From SPCTools

Contents 1 TPP 7.0.0 ARAFEL Release Notes 1.1 [General Changes:] 1.2 [UniMod Helper:] 1.3 [decoyFastaGenerator.pl:] 1.4 [mzParser] 1.5 [MSToolkit:] 1.6 [PeptideProphet:] 1.7 [PTMProphet:] 1.8 [SpectraST:] 1.9 [iProphet:] 1.10 [ProteinProphet:] 1.11 [InteractParser:] 1.12 [Quantic:] 1.13 [fetchDataset:] 1.14 [PepXMLViewer.cgi:] 1.15 [DIALib-QC:] 1.16 [StPeter:] 1.17 [tpp_gui.pl (a.k.a. PETUNIA) :] 1.18 [readMzXML:] 1.19 [plot-msms-js.cgi (a.k.a. Lorikeet Spectrum Viewer):] 1.20 [RefreshParser:] 1.21 [ProtXMLViewer] 1.22 [Seq2MS:] 1.23 [ASAPRatio:]

TPP 7.0.0 ARAFEL Release Notes

[General Changes:]

• install Seq2MS and PYTHON for windows to run it, with necessary python libs
• MacOS Native Build and Installer
• Native Build of clustalomega 1.2.2
• Native Build of kojak 2.1.0
• Native Build of magnum 1.3.2
• Add support for Selenocysteine (code provided by Jimmy)
• Adding CUDA supporting python version (Windows)
• Updated UniMod reference helper file
• Updated protXML schema to v10

[UniMod Helper:]

• Add 'most common' link to reach those mods more quickly; add link to Unimod.org to Landing Page

[decoyFastaGenerator.pl:]

• fix problem with not shuffling and outputting the last protein in the database and outputting the penultimate twice...problem discovered and reported by Seamus Morrone

[mzParser]

• Major Change #1:

• Added ability to read mzMLb file format. As with mz5 format, HDF is required. To compile with HDF support, use MZP_HDF compile time flag (replaces MZP_MZ5), which will include support for all HDF formats (MZ5 and mzMLb). Note that mzMLb.gz is not yet supported.

• Major Change #2:

• Made changes to improve mzML data converted from TIMSTOF instruments. Because different converters use different conventions when declaring data containing ion mobility (whether identified prior to the ion mobility array or AFTER it), default behavior of the RAMP interface was changed to read in the entire spectrum even if only header information is requested. This is because it wouldn't be possible to determine if there is ion mobility data without reading the spectrum data arrays under conventions used by some converters. This is potentially inefficient for legacy software that calls readHeader() and readPeaks() independently, so a better solution should be considered in the future. That being said, if readPeaks() is called after readHeader() for the same spectrum, the file is not parsed a second time and simply uses the data that was parsed in the readHeader() function call.

• fix spectrum flags to know the difference between having an ion mobility associated with the spectrum and having an actual ion mobility data array.

[MSToolkit:]

• update mzParser

[PeptideProphet:]

• VMC model pseudo-counts to prevent overclassification due to lack of data.

[PTMProphet:]

• Don't write the n-terminal 'n' when there is no modification at the n-terminus, to address Mike Hoopmann's request.
• change default minimum probability for analysis to 0, to allow the new iProphet NSM model using ptm information content to use all results in the file in an unbaised fashion.
• handle 0 intensity peaks which can occur rarely on some timsTOF data and causes PTMProphet to fail.
• fix distinction between PTMPro and USM type mods defined for SpectraST API, exposed by analysis as reported by Longping .. results in fewer WARNINGS when user doesn't specify all mods used in search at runtime of PTMProphet.

[SpectraST:]

• [spectrast::peaklist] don't populate 0 intensity peaks which can occur rarely on some timsTOF data and causes PTMProphet to fail.

[iProphet:]

• NSM model now weighs the evidence by ptm information content, significant speed-boost for NSP model.

[ProteinProphet:]

• NEW FEATURE TOPN=<num> uses <num> number of top peptide probabilities to compute the protein probability, 0 retains old behavior and is still the default ... for now .
• NEW FEATURE PROBX=<num> factor applied to the initial peptide probabilities (default: 0.999)
• Better handling of Windows line endings to FIX calculation of protein length and coverage when protein accession ends in a bar character
• BUGFIX * parsing protein descriptions from fasta files running on CentOS (reported by Jimmy)

[InteractParser:]

• BUGFIX * a option, remove any existing path to the data file before appending a new datapath to it, problem discovered by Yoonjung

[Quantic:]

• correct units in the usage statement

[fetchDataset:]

• Connect to PAtlas via SSL (v.0.8.3)
• Remove unused features and references to un-implemented ones (BDBags, MINIDs, PXD/PASS, python)
• UI changes to fetchdataset: accept URL only

[PepXMLViewer.cgi:]

• BUGFIX did not allow filtering by PTMProphet scores when only one PTM specified for PTMProphet, an issue discovered by Zhi.

[DIALib-QC:]

• Update to latest versions of assess_swathlib and DIALib-QC_RPlot
• rev.402 fixes typo

[StPeter:]

• New Feature -r to separate quantification "by run"
• New Feature -x to separate quantification "by run"
• bugfix when processing n-terminal modifications.

[tpp_gui.pl (a.k.a. PETUNIA) :]

• run Seq2MS from tpp_gui.pl
• Honor selected queue for non-search jobs!
• Allow to specify up to 999 threads (previous was 99)
• Fix minor typo and empty space formatting
• Clean up main menu; minor text updates for readability
• Highlight when node RAM is below 5% in cluster view
• Add extra command/filter/example help links to msconvert page
• Remove "expert" warning from its extra options
• Add suggestion to use MSConvertGUI in Windows
• Replace escapeHTML() with encode_entities()
• [tpp_files] Case-INsensitive sorting of files and dirs
• VMC Model checkbox on "Analyze Peptides" page

[readMzXML:]

• precursorMZ should report the monoisotopic peak selected for fragmentation, what was shown before under precursorMZ was the center of the isolation window, renamed to isolationMZ in this change... requested by Eric Deutsch based on his experimentation with monocle

[plot-msms-js.cgi (a.k.a. Lorikeet Spectrum Viewer):]

• add Seq2MS Generative Peptide Fragment Spectrum AI
• enable default mapping of fragments to Seq2MS generated spectra
• add mpep to Seq2MS call
• fix wrong MS1 being displayed bug identified by Eric Deutsch.
• Lorikeet determine width and height for spectrum page based on whether the display is a phone or desktop.
• Silence Typecast (ints do not float) and Buffer Overflow warnings -* bonus: default maxRT now shows up!
• clean up page layout
• Add TMT-18 reporter ions; minor formatting

[RefreshParser:]

• don't count proteins encoded as '-' for xl_type xl entries as UNMAPPED.
• BUGFIX UNMAPPED proteins were not showing up properly when xl_type is not recorded in pepXML, reported by Zhi

[ProtXMLViewer]

• Support 10x more peptides PER protein than previously (now 1e6!)

[Seq2MS:]

• Many changes to basic version including learning RTs and predicting RTs based on an RTCatalog, also encodings for more modifications based on proforma-style PTMs.

[ASAPRatio:]

• If quantifying only the CID charge, do not extract and process the data from all the other unused charge states, to significantly speed up processing.