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	= TPP 7.1.0 ALBEDO Release Notes =		= TPP 7.1.0 ALBEDO Release Notes =
	===[Known Bugs:]===		===[Known Bugs:]===
-	* Comet has a known bug searching MS3 data, [[xinteract:|xinteract]] option: -MULTI and [[InteractParser:|InteractParser]] option -m can be useful to make sense of MS3 data searched with this version of comet	+	* Comet has a known bug searching MS3 data,
		+	'''SOLUTION:'''[[http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.1.0_Release_Notes#.5Bxinteract:.5D xinteract]] option '''-MULTI''' and [[http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.1.0_Release_Notes#.5BInteractParser:.5D InteractParser]] option '''-m''' can be useful to make sense of MS3 data searched with this version of comet
		+
		+
		+	* Export of TSV data has a problem exporting StPeter values from ProtXMLViewer.pl when called over the CGI web-interface in this version.
		+	'''SOLUTION:'''
		+	1. As a backup, create a copy of the current TPP ProtXMLViewer.pl file: '''$(TPP_HOME)/cgi-bin/ProtXMLViewer.pl'''
		+	2. Using a text editor apply the following changes to [[https://sourceforge.net/p/sashimi/code/9290/tree//trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl?diff=9289 ProtXMLViewer.pl]]
	===[General:]===		===[General:]===
	* Use icons to differentiate the different TPP pages, should help those of us with millions of open tabs (not pointing fingers ... ;)		* Use icons to differentiate the different TPP pages, should help those of us with millions of open tabs (not pointing fingers ... ;)
		+
	===[apache 2.4 config:] ===		===[apache 2.4 config:] ===
-	* fix issue with Forbidden Access to /tpp on the webserver on MacOS	+	* fix issue with Forbidden Access to /tpp on the webserver

---

Current revision

Contents 1 TPP 7.1.0 ALBEDO Release Notes 1.1 [Known Bugs:] 1.2 [General:] 1.3 [apache 2.4 config:] 1.4 [protXML version 11:] 1.5 [digestdb:] 1.6 [PTMProphet:] 1.7 [plot-msms-utils.js:] 1.8 [Comet:] 1.9 [tpp_model.pl:] 1.10 [ProtXMLViewer:] 1.11 [ProteinProphet:] 1.12 [TPP:Models Page:] 1.13 [TPP::Main Page:] 1.14 [Petunia:] 1.15 [Petunia::Analyze Peptides] 1.16 [TPP::Magnum for Windows:] 1.17 [TPP::Kojak 2.1.0 for Windows:] 1.18 [common.mk:] 1.19 [Seq2MS_json.pl:] 1.20 [tpp_model.pl:] 1.21 [tpp_gui.pl:] 1.22 [PeptideProphet:] 1.23 [extern/MSToolkit:] 1.24 [common.mk:] 1.25 [Makefile:] 1.26 [DISCO:] 1.27 [HDF5:] 1.28 [PWIZ:] 1.29 [Petunia::Lib2HTML:] 1.30 [MSReader:] 1.31 [xinteract:] 1.32 [PepXMLViewer.cgi:] 1.33 [InteractParser:]

TPP 7.1.0 ALBEDO Release Notes

[Known Bugs:]

• Comet has a known bug searching MS3 data,

       SOLUTION:[xinteract] option -MULTI and [InteractParser] option -m can be useful to make sense of MS3 data searched with this version of comet

• Export of TSV data has a problem exporting StPeter values from ProtXMLViewer.pl when called over the CGI web-interface in this version.

       SOLUTION: 
       1. As a backup, create a copy of the current TPP ProtXMLViewer.pl file: $(TPP_HOME)/cgi-bin/ProtXMLViewer.pl
       2. Using a text editor apply the following changes to [ProtXMLViewer.pl]

[General:]

• Use icons to differentiate the different TPP pages, should help those of us with millions of open tabs (not pointing fingers ... ;)

[apache 2.4 config:]

• fix issue with Forbidden Access to /tpp on the webserver

[protXML version 11:]

• adding is_contributing_prob to distinguish from is_contributing_evidence

[digestdb:]

• add length range command line options for digested peptides

[PTMProphet:]

• BUGFIX issue with argument parsing, last arg was not getting set

[plot-msms-utils.js:]

• Seq2MS json parsing rt is now a string and needs parsing for this to work as before

[Comet:]

• update comet

[tpp_model.pl:]

• correct css link

[ProtXMLViewer:]

• color peptide probability based on is_contributing_prob (as opposed to is_contributing_evidence) when attribute is available.

[ProteinProphet:]

• catch and warn if TOPN setting is less than zero
• correctly calculate is_contributing_evidence for peptides when TOPN > 0 is enabled
• fix problem with calculating peptides that contribute probs when TOPN is limited, is_contributing_evidence attribute reports all peptides meeting minimum prob and minimum weight requirements (exactly as before), NEW attribute is_contributing_prob reports the peptides whose probabilities are included in the protein probability calculation...

[TPP:Models Page:]

• tpp.ico for TPP::Models

[TPP::Main Page:]

• tpp.ico for TPP::Main

[Petunia:]

• petunia.ico for Petunia
• xinteract, PeptideProphet and PTMProphet increase flexibility for setting options for analysis, allow extended modeling and experiment labeling options ... etc.
• additional flexibility for setting PTMProphet and xinteract options by Petunia
• ProphetModel.pl page decouple -n option from -u option, so that petunia can be used to analyze PTMs, unique peptide ions or unique peptide sequences by entrapment decoys
• add kojak params to New files options and fix some issues associated with creating a file with the correct name.
• add some basic help options with show/hide to help users
• add some basic help for experiment labels, mass difference models and model adjustment options

[Petunia::Analyze Peptides]

• Allow Petunia to set MASSDIFFMODE for PTMProphet using xinteract

[TPP::Magnum for Windows:]

• update Magnum to 1.3.4
• fix same path problem discovered in kojak on mingw::gcc compiled windows

[TPP::Kojak 2.1.0 for Windows:]

• path problem reported on spctools-discuss by Zeyu Wang

[common.mk:]

• fix issues with LDFLAGS

[Seq2MS_json.pl:]

• support for generating chimeric PSM

[tpp_model.pl:]

• diffvmc display new model

[tpp_gui.pl:]

• allow xinteract jobs to launch in parallel, useful when processing multiple files independently, also adding auto experiment labeling...
• allow executing xinteract jobs in parallel on a local linux server (without slurm)

[PeptideProphet:]

• VMC model: use the discrete model for VMC modeling as opposed to KDModel
• VMC: remove unused KDModel
• Prevent crash when no decoys are specified with MSFragger as the search engine
• new DIFFVMC model to complement the existing VMC-by-type model

[extern/MSToolkit:]

• BUGFIX running reSpect on DISCo generated mzML was observed throwing errors due to rampFileIn->fileName not being populated, using sCurrentFile instead

[common.mk:]

• adjust compilation linker flags for hdf5 on MacOS

[Makefile:]

• updates for new HDF5
• add the top level splash page to the files that need attention for make version-clean and make version

[DISCO:]

• updates for new PWIZ

[HDF5:]

• updated to 1.14.3 and patched
• hdf5 windows build on mingw
• adjust hdf5 linker flags for mac

[PWIZ:]

• updated
• requires HDF5 for MZ5 support
• changes for mingw build

[Petunia::Lib2HTML:]

• allow the the user to select user specific modifications for Lib2HTML by Petunia

[MSReader:]

• if scNum is 0 it is not useful as the lastReadScanNum

[xinteract:]

• new option -MULTI (InteractParser -m) to deal with comet files containing multiple precursors per possible spectrum number
• allow to specify unknown_decoy and use it in ProphetModels.pl in fully unsupervised modeling
• option to disable the new DIFFVMC model
• allow negatives in options to PTMProphet

[PepXMLViewer.cgi:]

• deal with comet files containing multiple precursors per possible spectrum number InteractParser option -m

[InteractParser:]

• new option -m to deal with comet files containing multiple precursors per possible spectrum number, encode spectrum names more uniquely based on scan number and precursor mz to allow multiple precursors per single scan number in one run
• new option -d to recalculate massdiffs for the search_hits