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- Protein identification terminology (4723 bytes)
1: ...to be highly redundant. Thus, we label each Atlas protein using the terminology below.
5: ...er 2009. This implementation allows you to select proteins based on the terminology below.
7: ===Protein Presence Levels===
8: Taken together, the set of proteins with a Presence Level label for any Atlas has th...
17: ... selection process, each set of indistinguishable proteins is considered to be a single entity, and the one...
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- Main Page (6445 bytes)
25: * statistical validation of peptide and protein identifications;
33: ==The [[Software:Firegoose, Gaggle, and PIPE|Protein Information and Property Explorer (PIPE)]]==
36: Once protein identifiers have been established with the TPP, t...
67: engines and protein sequences. All results of sequence and spectral l... - TPP:V5Feedback (11460 bytes)
42: * <s>legacy proteinprophet results: prot_wt_xml.pl: "The system canno...
80: * <s>Lumping these all together under "protein identifiers don't seem to be parsed correctly. C...
81: ** <s>Clicking on the protein link in the pepxmlviewer when viewing spectrast r...
84: ** Clicking on the protein link in the pepxmlviewer when viewing peptideprop...
85: ... so it won't crash. But it also doesn't find the protein'' - Software:Prequips (1386 bytes)
5: ...ss spectrometry data at the raw data, peptide and protein level. Furthermore, this data can be linked to ot... - Software:Prequips:Inclusion List Builder (3897 bytes)
32: ...clusion list runs, the corresponding peptide (and protein) identification in BioWorks tabular file format a... - TPP:Developer Documentation (23931 bytes)
52: ...e XSLT processor, Xalan, will also work fine with ProteinProphet. If you use it, just make sure it is inst...
234: #Go into database to retrieve all proteins corresponding to identified peptides
236: #ProteinProphet
237: ProteinProphet.pl interact.xml interact-prot.shtml XML_IN...
238: ...this point on, all analysis is on the output from ProteinProphet: interact-prot.xml - Software:Overview (3074 bytes)
9: ...ophet|PeptideProphet]], [[Software:ProteinProphet|ProteinProphet]], [[Software:XPRESS|XPRESS]], [[Software:...
44: ==Protein Crosslinking== - TPP:Files and Formats (299 bytes)
5: ;protXML: interchange of protein-level data; ISB-developed - TPP:7.0.0 Release Notes (6884 bytes)
21: ...roblem with not shuffling and outputting the last protein in the database and outputting the penultimate tw...
49: === [ProteinProphet:] ===
50: ...umber of top peptide probabilities to compute the protein probability, 0 retains old behavior and is still ...
52: ...X calculation of protein length and coverage when protein accession ends in a bar character
53: * BUGFIX * parsing protein descriptions from fasta files running on CentOS (... - Software:ProteinProphet (6941 bytes)
5: ...riginally developed at the SPC, part of the ISB. ProteinProphet is an integral part of the Trans-Proteomic...
8: ...when one peptide corresponds to several different proteins.
14: NOOCCAM: non-conservative maximum protein list
18: ... GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check pepti...
20: ASAP: compute ASAP ratios for protein entries - Software:XPRESS (1756 bytes)
5: ... for quantifying ratios of differentially labeled proteins.
8: ...XPRESS ratio present in a dataset and correct the protein expression averages by these average and median r...
11: ...e profiling of differentiation-induced microsomal proteins using isotope- coded affinity tags and mass spec... - Software:ASAPRatio (1791 bytes)
1: [[Image:ASAPRatio_GUI.jpg|right]]
6: Automated Statistical Analysis on Protein Ratio (ASAPRatio)
9: ... software quickly generates a list of interesting proteins based on their relative abundance, which is the ...
12: ...sold R. (2003) "Automated statistical analysis of protein abundance ratios from data generated by stable is... - Software:TPP (8915 bytes)
5: [[image:TPP.jpg|1200px]]
7: image:TPP.jpg|
14: ....proteomecenter.org/wiki/index.php?title=Software:ProteinProphet]]
63: [[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:P...
67: ===Protein Quantification=== - Software:XLink (3210 bytes)
1: [[Image:XLink Viewer.jpg|thumb|right]]
4: ...data derived from digested samples of crosslinked protein complexes.
14: ...database of crosslinker-modified species based on protein sequence(s), crosslinker and protease(s). Once cl...
24: "Integrative Protein Crosslinking Analysis Using Mass Spectrometry, Is... - Software:PeptideSieve (6357 bytes)
8: ...accurately identify proteotypic peptides from any protein sequence and offer starting points for generating...
10: ...e sequences. The program then returns which of a protein's peptides are most likely to be proteotypic for ...
13: ...ram first performs an ''in silico'' digest of the protein and then converts each of the peptides into chemi...
64: ...Observed_Proteins.txt AEBERSOLD_TABLE_S1_Observed_Proteins] - Formats:protXML (124 bytes)
1: A format for storage, exchange, and processing of protein identifications created from ms/ms-derrived pepti... - Software:Out2XML (2805 bytes)
35: ...b.fasta if running TPP on Linux. Thus, viewing of protein sequences in the TPP is impossible. - Software:Mascot2XML (2806 bytes)
24: -desc : generate protein description in pepXML output
25: ...rotein id as per Mascot result (default uses full protein ids in fasta file)
51: protein_endopeptidase : cut(P) nocuts(-) sense(C) - TPP:X!Tandem and the TPP (5454 bytes)
49: GROUP, protein - Software:SpectraST (70083 bytes)
7: ...orkflows, commonly known as shotgun proteomics, a protein sample of interest is first digested with a prote...
9: ...abase) searching. In sequence searching, a target protein (or translated DNA) database is used as a referen...
17: ...lational modification sites, if specified -- in a protein database are considered. Most of these putative p...
53: ...ing peptide identifications of library entries to protein sequence database of choice
85: ...ortation, automatic validation of search results, protein inference, and quantification and visualization. - Spectrast create.params (4398 bytes)
25: # Use protein list to filter library
26: useProteinList =
38: # Refresh protein mappings against FASTA file specified
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