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- TPP:V5Feedback (11460 bytes)
4: * Update the TPP wiki installation instructions
5: * Update the TPP wiki build instructions
31: * BUILD_LINUX instructions are way out of date. Also take a look at the BUI...
49: * <s>Clicking on the ions2 link to view the spectrum in comet results in th...
51: * <s>Clicking on the ions link in the comet pepxml view of the top 5 matchi... - Software:Prequips:Inclusion List Builder (3897 bytes)
1: ...ak detection and sequencing of selected precursor ions. The method has been described in detail in ''Sch... - TPP:7.0.0 Release Notes (6884 bytes)
27: ...out reading the spectrum data arrays under conventions used by some converters. This is potentially inef...
53: * BUGFIX * parsing protein descriptions from fasta files running on CentOS (reported by J...
70: * Update to latest versions of assess_swathlib and DIALib-QC_RPlot
76: * bugfix when processing n-terminal modifications.
86: * Remove "expert" warning from its extra options - Software:XPRESS (1756 bytes)
8: ...e expression values. Averages plus standard deviations are calculated for each protein expression value ...
12: [http://tools.proteomecenter.org/publications/Han-NatureBiotech.pdf download PDF] - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
2: |[[Image:alert.jpg|middle|left]]
3: ...les found in source code distribution for instructions on how to build TPP for the Linux platform.
70: ...ust INSTALL_DIR and TPP_DATADIR to match the locations you created above. Leave TPP_DATAURL and TPP_BASE...
148: ...ll this config file. This may vary among distributions, but this seems like a nice way to do it on Ubunt...
157: ... configuration. Next, set some appropriate permissions for the web server to write. With the first comma... - TPP:Sequest and the TPP (1847 bytes)
5: ...he TPP. For example, someone could write instructions for working with the GUI, with Bioworks, on the c...
8: ...is could possibly be different in more recent versions of Bioworks SEQUEST.
10: ...ly has minimal effect on the resulting identifications. - Software:SpectraST (70083 bytes)
1: ...designed primarily for shotgun proteomics applications. It is developed at the [http://www.systemsbiolog...
7: ... as tandem mass (MS/MS) spectra. Because peptide ions tend to fragment mostly along the peptide backbon...
11: ...ng, sequence searching in many proteomics applications.
17: ...se are considered. Most of these putative peptide ions considered in sequence searching are never observ...
21: ...ry simplistic (e.g., only including b- and y-type ions, at a fixed intensity), and do not resemble the e... - Spectrast.params (3605 bytes)
2: ### COMMON OPTIONS ##############################
26: # Spectra of peptide ions of a different kind of cysteine modification will...
38: # Whether to ignore library spectra of peptide ions with an unmodified cysteine - TPP Tutorial v1 (43187 bytes)
18: ...led samples, and validation of protein identifications, as well as tools for viewing raw LC/MS data, pep...
19: [[image:Pipeline_Tutorial.jpg]]
26: ...his guide uses the following typographical conventions:
62: ...ow the syntax necessary to run the program and options associated with the program.
83: ...th the user name and password. Below are instructions for making another account from a Cygwin shell. ... - Software:TIQAM (7374 bytes)
4: [[Image:TIQAMWorkFlow.jpg]]
10: .... Peptides are sorted within the proteins. Transitions are generated based on user criteria.
13: ...an be viewed to validate transitions. Best transitions can be exported for quantification.
16: ... are correctly defined. The names of the modifications in the csv file and on the modification page need...
20: * A csv file with the list of transitions and associated proteins. Such a file is generated... - Terry's blog (18394 bytes)
36: ...ion peaks vs. B-ion (correct for peptides where B-ions expected to be strong; I think these are certain ...
48: ...andem refinement because refinement breaks assumptions used by NTT modeling.
52: ...ntal limitation in MS/MS proteomics: modified versions of high abundance proteins are still abundant eno...
54: * '''Immonium ions''' -- single side chain fragments formed by combo...
77: ...t difficult to use on lots of data. Possible solutions: break up spectra into batches and run iProphet o... - TPP Tandem search (19915 bytes)
20: ...exe''. Run it and follow the installation instructions.'''
86: ...account the relevant static and variable modifications.
89: diff_search_options = 8.0 C 0.0 x 16.0 M
96: SEQUEST (diff_search_options). The 16.0 M accounts for the presence of oxidize...
154: <note> FILE LOCATIONS. Replace them with your input (.mzXML) file and o... - Software:TPP-MaRiMba (11021 bytes)
3: ...te MRM lists containing isotopically heavy transitions for use with isotopic labeling strategies such as...
10: ...RiMba interface provides the user with various options for MRM list creation and customization. The step...
14: ...d spectral library serves as the source of transitions for the ensuing MRM list. This spectral library c...
18: ... mapping options are included in the Filtering Options section (see Step 5 below). The provided protein ...
24: ...ogether, due to their unique m/z values. Modifications can be specified in the sequence by listing, to t... - PABST (4203 bytes)
4: ...oduce lists of peptides and (optionally) fragment ions for use in selected reaction
6: ...temsbiology.net/sbeams/cgi/PeptideAtlas/GetTransitions
8: ...proteomecenter.org/wiki/index.php?title=GetTransitionsAPI [here]].
12: ...of the top ''M'' (currently 8) potential fragment ions from each selected peptide is determined. Finall...
36: The best fragment ions for a given spectrum are determined by querying a... - GetTransitionsAPI (7941 bytes)
2: GetTransitions is a CGI script that allows users to query the pe...
3: The transitions retrieved are constrained by various parameters s...
6: to obtain transitions.
12: ... parameters that can be used to refine the transitions retrieved from the Atlas, some required and some ...
14: web UI to help further explain these options. - TPP:4.4.0 Release Notes (31941 bytes)
5: ...ially) through OSX source from all the usual locations (please see the section below, "Getting the softw...
28: New options
43: * Minor corrections to session handling
123: [various] add a bunch of missing initializations - stack and dynamically allocated memory cannot b...
135: [Pepc] update GWT and GChart to current versions and tweak color select code to satisfy IE8 - ReleasePlanning (12743 bytes)
15: ** Doesn't use web application conventions (single file in available-sites)
37: ...le as a very simple workflow manager. Selected options would be saved to a simple params file of key-val...
47: ...atasets looks on the EC2 nodes and local installations
124: ... listing (can be very slow) -- rely on file extensions? Implement AJAX?
173: ...filtering in Petunia (only affects Linux installations) - TPP:4.5.0 SVN Log (242349 bytes)
28: ...ic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx
43: ...ic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx
55: ...ic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx
56: ...ic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.h
60: ...ialization, replaced these with more generic functions that are easier to debug and work now. - TPP:4.6.0 Release Notes (4524 bytes)
3: ...ially) through OSX source from all the usual locations (please see the section below, "Getting the softw...
21: ...age shows all jobs run by user, including old sessions
30: * ''PepXMLViewer'' ions (''ions2'') link goes to ''Lorikeet'' viewer by default; ...
48: * Fixed double counting bug (under specific conditions) in ''ProphetModels.pl''
97: ...community who provided feedback and code contributions. - TPP:4.6.0 SVN Log (19654 bytes)
63: Report a,c,x,z ions (lost during upgrade to cyclone).
138: PTMProphet: Fix bug in enumerating all combinations of mods. Replaced recurring function with an ite...
259: [PepXMLViewer] Default ions2 link to Lorikeet, hide the link to old viewer (s...
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