools] [Analyze Peptides] - Software:XLink (3210 bytes)
1: [[Image:XLink Viewer.jpg|thumb|right]]
11: ...of a crosslinking reagent. Consequently, modified peptides should exist within a given spectrum as a doublet...
17: ...ased on mass inclusionlists created by iXLINK, to peptides included in iXLINK's preliminary sequence assignm... - Software:PeptideSieve (6357 bytes)
4: PeptideSieve has been returned to public distribution now ...
8: ...ve the ability to accurately identify proteotypic peptides from any protein sequence and offer starting poin...
10: ...s. The program then returns which of a protein's peptides are most likely to be proteotypic for each of fou...
13: ...gest of the protein and then converts each of the peptides into chemical property strings. The C++ program ...
16: ...):125-31. Computational prediction of proteotypic peptides for quantitative proteomics]. Mallick P, Schirle ... - Software:SpectraST (70083 bytes)
7: ...tides that are amenable to LC-MS/MS analysis. The peptides in the resulting mixture are chromatographically ...
9: ...l fragmentation pattern of each of these putative peptides, and compare the experimentally observed MS/MS sp...
35: ...ention time normalization using injected landmark peptides
36: * Support for glycopeptides ''(Contributor: Dr. Yingwei Hu)''
176: ... phosphorylation modification, and put the phosphopeptides in the library <code>phospho.splib</code>. - TPP Tutorial v1 (43187 bytes)
18: ... variety of mass spectrometer types, and assigned peptides using a wide variety of database search engines.
19: [[image:Pipeline_Tutorial.jpg]]
30: ...earning about one method to identify and quantify peptides and proteins using mass spectrometry. We have at...
198: PepXML files contain information about peptides derived from tandem MS data. PepXML files are ite...
212: [[Image:sequest_params.jpg]] - Software:ProbID (2453 bytes)
2: ProbID is a software tool designed to identify peptides from tandem mass spectra using a protein sequence...
7: ... This is the main package of software to identify peptides from MS/MS spectra using protein sequence databas... - Software:SuperHirn (11737 bytes)
1: [[Image:SuperHirnLogoThumb.jpg|right]]
5: * higher detection coverage of MS/MS sampled peptides ( i.e. higher number of MS/MS ids that map to ext...
10: * locked MS1 peak extraction of MS/MS sequenced peptides
36: [[Image:Prot.jpg|left]]
51: ..., M, Aebersold, R, Identification of cross-linked peptides from large sequence databases. Nature Methods - 5... - Glyco-peptide (2495 bytes)
11: ... Has database of existing transitions and ordered peptides, perhaps this can be used to filter list.
18: ...1800 peptides) and ovarian cell glycocapture (400 peptides) samples. Sent
48: ...chun announces he has generated list of 3464 glycopeptides from putative cancer biomarkers.
50: ...08-27 Bernd announces he has generated a list of peptides from surface proteins, proposes common export for...
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