From SPCTools

Contents 1 TPP 7.2.0 Bombogenesis Release Notes 1.1 [Known Bugs:] 1.2 [Petunia] 1.3 [Petunia::Analyze Peptides] 1.4 [Petunia::Decoy Databases] 1.5 [Petunia::FileBrowser:] 1.6 [tpp file browser] 1.7 [Petunia::Libra Conditions Generator] 1.8 [Unimod] 1.9 [PeptideProphetParser:] 1.10 [InteractParser:] 1.11 [ProtXMLViewer::StPeter:] 1.12 [Magnum:] 1.13 [Hardklor:] 1.14 [ShowXIC.cgi] 1.15 [PepXMLViewer] 1.16 [ploTPP] 1.17 [PWIZ] 1.18 [PTMProphet:] 1.19 [PepXMLViewer.cgi:] 1.20 [Lorikeet] 1.21 [Libra] 1.22 [BUGFIX:] 1.23 [MSToolkit:] 1.24 [DISCO:] 1.25 [ShowXIC.cgi:] 1.26 [comet-pepxml.cgi:] 1.27 [apache:] 1.28 [comet:] 1.29 [iProphet:] 1.30 [cuvalibre] 1.31 [Quetzal:] 1.32 [BUILD:] 1.33 [Landing Page] 1.34 [ProphetModels.pl:] 1.35 [Windows Installation:]

TPP 7.2.0 Bombogenesis Release Notes

[Known Bugs:]

• Building Comet from source fails using gcc > 12,

       SOLUTION:Use gcc <= 12 to compile from source, or go into Comet source directory and remove -std=c++14 from the Makefile

[Petunia]

• Libra parameters page:
  • Add support for multi-channel normalization
  • Add support for deuterated isotopes (CD,ND)
• Also move Libra-related javascript to .js file for ease of editing
• BUGFIX record correct normalization channel(s) when user skips some channels to quantify
• Point to latest PWiz; add "Daltons"

[Petunia::Analyze Peptides]

• New features, allow to label experiments by a portion of the file name, so that files belonging to the same experiment can be tagged with one experiment label. Useful for better analyses incorporating NSE.

[Petunia::Decoy Databases]

• decoyFastaGenerator.pl user interface option to select number of independent decoy sets generated

[Petunia::FileBrowser:]

• NEW FEATURE add link ShowTIC to display the Total Ion Current for mzML/mzXML data.
• Move code for (new) TIC link to a more appropriate location; add mouse-over text to it
• ShowTIC should open in a new browser tab

[tpp file browser]

• Add ability to store and retrieve recent file names via localStorage.tppRecentFiles

[Petunia::Libra Conditions Generator]

• Add provisional support for TMT-35 in Libra Conditions generator

[Unimod]

• Update UNIMOD data
• update to latest definitions

[PeptideProphetParser:]

• update usage statement
• BUGFIX fix crash that occurs when a nonparametric model has to revert to a parametric model due to lack of decoys and ONEFVAL is used.
• compute same prior whether or not DECOYPROBS is enabled, so DECOYPROBS should have no effect on the model, only an effect on known decoy PSMs now having a probability value, also try to honor NODIFFVMC flag better!
• BUGFIX DIFFVMC model was counting static mods as variable, this code allows SearchResults to compare each PSM modification to the list of variable mods to determine that it isVarMod before adding it to the variable modification list for that PSM.
• BUGFIX crash when RTmodel is enabled but NONTT is used so ntts are not available.
• BUGFIX NODIFFVMC was not working, also make messages more meaningful when ACCMASS model is not utilized on purpose

[InteractParser:]

• option -k to keep original spectrum names rather than changing them, requested for Mango pipeline.

[ProtXMLViewer::StPeter:]

• BUGFIX ExportTSV, stpeter values were not being output correctly from ProtXMLViewer ExportTSV button...

[Magnum:]

• BUGFIX magnum was stuck in infinite loop due to zero intensity peaks in mzML file (Kristian's data), this change will not add a non-positive intensity value peak to a spectrum, unless doing so to make a mask.

[Hardklor:]

• when adding a zero intensity peak to a Spectrum on purpose it is a mask, so allow the library to add it by flagging mask=true

[ShowXIC.cgi]

• New Feature, if the target mz is non-positive extract the TIC instead of the XIC.
• code readability and wider range for TIC

[PepXMLViewer]

• Style zero-value (no signal) Libra ratios as gray instead of blue
• Bugfix Libra filters not showing up when adding columns to display
• Add massdiff filter
• Minor layout cleanup and code simplification
• Fix text: precursor m/z is not (typically) measured in seconds...
• Add input for user-specified PXD id; enables links to USI page and Quetzal annotator

[ploTPP]

• Add overlay for single and double amino acid mass gain/loss (in blue)

[PWIZ]

• tidy up new msi setup...

[PTMProphet:]

• BUGFIX, correct analysis on open search datasets (identified by Zhi), were stacking of user defined variable modifications and mass differences was not possible, so they had to be analyzed in NOSTACK mode. This change makes it possible to analyze this data with PTMProphet in MASSDIFFMODE and allowing for stacking.
• raise default MINPROB to 50%, per Eric's request
• BUGFIXES associated with MASSDIFFMODE and returning all PTM site probabilities equal to 0, under certain conditions using MSFragger and high lability open searches identified by Kristian.
• process PTMs specified only in the spectrum_query elements, i.e. not provided in the search parameters or PTMProphet command, for instance PEFF mods (which should only appear along the peptide backbone, not on peptide termini like other mods). Changed based on a feature request from Zhi

[PepXMLViewer.cgi:]

• display the peptide_massdiff even if stacked with another modification, by extracting it from the search_hit as a fall back measure...

[Lorikeet]

• Add TMT(Pro)-35
• Add input for user-selected MS1 scan, with +/- convenience buttons; clean up some code
• Auto-detect losses from mod peptide and add to Lorikeet custom peptide
  • Losses: Phospho, Oxydation, Formyl, C-linked hexose (same as those in the .cpp file)
• Clean up Javascript...
• Get Seq2MS source from the brower window if not set by user
• Send Seq2MS AI generated spectra to Quetzal/Coatl
• Integrate with Quetzal/Coatl
• a few javascript and html bugfixes
• display Seq2MS on the main spectrum tab
• send max RT to Seq2MS predictor
• default Seq2MS settings left blank, which allows plot-msms-utils.js to set the values

[Libra]

• Add support for multi-channel normalization (useful for quantifying deuterated reporters of TMT-35)
  • Libra will exit with error if list size does not match number of channels, or if a channel value is incorrect
  • Usage: <normalization type="999" series="<STRING>"/>
  • <STRING> is a comma-separated list that specifies which channel to normalize against
  • e.g. to normalize non-D channels to channel 1, and the rest to channel 8:

  <normalization type="999" series="1,1,1,8,1,8,1,8,1,8,1,8,1,8,1,8,1,8,1,8,1,8,1,8,1,8,1,8,1,8,8,8"/>

• Fix a few potential buffer overflow conditions
• Minor code clean up and pruning (code commented out 19 years ago is likely not about to get used...)
• Add link to Quetzal annotator (includes general-purpose Javascript helper for facilitating this linking)

[BUGFIX:]

• post_to_spectrast.html has been broken since peptideatlas changed urls...fixed for now
• front page lorikeet missing links

[MSToolkit:]

• BUGFIX check for frame before scan in case there are both, but frame indicates timsTOF PASEF, which was failing in DISCo.

[DISCO:]

• BUGFIX timsTOF PASEF, which was failing for Zhi on recently converted mzML data using diapysef

[ShowXIC.cgi:]

• Upgrade to d3 version 4, and make more visually appealing.
• when a peak is not found, fill in the graph with 0 intensity at that RT
• code cleanup

===[Seq2MS]===:

• convert a few common unimod ptms to Seq2MS understood ptms
• BUGFIX place the mod at the correct site in the peptide!
• switching to POST
• code reorganisation to improve durability
• [seq2ms server:] add fail safe error handling for unknown requests, also remove hardcoded settings to make configurable
• configure Seq2MS local server and default model settings
• run as a server in the background on Windows.
• configure server during install on Windows
• install seq2ms server batch file on Windows
• process without the seq2ms server when it is off

[comet-pepxml.cgi:]

• BUGFIX, buffer size was too big for newer systems...also compare PSMs based on run_name, start/end scan and charge, not based on identities of spectrum_names which can have different paddings for scan numbers.

[apache:]

• upgrade to apache 2.4 for windows
• update default http configs to apache 2.4

[comet:]

• upgrade to comet 2024.02 rev 0

[iProphet:]

• controls to tune NRS and NSE. Also, flag to allow excluding proteins (provides significant speed boost under specific conditions, e.g. incorporating Tesorai results)

[cuvalibre]

• First pass check-in, with some expected areas to-fix (e.g. retrieving spectra). Also add Quetzal mini-image for links
• rearrange code for installation and compartmentalization
• adjust layout; simplify code
• ===[RumAndCoke]=== Initial commit; tool still in Beta

[Quetzal:]

• first commit
• configure for local site
• tidy up and link to ProteomeXchange
• ===[Coatl:]=== BUGFIX don't close Quetzal Window

[BUILD:]

• html targets cuvalibre and quetzal are compartmentalized, built and installed ... will likely need changes to apache server config to enable quetzal and cuvalibre

[Landing Page]

• Add link to Gene Ontology; bump version link to release notes; style Welcome message

[ProphetModels.pl:]

• change the way uncertainty is computed, per Eric's suggestion...whiskers are longer now

[Windows Installation:]

• options for setting Seq2MS Local Server parameters
• reconfigure installation with options for Seq2MS and make it easy to start the server...if server is not started Seq2MS should still work but much slower for every new peptide
• BUGFIX new dependecies required for apache 2.4