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- TPP:Developer Documentation (23931 bytes)
33: ...rograms (children of Parser.cxx) parse pepXML and protXML with the constrain that all text be enclosed w...
52: ...e XSLT processor, Xalan, will also work fine with ProteinProphet. If you use it, just make sure it is i...
152: # ISB-Tools Trans Proteomic Pipeline directives
184: [http://tools.proteomecenter.org/configure.html]
234: #Go into database to retrieve all proteins corresponding to identified peptides - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11579 bytes)
2: |[[Image:alert.jpg|middle|left]]
64: ...http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline
79: ...e package. This will start by unpacking Boost and ProteoWizard and compile all that and then compile the...
119: /bin/rm -rf trans_proteomic_pipeline
175: ...uick Comet search and a PeptideProphet->iProphet->ProteinProphet->mzIdentML processing, try this recipe: - TPP Tutorial v1 (43187 bytes)
1: =Trans Proteomic Pipeline (TPP) Tutorial=
15: ...tical identification and quantitative analysis of proteins with mass spectrometry, this tutorial was des...
17: ==About Trans-Proteomic Pipeline==
18: ...w LC/MS data, peptide identification results, and protein identification results. The XML backbone of th...
19: [[image:Pipeline_Tutorial.jpg]] - Software:SuperHirn (11737 bytes)
1: [[Image:SuperHirnLogoThumb.jpg|right]]
11: * parsing of protXML data updating MS/MS ids with ProteinProphet probabilities
19: ...eted peptide/protein profiling: Correlate peptide/protein profile vs. a given target profile
24: ...now be downloaded from the download page: [http://prottools.ethz.ch/muellelu/web/SuperHirn.php go to dow...
28: ...nical manuscript (Mueller et al.), follow [http://prottools.ethz.ch/muellelu/web/Latin_Square_Data.php t... - Terry's compbio links (11123 bytes)
112: [http://pipe.systemsbiology.net The Pipe] Protein Information and Property Explorer, developed a...
114: [http://www.expasy.org/sprot Swiss-Prot] curated protein sequence database
118: ...t release 56.6 of 16-Dec-08 contains 20,333 human proteins.
122: ...re not, according to Clamp et al, "Distinguishing protein-coding and noncoding genes in the human genome...
127: ===ISB proteomics informatics=== - Terry's blog (18394 bytes)
5: ...vid's latest flags as in finishtandemsearch, plus PROTLEN,
7: then run showProteins.pl -C 0.9
9: ====incorporating Swiss-Prot data into PeptideAtlas====
10: Look at several Swiss-Prot entries from different species in XML format; com...
11: ...ic. Load these fields into a new biosequence_swissprot_attr table - Building Peptide Atlas (26978 bytes)
1: ...ow. Data from a single species, or sometimes a subproteome such as plasma or liver, are combined into su...
14: ...ted experiments. For example, a project may study proteins found in normal and diseased liver, and may i...
16: ...erent DBs may result in proliferation of UNMAPPED protIDs (not sure about this).
30: *To register experiments, go to SBEAMS Home > Proteomics > Manage Data > Experiments
38: ...ions> interact-combined.pep.xml interact-combined.prot.xml - TPP:4.3.0 Release Notes (13496 bytes)
1: Trans-Proteomic Pipeline (TPP) 4.3.0 release notes
6: We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 4.3.0 (4.3 ...
73: ...re to calculate decoy-estimated PSM, peptide, and protein FDR.
75: ...otes available at the SPCtools wiki, http://tools.proteomecenter.org/wiki/index.php?title=Software:Mayu
77: ...entification false discovery rates for very large proteomics datasets generated by tandem mass spectrome... - 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...
17: ... preferred identifier (for human and mouse, Swiss-Prot primary splice variant) is the one labeled canoni... - SearchProteins (2190 bytes)
1: ...n accessions, one per line. Then, go to the SearchProteins tab in PeptideAtlas (made available in Oct. 2...
3: ...Atlas (for example, for human that would be Swiss-Prot, IPI, or Ensembl), or from one of the databases t...
5: SP (Swiss-Prot)
19: ... Plasma Atlases were built with IPI+Ensembl+Swiss-Prot -- and the versions of IPI and Ensembl are more r...
21: ...as build you have selected doesn't recognize your protein identifier, it will report UNKNOWN. Reasons fo... - Recipe for generating proteotypic peptides for example database (10354 bytes)
1: Notes creating proteotypic peptide information - based on Human 2009-...
21: ...cessions are correct, filter decoys and trim long proteins longer than 8999 AA (which choke Peptide Siev...
45: ln -s /net/db/projects/PeptideAtlas/ExternalData/proteotypic/bin/PepSieve_20080530/peptideSieve_080527/...
46: ln -s /net/db/projects/PeptideAtlas/ExternalData/proteotypic/bin/PepSieve_20080530/peptideSieve_080527/...
57: ...b_no-decoys.fasta -p results.PS -d results.PDP -o proteotypic_merged.tsv - Msconvert Capabilities (15313 bytes)
23: results written to file /proteomics/gsun/trapper-test/trapper/interact-prob.pep...
50: results written to file /proteomics/gsun/trapper-test/trapper/interact-ipro.pep...
54: Mayu decoy-based protein FDR analysis on interact-ipro.pep.xml
62: PSM FDR Protein IDs Decoys Protein FDR (lower bound)
64: True protein ID count may be lower if redundancy in databas... - PeptideAtlas:Chromosomal coverage (4563 bytes)
1: ...uch a depiction, one must restrict the listing to proteins from a single chromosome on a human build.
6: ...and from the new menu that appears select "Browse Proteins"
11: *To adjust the level of selectivity for the proteins in the build use the "Presence Levels" and "R...
12: ...d of "No redundant relationships" provides repeat proteins.
13: ...protein is the canonical protein for almost every protein. - ReleasePlanning (12743 bytes)
8: ...pXML cannot be found at the path specified in the protXML, try to see if there’s a file of the same na...
58: ** prot_wt_xml.pl
78: * (Joe) Fix Proteowizard builds on Linux so that they support HDF5...
98: * Update the ProtXML schema for ASAPRatio change AND for n_distinct...
100: * Update ProtXMLViewer.pl to display n_distinct_sequences if pr... - TPP SEWW Demo2012 (29568 bytes)
9: ...to ''Petunia'' by double-clicking on the '''Trans-Proteomic Pipeline''' flower icon on your Desktop or t...
38: ...n and you should now see the template ''Tandem To Protein Prophet Template''. Loading this ''simple_tem...
71: ''TandemToProteinProphetTemplate'' in the ''Templates'' grid is ...
117: :''This fasta file contains the Yeast protein sequences''
245: ...mecenter.org/wiki/index.php?title=Image:PlotModel.JPG IMG:PlotModel] which shows graphically how succes... - PeptideAtlas Pipeline Retool 2012/13 (1625 bytes)
6: 00. Start with iPro and ProtPro results, refreshed to ref DB
17: ...06 in parallel for Gold (prot FDR=1%) and Silver (prot FDR=5%) builds.'''
28: then run ProtPro on all expts combined
32: ...,sc. Compile protein identifications and estimate protein concentrations
34: ..._probs.tsv, gather peptides mapping to identified proteins down to 1% peptide FDR.''' - Software:MZIdentML (1801 bytes)
3: MZIdentML is an emerging standard in the proteomic community. [http://psidev.info/mzidentml-1_1...
6: ...single document. In particular the combination of prot.xml and pep.xml is supported. If you use this com...
8: ...am waiting to see if they are adopted by the main proteo wizard team.
14: MyDirectory>idconvert --mzIdentML interact.prot.xml
15: ...nd into a file whose name will be the name of the prot.xml file with .mzid appended. NOTE in the command... - TPP:4.6.2 Release Notes (2282 bytes)
3: Trans-Proteomic Pipeline (TPP) software, release 4.6.2 is a ...
34: "http://tools.proteomecenter.org/wiki/"
37: "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP" - TPP:4.7.0 Release Notes (9008 bytes)
2: Trans-Proteomic Pipeline (TPP) software, release 4.7.0 is a ...
7: * '''compareProts_ClusterHM.pl''':
8: ** tool for building heatmaps comparing different ProteinProphet results
14: * New '''ProtXML Viewer''' (beta):
19: ** Displays protein annotation via AJAX call, with show/hide divs - TPP:4.8.0 SVN Log (42174 bytes)
21: [ProtXMLViewer] Added NSP bin link (goes to models page...
25: ...atio pvalue] Write pvalue raw data and model into protXML (using a tmp file) so other tools can display/...
39: * Changed element name "protein_summary" to "protein_summary_header" for
40: ...e source_files and source_files_alt attributes in prot.xml files
63: [ProtXMLViewer]
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