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	* 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 on MacOS
-	[protXML version 11:]	+	===[protXML version 11:] ===
-	adding is_contributing_prob to distinguish from is_contributing_evidence	+	* adding is_contributing_prob to distinguish from is_contributing_evidence
-	[digestdb:]	+	===[digestdb:] ===
-	add length range command line options for digested peptides	+	* add length range command line options for digested peptides
-	[PTMProphet:]	+	===[PTMProphet:] ===
-	BUGFIX issue with argument parsing, last arg was not getting set	+	* BUGFIX issue with argument parsing, last arg was not getting set
-	[plot-msms-utils.js:]	+	===[plot-msms-utils.js:] ===
-	Seq2MS json parsing rt is now a string and needs parsing for this to work as before	+	* Seq2MS json parsing rt is now a string and needs parsing for this to work as before
-	[Comet:]	+	===[Comet:]===
-	update comet	+	* update comet
-	[tpp_model.pl:]	+	===[tpp_model.pl:] ===
-	correct css link	+	* correct css link
-	[ProtXMLViewer:]	+	===[ProtXMLViewer:] ===
-	color peptide probability based on is_contributing_prob (as opposed to is_contributing_evidence) when attribute is available.	+	* color peptide probability based on is_contributing_prob (as opposed to is_contributing_evidence) when attribute is available.
-	[ProteinProphet:]	+	===[ProteinProphet:] ===
-	catch and warn if TOPN setting is less than zero	+	* catch and warn if TOPN setting is less than zero
-	correctly calculate is_contributing_evidence for peptides when TOPN > 0 is enabled	+	* 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 repor	+	* 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 repor
	ts the peptides whose probabilities are included in the protein probability calculation...		ts the peptides whose probabilities are included in the protein probability calculation...
-	[TPP:Models Page:]	+	===[TPP:Models Page:]===
-	tpp.ico for TPP::Models	+	* tpp.ico for TPP::Models
-	[TPP::Main Page:]	+	===[TPP::Main Page:]===
-	tpp.ico for TPP::Main	+	* tpp.ico for TPP::Main
-	[Petunia:]	+	===[Petunia:]===
-	petunia.ico for Petunia	+	* petunia.ico for Petunia
-	xinteract, PeptideProphet and PTMProphet increase flexibility for setting options for analysis, allow extended modeling and experiment labeling options ... etc.	+	* 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	+	* 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	+	* 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 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 options with show/hide to help users
-	add some basic help for experiment labels, mass difference models and model adjustment options	+	* add some basic help for experiment labels, mass difference models and model adjustment options
-	[Petunia::Analyze Peptides]	+	===[Petunia::Analyze Peptides] ===
-	Allow Petunia to set MASSDIFFMODE for PTMProphet using xinteract	+	* Allow Petunia to set MASSDIFFMODE for PTMProphet using xinteract
-	[TPP::Magnum for Windows:]	+	===[TPP::Magnum for Windows:] ===
-	update Magnum to 1.3.4	+	* update Magnum to 1.3.4
-	fix same path problem discovered in kojak on mingw::gcc compiled windows	+	* fix same path problem discovered in kojak on mingw::gcc compiled windows
-	[TPP::Kojak 2.1.0 for Windows:]	+	===[TPP::Kojak 2.1.0 for Windows:] ===
-	path problem reported on spctools-discuss by Zeyu Wang	+	* path problem reported on spctools-discuss by Zeyu Wang
-	[common.mk:]	+	===[common.mk:] ===
-	fix issues with LDFLAGS	+	* fix issues with LDFLAGS
-	[Seq2MS_json.pl:]	+	===[Seq2MS_json.pl:]===
-	support for generating chimeric PSM	+	* support for generating chimeric PSM
-	[tpp_model.pl:]	+	===[tpp_model.pl:]
-	diffvmc display new model	+	* diffvmc display new model
-	[tpp_gui.pl:]	+	===[tpp_gui.pl:] ===
-	allow xinteract jobs to launch in parallel, useful when processing multiple files independently, also adding auto experiment labeling...	+	* 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)	+	* allow executing xinteract jobs in parallel on a local linux server (without slurm)
-	[PeptideProphet:]	+	===[PeptideProphet:] ===
-	VMC model: use the discrete model for VMC modeling as opposed to KDModel	+	* VMC model: use the discrete model for VMC modeling as opposed to KDModel
-	VMC: remove unused KDModel	+	* VMC: remove unused KDModel
-	Prevent crash when no decoys are specified with MSFragger as the search engine	+	* Prevent crash when no decoys are specified with MSFragger as the search engine
-	new DIFFVMC model to complement the existing VMC-by-type model	+	* new DIFFVMC model to complement the existing VMC-by-type model
-	[extern/MSToolkit:]	+	===[extern/MSToolkit:] ===
-	BUGFIX running reSpect on DISCo generated mzML was observed throwing errors due to rampFileIn->fileName not being populated, using sCurrentFile instead	+	* BUGFIX running reSpect on DISCo generated mzML was observed throwing errors due to rampFileIn->fileName not being populated, using sCurrentFile instead
-	[common.mk:]	+	===[common.mk:]
-	adjust compilation linker flags for hdf5 on MacOS	+	* adjust compilation linker flags for hdf5 on MacOS
-	[Makefile:]	+	===[Makefile:] ===
-	updates for new HDF5	+	* updates for new HDF5
-	add the top level splash page to the files that need attention for make version-clean and make version	+	* add the top level splash page to the files that need attention for make version-clean and make version
-	[DISCO:]	+	===[DISCO:] ===
-	updates for new PWIZ	+	* updates for new PWIZ
-	[HDF5:]	+	===[HDF5:] ===
-	updated to 1.14.3 and patched	+	* updated to 1.14.3 and patched
-	hdf5 windows build on mingw	+	* hdf5 windows build on mingw
-	adjust hdf5 linker flags for mac	+	* adjust hdf5 linker flags for mac
-	[PWIZ:]	+	===[PWIZ:] ===
-	updated	+	* updated
-	requires HDF5 for MZ5 support	+	* requires HDF5 for MZ5 support
-	changes for mingw build	+	* changes for mingw build
-	[Petunia::Lib2HTML:]	+	===[Petunia::Lib2HTML:] ===
-	allow the the user to select user specific modifications for Lib2HTML by Petunia	+	* allow the the user to select user specific modifications for Lib2HTML by Petunia
-	[MSReader:]	+	===[MSReader:]===
-	if scNum is 0 it is not useful as the lastReadScanNum	+	* if scNum is 0 it is not useful as the lastReadScanNum
-	[xinteract:]	+	===[xinteract:] ===
-	new option -MULTI (InteractParser -m) to deal with comet files containing multiple precursors per possible spectrum number	+	* 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	+	* allow to specify unknown_decoy and use it in ProphetModels.pl in fully unsupervised modeling
-	option to disable the new DIFFVMC model	+	* option to disable the new DIFFVMC model
-	allow negatives in options to PTMProphet	+	* allow negatives in options to PTMProphet
-	[PepXMLViewer.cgi:] d	+	===[PepXMLViewer.cgi:] ===
-	deal with comet files containing multiple precursors per possible spectrum number InteractParser option -m	+	* deal with comet files containing multiple precursors per possible spectrum number InteractParser option -m
-	[InteractParser:]	+	===[InteractParser:] ===
-	new option -m to deal with comet files containing multiple precursors per possible spectrum number	+	* 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
-	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
-	New Option -d to recalculate massdiffs for the search_hits	+

---

Revision as of 21:38, 21 June 2024

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

TPP 7.1.0 ALBEDO Release Notes

[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 on MacOS

[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 repor

ts 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