From SPCTools

Revision as of 06:56, 20 May 2022 Luis (Talk | contribs) ← Previous diff		Current revision Luis (Talk | contribs) (→Known Issues)
Line 8:		Line 8:
-	= Major Changes (current to r8638) =	+	= Major Changes =
-	* Inclusion of '''Magnum''' search engine for open-mass and adduct identification (v 1.0.0. alpha 6)	+	* Inclusion of '''Magnum''' search engine for open-mass and adduct identification (v 1.0.0. alpha 7)
		+
Line 57:		Line 58:
	* ''ShowXIC''		* ''ShowXIC''
	** add user cgi controls for retention time, ms level, and isolation m/z		** add user cgi controls for retention time, ms level, and isolation m/z
		+
		+	* ''clips''
		+	** New option -X <string> to skip indexing of proteins with names that start with <string> (e.g. DECOY_)
Line 159:		Line 163:
	* ''msnExtract''		* ''msnExtract''
	** correct memory bug		** correct memory bug
		+
		+	* ''promast''
		+	** trim whitespace when reading peptides from text file
	* ''mzParser''		* ''mzParser''
Line 188:		Line 195:
	* Improved ThreadPool		* Improved ThreadPool
	* Update Apache ReWrite rule for opening protXML files in (new) viewer when in directory browsing mode		* Update Apache ReWrite rule for opening protXML files in (new) viewer when in directory browsing mode
		+	* Windows installer creates default tmp dir in main TPP installation
		+	* Fix bugs with default links in various visualization tools when installing TPP and/or data in non-default locations in Windows
		+	* Update links to PeptideAtlas
	* Update code to c++14 standard		* Update code to c++14 standard
	* Add newly required windows libs		* Add newly required windows libs
Line 195:		Line 205:
	= Known Issues =		= Known Issues =
-		+	* On non-standard Windows installations:
		+	** the javascript file browser may not work properly in certain circumstances
		+	** the Desktop link to TPP may not work
	= Getting the TPP Software =		= Getting the TPP Software =

---

Current revision

Trans-Proteomic Pipeline (TPP) software, release 6.1.0 is a major release of TPP that contains new features, improvements, and fixes to 6.0.0. The software is available for Windows as well as Linux (and unofficially) for OSX from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server). For advanced users who need to customize the TPP, or for those who run on Linux or OS X, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

For installation help, please see TPP:5.2_Installation (same as for 6.1.0)

Previous release notes are available at TPP:6.0.0_Release_Notes

Contents 1 Major Changes 2 New Features 3 Improvements/Changes/Bug Fixes 4 Miscellaneous 5 Known Issues 6 Getting the TPP Software 7 Acknowledgements

Major Changes

• Inclusion of Magnum search engine for open-mass and adduct identification (v 1.0.0. alpha 7)

New Features

• PeptideProphet
  • New Variable Modification Count (VMC) model

• xinteract
  • new option -n (InteractParser) -NATIVE (xinteract) to rewrite spectrum names with native scan numbers to fix issue with MSFragger splitting of searches
  • user settable isolation interference -f<tolerance> option; record into pepXML
  • allow to specificy MASSWIDTH= for PeptideProphet open-mass search modeling

• Petunia
  • Add support for Magnum
  • Added ability to launch jobs to SLURM cluster
    • comet, tandem, and msconvert use the corresponding ISB-specific "q" scripts
    • other high CPU tasks are submitted via srun on to the urgent queue
    • number of cores requested match threads requested by user (default=1)
    • user chooses if running on cluster or local machine
    • Do not allow selection of local machine to run CPU-intensive jobs at ISB
    • new monitoring code to determine when job is done
    • new page that displays queue and cluster status
    • Removed old SGE cluster options

• PepXMLViewer
  • display MZ of the measured precursor and allow to filter on MZ and RT
  • display Evalue from Magnum results
  • support for additional columns for ACCMASS, ZACCMASS, and co-isolation interference
  • show peptide_adduct and peptide_massdiff fields as links to Unimod mass +- 1 Da in html mode.

• Tandem2XML
  • Implement N15 support

• SpectraST
  • support for x-ions
  • look for nTermMods when the amino acid is 'n'
  • enhance api with routines helpful for reSpect and speed

• DISCO
  • improve sensitivity of analysis
  • add function smoothForGrid to allow processing of fragments that have a different grid (number of datapoints) than precursor ms1 signal for irregular DIA methods.

• SPACEPro
  • Improved quant starting point to be the PSM with the highest TIC when multiple PSMs map to the same precursor signal.
  • Added quant support for multiple FAIMS CVs.

• ShowXIC
  • add user cgi controls for retention time, ms level, and isolation m/z

• clips
  • New option -X <string> to skip indexing of proteins with names that start with <string> (e.g. DECOY_)

• Updated to Comet 2022.01.0 and related params file
• Update to Kojak 2.0.0 alpha-16 and related conf file
• Upgrade to version v1.23 of pepXML schema
• Include ProteoWizard tools v3.0.22088

Improvements/Changes/Bug Fixes

• PeptideProphet
  • increase sensitivity of Comet nonparam model by reducing the bandwidth
  • add more explanatory messages and fail proof when KDModels cannot initialize for some off reason (e.g. all values are the same)
  • when encountering a PSM with an absolutec adduct mass that is greater 1e-12 and an absolute mass difference less that 1e-12, treat the adduct mass as the mass difference of the PSM for PeptideProphet modelling purposes
  • LOWMEM option that cannot revert to unsupervised method
  • instead of crashing and exiting after this message actually enable "revert to fully unsupervised" model when no decoys are to be found

• xinteract
  • make -THREADS= parameter apply to PeptideProphet and iProphet.
  • Set search_engine to 'MSFragger' if it is actually MSFragger results, overriding XTandem hack
  • ensure order of aminoacid_modifications appearing before terminal_modifications for schema compliance
  • Implement mzFile open retry (upto 100 times) for problems opening files over NFS the first try

• Petunia
  • Always sort files and directories
  • update location of PWiz/msconvert in Windows
  • Added extra user params input box for Percolator
  • Updated link to Comet project page
    • link to new site for newer comet params help; leave older ones in place

• PepXMLViewer
  • allow program to run even if WEBSERVER_TMP is not set (can happen when run on commandline)
  • option to skip running tpp_models.pl

• madcaps
  • convert carriage returns to < br > when displaying error messages in JS/HTML

• PTMProphet
  • deal with adducts and massdiffs in MASSDIFFMODE, only localize commandline specified modifications (other variable mods stay put)
  • multi-threading improvements
  • print mod_info tags even if PSM contains unknown modifications.
  • mz file reading retry and more informative error message, and processing of PSMs with a static_mod and a variable_mod (not specified to PTMProphet) on one site
  • report static and variable mod combined at one site as composite mod (not as single var mod)
  • don't use more threads than allowed
  • report non-localized variable mods in the pepXML file (reported by Eric)
  • fixed a problem with first search_score not being reported under some conditions in MASSDIFFMODE with Magnum
  • print the search_scores right after ptmprophet_analysis.
  • add a token collision warning and makes sure latest changes for massdiffmode work on PSMs with partial variable mod specification to ptmprophet
  • special cases debugged for n-terminal ptm containing peptides
  • adduct and massdiffs for magnum with multiple hit_rank=1 search_hits
  • improve handling of multiple PTMs on one site
  • fix bug found by Tami associated with PTM variable mod combined with a static mod, also fixed a deadlock.
  • fix a couple of bugs with reporting modifications also with pepXML schema noncompliance
  • correct bug of not writing the result file (reported by Tami)
  • correct some issue on MSFragger massdiff data (reported by Mike Riffle)
  • correct issue with n[43] appearing as n[43][43]
  • don't print same tags twice
  • fix bug associated with static mods on the n-terminus
  • correct default FRAGPPMTOL values

• Libra
  • Fixed SPS/MS3-based quant analysis in LibraPeptideParser
    • Briefly, when an identified MS2 scan does not have a paired MS3 scan, DO NOT default back to quantifying the peptide from the MS2 scan
    • This behavior is guaranteed to fail when using, for example, TMTpro16 label with ion trap MS2 scans, because such scans cannot resolve the TMT channels. Instead, those scans simply report no quantitation.
  • Throw error if smallest mz difference between any 2 channels is less than 2 x specified mass window
  • user defined intensity pseudocounts
  • fix bug with processing multiple run data (reported by Will Comstock)

• reSpect
  • option PRECURSOR to add precursorMZ information from the pepXML file
  • generate a scanID that is compatible with the pwiz parser for files where scanID is not populated
  • use user mods and don't rely on any default mods
  • MANGO mode
  • read more inputs, outputs ms2 data for mango pipeline
  • ID the spectrum by the IdString
  • mzFile open retry (upto 100 times) for problems opening files over NFS on the first try

• tpp2mzid
  • Adds modifications from PTMProphet parameters to the SpectrumIdentificationProtocol for a database search
  • Fixed conversion issues with some PTMProphet modification annotations
  • Fixed bug in handling peptide elements without indistinguishable peptide elements
  • Added version identifier for the NeoPepXMLParser library that is under the hood.

• RTCatalog
  • adjust Display values
  • correct PEAKVIEW PTM encoding
  • improve outlier detection
  • fix parsing of search_results with multiple search_hit hit_rank=1 peptides

• quantic
  • use user mods and don't rely on any default mods
  • only autocompute mzTol if not specified by the user as a non-negative value
  • fix bugs associated with usage of ptmprophet+quantic on open search data

• mzTrace
  • multithreaded
  • implementing RT window to extract a given mz
  • NOPEAKS option to speed up performance when peak detection is not required
  • using localized smoothing for speed

• msnExtract
  • correct memory bug

• promast
  • trim whitespace when reading peptides from text file

• mzParser
  • Increased additional precursor buffer to accommodate 10 or more precursor ions per spectrum, such as during SPS collection of MS3 spectra.
  • Fixed duplication of precursor elements introduced during r8143

• NeoPepXMLParser
  • Adding new elements to parse
  • Fixed a typo when parsing CV and fixed N-terminal mod parsing.

• NeoPepXMLParser
  • Adding new elements to the API for handling Libra-quantified Proteins
  • Updated the API for handling peptide elements

• mzIMLTools
  • Update modification table for mTRAQ8plex
  • Added formylation to the modification table
  • Updated modification param addition to be a bit smarter, and to use fuzzy math for different user precisions on modification masses.
  • speed improvements.

• MSToolkit
  • align mzParser with TPP version

Miscellaneous

• Don't print model when no bins exist for schema compliance
• Add links to 6.1.0 release notes and to Magnum, and update link to Comet on Landing Page
• Improved ThreadPool
• Update Apache ReWrite rule for opening protXML files in (new) viewer when in directory browsing mode
• Windows installer creates default tmp dir in main TPP installation
• Fix bugs with default links in various visualization tools when installing TPP and/or data in non-default locations in Windows
• Update links to PeptideAtlas
• Update code to c++14 standard
• Add newly required windows libs
• Update Boost library to v1.76

Known Issues

• On non-standard Windows installations:
  • the javascript file browser may not work properly in certain circumstances
  • the Desktop link to TPP may not work

Getting the TPP Software

• Download the TPP version 6.1.0 native windows installer (TPP_Setup_6.1.0.exe) from the Sashimi SourceForge project file release page:

 http://sourceforge.net/projects/sashimi/files/

• Everyone is encouraged to read and contribute to our wiki, at

 http://tools.proteomecenter.org/wiki/

• For guides to installing and using our software, please see our wiki:

 http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

• For downloading the source code, please go to the following link:

 http://sourceforge.net/projects/sashimi/files/ and find the 6.1.0 source code .tgz package

• Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_6-1-0

• For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki.

Acknowledgements

The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers who contributed to this release from ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.