TPP:5.2.0 SVN Log
From SPCTools
Revision as of 01:29, 9 August 2018
r7671 | real_procopio | 2017-11-03 16:21:35 -0700 (Fri, 03 Nov 2017) | 1 line
[comet] Delete previous versions
r7672 | real_procopio | 2017-11-06 15:02:29 -0800 (Mon, 06 Nov 2017) | 1 line
Removing obsolete/unused cgis and references to them (mostly old protXML viewer helpers)
r7673 | real_procopio | 2017-11-06 15:53:29 -0800 (Mon, 06 Nov 2017) | 1 line
[pepXMLViewer] Freshen up the help page to reflect current state of viewer, and clean up grammar/spelling. More work needed...
r7674 | real_procopio | 2017-11-07 17:40:03 -0800 (Tue, 07 Nov 2017) | 7 lines
[ProtXMLViewer] - Attempt to guess organism from Uniprot annotations (OS=xxx yyy) - Give breakdown of number of entries, single hits, spectra, etc by organism - Update Gaggle format for export to Firegoose/Chrome Goose (if they ever work fully again...) - Reduced size of font for entry id
r7675 | mhoopmann | 2017-11-09 13:51:14 -0800 (Thu, 09 Nov 2017) | 3 lines
Changed how modifications are tracked and handled. No longer requires lookup table to reconcile differences in search parameters and pepXML output when representing peptide sequences. Some potential issues likely remain when reading pepXML from msgfplus with n-terminus modifications.
r7676 | eng_jk | 2017-11-09 14:26:18 -0800 (Thu, 09 Nov 2017) | 2 lines
fix parsing non-matching strings into correct variable
r7677 | dshteyn | 2017-11-15 11:11:44 -0800 (Wed, 15 Nov 2017) | 1 line
New features in PTMProphet
r7678 | dshteyn | 2017-11-17 17:53:53 -0800 (Fri, 17 Nov 2017) | 1 line
PTMProphet: multi-threading
r7679 | real_procopio | 2017-11-20 12:43:42 -0800 (Mon, 20 Nov 2017) | 1 line
[Prospector] Adding support for ProteinProspector
r7680 | real_procopio | 2017-11-20 12:53:54 -0800 (Mon, 20 Nov 2017) | 1 line
[general] Removing old unused PeptideProphetMain (dates from we only supported SEQUEST and MASCOT); also remove similar old unused code from MixtureModel
r7681 | real_procopio | 2017-11-21 10:44:55 -0800 (Tue, 21 Nov 2017) | 1 line
[XPRESS] Bugfixes: fix logic for actually reporting intensity-based ratios when using -H or -L options; fix typo in heavy_intensity_scan tag name
r7682 | real_procopio | 2017-11-21 10:54:36 -0800 (Tue, 21 Nov 2017) | 1 line
[PepXMLViewer] Added (and fixed) support for XPRESS fields: light_area, heavy_area, light_intensity, heavy_intensity, intensity_ratio
r7683 | real_procopio | 2017-11-21 11:00:00 -0800 (Tue, 21 Nov 2017) | 1 line
[Petunia] Added support for reporting intensity-based ratios in XPRESS
r7684 | dshteyn | 2017-11-22 12:37:26 -0800 (Wed, 22 Nov 2017) | 1 line
ProteinProphet: compute exact error rates based on existing probabilities of all proteins, rather than applying artibtrary minimum probability thresholds, at request of Kristian for use with StPeter.
r7685 | dshteyn | 2017-11-22 12:39:05 -0800 (Wed, 22 Nov 2017) | 1 line
PTMProphet: synchronize opening the file with cramp
r7686 | dshteyn | 2017-11-23 10:19:25 -0800 (Thu, 23 Nov 2017) | 1 line
PTMProphet: improvements for faster execution for single and multi-threading.
r7687 | dshteyn | 2017-11-24 09:10:43 -0800 (Fri, 24 Nov 2017) | 1 line
PTMProphet: fix compilation error ...
r7688 | dshteyn | 2017-11-27 15:53:02 -0800 (Mon, 27 Nov 2017) | 1 line
mzParser: fix bug associated with reading scan headers using the scan index, for files that are filtered for a subset of scans. Throw error and revert to linear lookup when the index doesn't access the requested scan number.
r7689 | dshteyn | 2017-11-27 15:55:48 -0800 (Mon, 27 Nov 2017) | 1 line
InteractParser: fix bug reported by Kristian on filtered mzML files. Append file extension to the data file path.
r7690 | real_procopio | 2017-11-27 18:02:05 -0800 (Mon, 27 Nov 2017) | 1 line
[PepXMLViewer] Report number of *_UNMAPPED protein entries, when present, and disable links to sequence viewer from such entries; Display list of search engines when viewing iProphet results
r7691 | real_procopio | 2017-11-29 12:58:08 -0800 (Wed, 29 Nov 2017) | 6 lines
[updatepaths] - Ensure new directory is an absolute path - Make sure we are updating the desired attribute's value (and not some other matching string within the tag) - Perform extension-free check only if original file name is not found (fixes case when pepXML reference files within a protXML file got mismapped like so: interact.pep.xml --> interact.prot.xml) - Remove duplicated documentation
r7692 | real_procopio | 2017-11-29 13:21:08 -0800 (Wed, 29 Nov 2017) | 1 line
[RefreshParser] Report number of _UNMAPPED entries
r7693 | real_procopio | 2017-11-29 18:22:04 -0800 (Wed, 29 Nov 2017) | 1 line
[InteractParser] Apply -C (correct charge states) automatically for OMSSA files (as per usage statement!); clean up usage statement and enzyme display, as well as some unused code
r7694 | dshteyn | 2017-11-30 10:00:40 -0800 (Thu, 30 Nov 2017) | 1 line
PTMProphet: fix bug of skipping some pepXML tags in multithreaded execution.
r7695 | real_procopio | 2017-11-30 16:04:20 -0800 (Thu, 30 Nov 2017) | 1 line
Delete old, corrupted (unreadable) file
r7696 | real_procopio | 2017-11-30 18:18:11 -0800 (Thu, 30 Nov 2017) | 1 line
[subsetdb] Bump buffer to 500k bytes to accommodate super long PEFF description lines (longest so far observed is 210k chars!)
r7697 | real_procopio | 2017-11-30 19:46:32 -0800 (Thu, 30 Nov 2017) | 6 lines
[madcaps] - Use case-sensitive option (-C) when calling subsetdb for faster performance (>100x faster with PEFF files!) - Bolden keywords (KEY=) in protein annotations - Provide direct link to neXtProt proteomics page for "nxp:NX_" entries - Adjust width and alignment of sequence zoom window
r7698 | dshteyn | 2017-12-01 16:33:13 -0800 (Fri, 01 Dec 2017) | 1 line
PTMProphet bug fixes associated with check in of newest features.
r7699 | real_procopio | 2017-12-01 17:39:18 -0800 (Fri, 01 Dec 2017) | 1 line
[subsetdb] For case-insensitive searches, only apply toupper() to chars in the range a-z - this boosts performace by an order+ of magnitude when processing PEFF databases; remove unused SUBSET_SIZE define
r7700 | real_procopio | 2017-12-01 18:47:47 -0800 (Fri, 01 Dec 2017) | 1 line
[PTMProphet] Report processing progress in one line (overwriting itself), instead of creating a new one each time, to save space on output. It can get funky with multiple threads, so a threadsafe cleanup might be desired
r7701 | dshteyn | 2017-12-04 11:18:35 -0800 (Mon, 04 Dec 2017) | 1 line
ProteinProphet: expand isotopic offsets considered for mass diff to -1,0,1,2,3 per Alexey request for Open Mass Searching (e.g MSFragger).
r7702 | real_procopio | 2017-12-14 11:45:25 -0800 (Thu, 14 Dec 2017) | 1 line
[ramp] Also delete scan headers cache when "closing" file
r7703 | dshteyn | 2017-12-15 10:24:44 -0800 (Fri, 15 Dec 2017) | 1 line
PTMProphet: BUGFIX neutral losses were not being picked up from the commandline nor utilized correctly; FEATURE auto enable DIRECT mode under specific conditions.
r7704 | dshteyn | 2017-12-15 11:13:42 -0800 (Fri, 15 Dec 2017) | 1 line
DISCO: report number of precursors being tracked. Improve code for tracking the precursors near their local peak maxima to improve efficiency.
r7705 | real_procopio | 2017-12-15 13:43:12 -0800 (Fri, 15 Dec 2017) | 9 lines
[XPRESS] - Implement calculation of protein ratios based on peptide peak intensities (new -i option in XPressProteinRatioParser) - Added new "ratio_basis" attribute to protXML (possible values are "area" and "intensity") - Added usage statement to XPressProteinRatioParser - Establish a floor (0.001) and ceiling (999.0) for intensity-based peptide ratios (as is done for area-based ratios). Also report "-1" when no ratio can be calculated. - Remove unsused -C option from XPressPeptideParser usage statement (and minor clean-up) - Fix various memory leaks and minor code clean-up
r7706 | real_procopio | 2017-12-15 14:05:00 -0800 (Fri, 15 Dec 2017) | 7 lines
[PepXMLViewer] - Added support for XPRESS label-free analysis; new fields are:
peak_area (default), first_scan, last_scan, peak_intensity, peak_intensity_scan
- Implement background color gradient for intensity-based XPRESS ratios - Minor code simplification for better performance
r7707 | real_procopio | 2017-12-15 14:14:08 -0800 (Fri, 15 Dec 2017) | 1 line
[tpp_models] Added support for XPRESS label-free analysis parameters
r7708 | real_procopio | 2017-12-15 14:20:05 -0800 (Fri, 15 Dec 2017) | 1 line
[Petunia] Added option to run XPRESS label-free analysis; re-arranged XPRESS options for more logical/visual flow
r7709 | real_procopio | 2017-12-15 14:24:08 -0800 (Fri, 15 Dec 2017) | 1 line
[ProtXMLViewer] Added label when viewing intensity-based ratios from XPRESS
r7710 | real_procopio | 2017-12-15 15:01:29 -0800 (Fri, 15 Dec 2017) | 6 lines
[ProteinProphet] - Implement XPRESS_INT parameter to run XPressProteinRatioParser with new -i option - Don't report raw_intensity when unavailable - Partial fixes for memory leaks, some code clean-up
r7711 | real_procopio | 2017-12-15 15:07:52 -0800 (Fri, 15 Dec 2017) | 1 line
[xinteract] Change meaning of -Ot option; it now will pass PLOTPNG option to ProteinProphet (replacing long-vacated NOPLOT option)
r7712 | real_procopio | 2017-12-15 17:47:09 -0800 (Fri, 15 Dec 2017) | 1 line
[batchcoverage] Fix memory leaks, clean up code
r7713 | eng_jk | 2017-12-19 15:50:20 -0800 (Tue, 19 Dec 2017) | 2 lines
set default number of isotope peaks (-p) to "1" as stated in xinteract usage statement
r7714 | real_procopio | 2017-12-19 16:16:03 -0800 (Tue, 19 Dec 2017) | 1 line
[InteractParser] Fix bug that mangled spectrum names from files that contain a dot in their names; also fixed bad logic (from r6329) that prevented fallback capture of scans and charge from spectrum names; and while we're at it, plug various memory leaks
r7715 | real_procopio | 2017-12-19 18:59:14 -0800 (Tue, 19 Dec 2017) | 1 line
[cygwin] Remove all references to cygpath -- the first of several steps to remove long-unmaintained and deprecated cygwin code
r7716 | real_procopio | 2017-12-20 11:32:08 -0800 (Wed, 20 Dec 2017) | 1 line
[cygwin] Remove all references to WINDOWS_CYGWIN -- the second of several steps to remove long-unmaintained and deprecated cygwin code
r7717 | mhoopmann | 2017-12-20 15:04:57 -0800 (Wed, 20 Dec 2017) | 2 lines
Cosmetic changes to verbage during use. Removed exporting of non-normalized results and removed unintended creation of text files used during testing.
r7718 | real_procopio | 2017-12-20 15:48:17 -0800 (Wed, 20 Dec 2017) | 1 line
[Petunia] Remove StPeter option for exporting non-normalized results
r7719 | dshteyn | 2017-12-25 23:40:00 -0800 (Mon, 25 Dec 2017) | 1 line
Correcting windows compilation problems...
r7720 | dshteyn | 2017-12-26 10:18:38 -0800 (Tue, 26 Dec 2017) | 1 line
Fix mingw compilation issue of tandem.
r7721 | dshteyn | 2017-12-26 11:14:04 -0800 (Tue, 26 Dec 2017) | 1 line
Enable SIMD in tandem code to compile under MINGW gcc
r7722 | mhoopmann | 2017-12-27 11:02:11 -0800 (Wed, 27 Dec 2017) | 3 lines
Fixed bug that skipped n-terminally modified peptides. And very minor other bits of code cleaning.
r7723 | mhoopmann | 2017-12-27 11:28:50 -0800 (Wed, 27 Dec 2017) | 2 lines
Adding alternative enzyme names and fixing incorrect expression for TrypChymo
r7724 | mhoopmann | 2018-01-16 15:34:39 -0800 (Tue, 16 Jan 2018) | 3 lines
[STPETER]: Use natural log fragment ion peak values.
r7725 | dshteyn | 2018-02-27 11:24:45 -0800 (Tue, 27 Feb 2018) | 1 line
DISCO: streamline parallel execution, fix file output of intermediate results on Windows, remove RT in secs correction factor, upgrade threading to use c++11 standard library
r7726 | dshteyn | 2018-02-27 14:33:33 -0800 (Tue, 27 Feb 2018) | 1 line
Makefile: enable -std=c++11 for sufficiently high versions of gcc
r7727 | dshteyn | 2018-02-27 15:32:05 -0800 (Tue, 27 Feb 2018) | 1 line
MzXML2Search: take advantage of the index to faster read spectrum headers with mzParser.
r7728 | dshteyn | 2018-02-27 15:36:11 -0800 (Tue, 27 Feb 2018) | 1 line
RTCatalog: Allow for negative RT values as some iRTs can be negative, use unsigned long instead of ints for larger datasets.
r7729 | dshteyn | 2018-02-27 15:38:55 -0800 (Tue, 27 Feb 2018) | 1 line
Mascot2XML: more descriptive warning messages for poorly formatted Mascot results, and allow conversion to proceed after reporting the issues.
r7730 | dshteyn | 2018-02-27 15:45:36 -0800 (Tue, 27 Feb 2018) | 1 line
Tandem2XML: new options in Tandem2XML to allow it to work with newer versions of tandem and format spectrum names for TPP according t TPP conventions.
r7731 | dshteyn | 2018-02-27 15:50:44 -0800 (Tue, 27 Feb 2018) | 1 line
RTCatalog: prevent overwriting existing files.
r7732 | dshteyn | 2018-02-27 17:49:58 -0800 (Tue, 27 Feb 2018) | 1 line
Tag.h: including system types header.
r7733 | dshteyn | 2018-02-27 18:42:00 -0800 (Tue, 27 Feb 2018) | 1 line
ShowXIC.cgi: user settable MAXPPM error tolerance.
r7734 | dshteyn | 2018-02-27 18:46:52 -0800 (Tue, 27 Feb 2018) | 1 line
InteractParser: report TIC and S2N in pepXML
r7735 | dshteyn | 2018-02-27 18:48:19 -0800 (Tue, 27 Feb 2018) | 1 line
Spectrum Viewer: faster reading of spectra by use of index
r7736 | dshteyn | 2018-02-27 18:49:58 -0800 (Tue, 27 Feb 2018) | 1 line
PepXMLViewer: plot histograms with 1000 bins by default.
r7737 | dshteyn | 2018-02-27 18:53:27 -0800 (Tue, 27 Feb 2018) | 1 line
InteractParser: compile with gsl for stats.
r7738 | dshteyn | 2018-02-27 18:55:50 -0800 (Tue, 27 Feb 2018) | 1 line
SpectraST: New function for returning the nearest peak to a given mz value in a spectrum; default constructor for Peptide
r7739 | dshteyn | 2018-02-27 19:04:10 -0800 (Tue, 27 Feb 2018) | 1 line
PTMProphet: use the max of user set mz tolerance and PSM massdiff to localize
r7740 | dshteyn | 2018-02-27 19:07:31 -0800 (Tue, 27 Feb 2018) | 1 line
PeptideProphet: tell Mascot user which scores are missing
r7741 | dshteyn | 2018-02-27 19:15:19 -0800 (Tue, 27 Feb 2018) | 1 line
PeptideProphet: SpectraST modeling correct errors in initial settings.
r7742 | dshteyn | 2018-02-27 19:19:41 -0800 (Tue, 27 Feb 2018) | 1 line
iProphet: make use of spectrum_label when available.
r7743 | dshteyn | 2018-02-27 19:22:47 -0800 (Tue, 27 Feb 2018) | 1 line
reSpect: when multiple spectra of the same scan number are in the same analysis, only process the highest probability PSM
r7744 | dshteyn | 2018-02-27 19:36:28 -0800 (Tue, 27 Feb 2018) | 1 line
HardKlor: allow modeling of intesities less than 1
r7745 | dshteyn | 2018-02-27 19:40:20 -0800 (Tue, 27 Feb 2018) | 1 line
ProteoWizard: set centroid CV term
r7746 | dshteyn | 2018-02-28 17:07:41 -0800 (Wed, 28 Feb 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
r7747 | dshteyn | 2018-02-28 17:36:16 -0800 (Wed, 28 Feb 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
r7748 | dshteyn | 2018-02-28 17:38:11 -0800 (Wed, 28 Feb 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
r7749 | dshteyn | 2018-03-01 09:01:35 -0800 (Thu, 01 Mar 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
r7750 | dshteyn | 2018-03-05 10:00:34 -0800 (Mon, 05 Mar 2018) | 1 line
Use std::isnan to allow pwiz to compile.
r7751 | dshteyn | 2018-03-05 11:02:07 -0800 (Mon, 05 Mar 2018) | 1 line
including <cmath> to address isnan compiling issues
r7752 | real_procopio | 2018-03-09 16:12:42 -0800 (Fri, 09 Mar 2018) | 1 line
[tpp_models] Capture and display Phospho models, when available
r7753 | dshteyn | 2018-03-14 09:17:30 -0700 (Wed, 14 Mar 2018) | 1 line
Adding back protovis which is utilized in RTCatalog for drawing RT gradient corrections page...
r7754 | dshteyn | 2018-03-14 10:19:25 -0700 (Wed, 14 Mar 2018) | 1 line
RTCatalog: new option DISCO to allow building catalog from DISCO/DIAUmpire results.
r7755 | dshteyn | 2018-03-14 17:15:38 -0700 (Wed, 14 Mar 2018) | 1 line
Upgrading PWIZ ...
r7756 | dshteyn | 2018-03-14 23:30:00 -0700 (Wed, 14 Mar 2018) | 1 line
Upgrading PWIZ ...
r7757 | dshteyn | 2018-03-15 09:39:39 -0700 (Thu, 15 Mar 2018) | 1 line
Upgrading PWIZ ...
r7758 | dshteyn | 2018-03-15 10:16:42 -0700 (Thu, 15 Mar 2018) | 1 line
Upgrading PWIZ ...
r7759 | dshteyn | 2018-03-15 14:02:47 -0700 (Thu, 15 Mar 2018) | 1 line
Updating PWIZ ...
r7760 | mhoopmann | 2018-03-15 14:10:28 -0700 (Thu, 15 Mar 2018) | 3 lines
[mzIMLTools]: fixed bug when copying a string. (old commit finally let through now that sourceforge is working again).
r7761 | dshteyn | 2018-03-19 09:55:29 -0700 (Mon, 19 Mar 2018) | 1 line
Fix problem with windows build not copying the pwiz msi to the staging area ...
r7762 | real_procopio | 2018-03-21 12:22:41 -0700 (Wed, 21 Mar 2018) | 1 line
[indexmzXML] New wrapper to run indexer, which renames .new file (if generated). Have Petunia call this instead of running the executable directly to avoid mis-communication to user when no .new file is created (i.e. index was good)
r7763 | dshteyn | 2018-03-26 15:17:33 -0700 (Mon, 26 Mar 2018) | 1 line
Fix runtime bug with using boost regex match extra flag ... was crashing PepXMLViewer.
r7764 | dshteyn | 2018-03-26 15:49:07 -0700 (Mon, 26 Mar 2018) | 1 line
Fix runtime bug with using boost regex match extra flag ... was crashing PepXMLViewer.
r7765 | dshteyn | 2018-04-26 10:04:51 -0700 (Thu, 26 Apr 2018) | 1 line
cramp: use the index for faster lookups.
r7766 | dshteyn | 2018-04-30 12:01:10 -0700 (Mon, 30 Apr 2018) | 1 line
cramp: use index for speed in reading peakLists...
r7767 | dshteyn | 2018-05-10 14:12:37 -0700 (Thu, 10 May 2018) | 1 line
Lorikeet: Display Annotated Ion Current
r7768 | dshteyn | 2018-05-10 14:20:36 -0700 (Thu, 10 May 2018) | 1 line
Lorikeet: Display Annotated Ion Current
r7769 | dshteyn | 2018-05-14 15:53:32 -0700 (Mon, 14 May 2018) | 1 line
PTMProphet: make options to set N-term and C-term fragment ions for PTMProphet to consider.
r7770 | dshteyn | 2018-05-14 16:39:58 -0700 (Mon, 14 May 2018) | 1 line
compute_p: simple utility to compute p-values for some common distributions using GSL.
r7771 | dshteyn | 2018-05-16 16:11:05 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: use ppm fragment tolerance.
r7772 | dshteyn | 2018-05-16 16:19:43 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: merging copies ...
r7773 | dshteyn | 2018-05-16 16:34:23 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: use PPM for auto tolerance selection ...
r7774 | dshteyn | 2018-05-16 22:19:51 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: correct problem in previous checkin...
r7775 | dshteyn | 2018-05-18 10:03:36 -0700 (Fri, 18 May 2018) | 1 line
PTMProphet: test for NULL pointer to prevent crashes ...
r7776 | dshteyn | 2018-05-21 08:51:49 -0700 (Mon, 21 May 2018) | 1 line
DiscoFilter: Test for spectrum list bounds overruns as QE DIA data may not have complete cycles...
r7777 | real_procopio | 2018-05-31 17:36:38 -0700 (Thu, 31 May 2018) | 1 line
Bump version as we prepare for a pre-release candidate
r7778 | dshteyn | 2018-07-09 10:25:49 -0700 (Mon, 09 Jul 2018) | 1 line
Mascot2XML: updates to allow handling of newer mascot results ...
r7779 | dshteyn | 2018-07-09 10:29:05 -0700 (Mon, 09 Jul 2018) | 1 line
RTCalculator: function to read coefficients from a user specified file
r7780 | dshteyn | 2018-07-09 10:32:54 -0700 (Mon, 09 Jul 2018) | 1 line
RTCatalog: when reading catalog ignore the header line. Report RT in minutes.
r7781 | dshteyn | 2018-07-09 10:33:57 -0700 (Mon, 09 Jul 2018) | 1 line
Objects for handling Magnum and Morpheus results...
r7782 | dshteyn | 2018-07-09 10:36:02 -0700 (Mon, 09 Jul 2018) | 1 line
Add option to store the RTCatalog coefficients file when using it in PeptideProphet modeling.
r7783 | dshteyn | 2018-07-09 10:38:11 -0700 (Mon, 09 Jul 2018) | 1 line
QUANTIC: first commit ...
r7784 | dshteyn | 2018-07-09 10:38:29 -0700 (Mon, 09 Jul 2018) | 1 line
QUANTIC: first commit ...
r7785 | dshteyn | 2018-07-09 10:44:54 -0700 (Mon, 09 Jul 2018) | 1 line
DISCO: updates and implement support for analysis of simply formated RT mz tables files...
r7786 | dshteyn | 2018-07-09 10:46:47 -0700 (Mon, 09 Jul 2018) | 1 line
PeptideProphet: support for Magnum ...
r7787 | dshteyn | 2018-07-09 10:47:10 -0700 (Mon, 09 Jul 2018) | 1 line
PeptideProphet: support for Morpheus ...
r7788 | dshteyn | 2018-07-09 10:48:33 -0700 (Mon, 09 Jul 2018) | 1 line
Makefile support for Magnum, Morpheus and new DISCO functionality ...
r7789 | dshteyn | 2018-07-09 10:51:09 -0700 (Mon, 09 Jul 2018) | 1 line
Support for Magnum, Morpheus and new RT model functionality in PeptideProphet
r7790 | dshteyn | 2018-07-09 10:52:18 -0700 (Mon, 09 Jul 2018) | 1 line
Support for new RT model functionality in PeptideProphet ...
r7791 | dshteyn | 2018-07-09 10:56:29 -0700 (Mon, 09 Jul 2018) | 1 line
PTMProphet: Use bootstrapped fragment PPM tolerance when left unspecified ...
r7792 | dshteyn | 2018-07-09 10:58:49 -0700 (Mon, 09 Jul 2018) | 1 line
Support for Magnum and new RT model functionality in PeptideProphet
r7793 | dshteyn | 2018-07-09 11:00:38 -0700 (Mon, 09 Jul 2018) | 1 line
InteractParser: record base peak intensity in pepXML.
r7794 | dshteyn | 2018-07-09 11:03:27 -0700 (Mon, 09 Jul 2018) | 1 line
PepXMLViewer: change to allow export of PTMProphet features and Quantic results ...
r7795 | dshteyn | 2018-07-09 11:05:15 -0700 (Mon, 09 Jul 2018) | 1 line
Xinteract: support for new RT model functionality in PeptideProphet
r7796 | dshteyn | 2018-07-09 11:06:14 -0700 (Mon, 09 Jul 2018) | 1 line
Makefile: support for Magnum and Morpheus
r7797 | dshteyn | 2018-07-09 11:22:31 -0700 (Mon, 09 Jul 2018) | 1 line
Tools to generate quantitative volcano plots on Proteins and Peptides ...
r7799 | henryhlam | 2018-07-24 22:34:00 -0700 (Tue, 24 Jul 2018) | 1 line
[SpectraST] Fix MSP import of latest NIST HCD libraries.
r7801 | henryhlam | 2018-07-25 00:29:10 -0700 (Wed, 25 Jul 2018) | 1 line
[SpectraST] PepXML import allows modification specified as SpectraST-recognized mod names (in place of "mass" in mod_aminoacid_mass). This is a temporary fix until we have better ways of specifying mods in PepXML.
r7802 | dshteyn | 2018-08-06 17:20:04 -0700 (Mon, 06 Aug 2018) | 1 line
PepXMLViewer: report new stats norm_entropy and mean_best_prob.
r7803 | real_procopio | 2018-08-07 18:39:37 -0700 (Tue, 07 Aug 2018) | 1 line
[comet] New version 2018012
r7804 | real_procopio | 2018-08-07 18:48:07 -0700 (Tue, 07 Aug 2018) | 1 line
[version] 5.2.0(beta)0 pre-release
r7805 | real_procopio | 2018-08-08 11:05:30 -0700 (Wed, 08 Aug 2018) | 1 line
[comet] Fix Makefile target for unpacking comet sources
