TPP:6.0.0 Release Notes

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Trans-Proteomic Pipeline (TPP) software, release 6.0.0 is a major release of TPP that contains new features, improvements, and fixes to 5.2.0. 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 6.0.0)

Previous release notes are available at TPP:5.2.0_Release_Notes

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

[edit]

Major Changes

Added new TPP "Landing" page for local installation
- Mostly links to local TPP interfaces, external resources, release notes, and related info
- becomes new default location of TPP link (instead of Petunia)

Added support for fetching remote spectra via their Universal Spectrum Identifier (USI) in Lorikeet
- Enables interactive examination and interrogation of spectra stored in public repositories (only PeptideAtlas so far)
- Can be displayed standalone or butterfly-style for comparison against currently loaded spectrum

Major updates to ASAPRatio peptide UI:
- Add button to list IDs info in a table and overlay onto chromatogram (calls qsir via AJAX/json)
  - Added qsir utility to extract all CIDs info within specified scan and m/z ranges
- Enable mouse drag for selection of scan range and background (with toggle)
- Simultaneous adjustment of light+heavy scan ranges by holding down <shift> while dragging mouse
- Highlight input elements that have changes
- Add toggle to display relative vs absolute y-scale ranges
- Added 'X' to zero out background
- Cease using gnuplot/png images and instead use flot.js
- New L&F

Major revamp of ASAPRatio protein UI:
- New page layout: single table with collapsible peptide sections
- Added more obvious "accepted" status for peptides, peaks, spectra
- Added NTT and mapping uniqueness flags to peptide bar
- Added background color quant scale
- Added link to MADCAPS
- Fixed links to PepXMLViewer; Lorikeet; TPP Models
- Added pop-up messages window
- Fixed memory overrun when building mods in spectrum links

New tool fixPepXMLScan that can update (to a new file - no overwriting) pepXML files that have scan indexes that do not match the mzML files.

New tool MikesMagicalMzMLShrinker to shrink mzML files.
- Its most basic functions remove white space and truncate user-defined identifier tags to a minimal size.
- More advanced features adds MS-Numpress compression to the files. No matter what, the data are zlib compressed (if they were not zlib compressed previously).
- Only works with mzML files. Not for mzXML. Not for mzML.gz. However, for mzML.gz, you can gunzip it, magically shrink it, then gzip it back up.

New utility msnExtract for extracting fragment spectra

New tool PepExtract
- simple single command tool to run comet, PeptideProphet, iProphet, PTMProphet and then export results as xls
- tpp/bin and tpp/cgi-bin have to be in the PATH

New tool SPACEPro to quantify and evaluate digestion efficiency at the PSM, peptide, and protein levels.

New utility StPeter2Matrix for combining multiple StPeter analyzed ProtXML files into a single 2-dimension data matrix of protein abundances.
- The application reconciles differences in protein grouping that occur among the different ProtXML files, and error rates (at least for now) are controlled using a single ProteinProphet analysis of all the combined datasets.

New Tools: mzTrace, rtExtract, DidIScanThat, DIALib-QC (v1.2), QuanticProteinParser

MADCAPS replaces old comet-fastadb.cgi as the default protein sequence viewer in TPP
- A link to the old viewer is still provided in MADCAPS

New tool PPSX for Peptide-Protein Sequence eXploration. Mostly a front-end to promast

New tool ptm2plot -- extracts PTM peptides and site probs from pepXML and creates files for visualizing in ploTPP

New tool quiddist to query peptide ID info and overlay it onto DidIScanThat output
- takes in extra (optional) list of pepXML files
- Launch this tool from Petunia instead of DidIScanThat
- Show results in TPPcel table, with links to PepXMLViewer for each scan with an ID

New tool TPPcel to visualize sets of similar tables in TPP
- Can load data via a few flavors of json, TSV (first 2 columns only), name=value lines, and various params files
- Can display data from multiple source files side by side to allow comparison of values, including ability to see only rows with non-equal values
- Simple one-click bar chart mechanism
- Experiment labels used in table headers are user-editable
- Able to receive "postMessages" from other TPP tools which trigger auto-loading of a new file
- Ability to Copy-Table-To-Buffer-As-TSV
- Includes js FileBrowser for ease of data loading

New Unimod helper utility to view and add Unimod mass mods via pop-up widget
- list can be multiply filtered by user-specified string(s)
- user chooses from potential sites
- value of input element is set to conform to parameters format (comet/msfragger, kojak, tandem) and field type
- highlights associated input text field
- link to Unimod entry
- Added custom unimod.json to enable above (generated via local script from unimod xml export)
- Used in Petunia (comet etc params) and Lorikeet (custom user peptide)

New TPPFileChooser utility to browse/choose files or directories to view/load via pop-up widget
- Added to Pep3D, ploTPP, PPSX, PepXMLViewer, ProtXMLViewer
- Able to sort/filter by name, size, and date
- Keeps directory history
- Can be repositioned via mouse-drag
- Uses new cgi to serve directory listing via json

New RACI library (Random Access Compressed Ifstream)
- This small library (libraci in TPP) can be used in place of pwiz::util::random_access_compressed_ifstream
- It is actually the same-ish code, but deboosted in favor of STL, and without the need to drag the entire ProteoWizard with it.
- Simple, lightweight, and you can still read pep.xml.gz files

New NeoMzMLParser API -- a new, object API for reading and writing mzML files. Also supports scan-by-scan iterative reading or writing.
New NeoPepXMLParser API -- a new C++ API for reading and writing PepXML files. This is intended to *eventually* replace the libpepxml currently in TPP.
New NeoProtXMLParser API -- a new C++ API for reading and writing ProtXML files. This is intended to *eventually* replace the libprotxml currently in the TPP.

TIMS-TOF support for DISCO

Cleavable linker based neutral loss quantitation with Quantic

Quantic results integrated with ProteinProphet on protein level

multithreaded execution of PeptideProphet

PTMProphet can localize adducts and massdiffs

Updated Look and Feel for most interfaces and viewers

[edit]

New Features

Lorikeet
- Added ability to read and display spectral library entries alongside acquired spectrum (e.g. SpectraST)
  - Initial "butterfly" dual spectra plotting code courtesy of Bai Mingze
  - New button to remove butterfly spectrum entry
- Add interactive utility to add custom user interpretation of spectrum:
  - Displayed on separate tab, able to animate
  - Can enter sequence, charge state, and mass modifications
  - Dynamically display m/z of new peptide as user enters sequence/charge/mods, and compare to acquired m/z, showing diff in Da and ppm
  - New Unimod Helper to find mass mods
  - No support for custom neutral losses in custom view

novor2xml
- Add option to write one FASTA pseudo-protein per peptide
- After conversion, call EnzymeDigestionParser to calculate NMC
- Special handling for terminal mods (format not as advertised in docs!)
- set protein name to "_UNMAPPED" as per TPP convention and add helpful description
- Preprend peptide sequence to UNMAPPED protein name in order to get better protein mapping stats within PepXMLViewer
- clarify errors and warnings; minor changes to output to ease file comparison

Petunia
- Major updates for AWS / amztpp integration
  - Added explicit control to start/stop amztpp (local background process)
    - process must be started here in order to launch searches
  - Added 6 options for EC type to launch, as well as max.instances and %utilization
  - Show last 20 lines of status
  - Enable deletion of files in S3 bucket
  - Show recently completed AWS services
  - Revamped look and feel
  - Add links to (external) management consoles
  - Show number of jobs queued in page title
  - Cleaned up logic of queued vs finished jobs
  - Specify output directory for AWS Comet searches
  - Minor text changes for clarity, and warning of charges on AWS
- Added utility to Add a New File in File Browser via pop-up widget
  - choice of: blank (text); comet, tandem, or various msfragger params
  - user chooses name; file is first written in /tmp, then moved to target dir
- Added interfaces for Mike's Magical Mystery Tool (mzML shrinker), DIALib-QC, DidIScanThat, clips (indexing of PEFF files), SPACEPro (enzyme digestion efficiency and quant)
- Added link to display command-line usage of most major tools (via async call)
- Added "dry run" option checkbox to most tools: shows command line but does not execute it
- Add "re-run" commands link, with warning/confirmation alert
- Display Tool Name on mouse-over in main menu for most major tools (e.g. "StPeter")
- Add initial support for MSFragger
- Add option to use promast in xinteract and re-map database pages
- Add new de Bruijn option to decoy fasta generator, make it the default

PepXMLViewer
- 64-bit support for large files
- Update to new L&F
- Add new js FileBrowser widget to assist in file loading
- Add tpp AlertBox for error messages
- Added PEFF-related fields, with options to filter and sort on:
  - num_saavs_min : when mapping to several proteins, the peptide sequence with minimal number of aa subs
  - num_saavs_max : when mapping to several proteins, the peptide sequence with maximal number of aa subs
  - peff_mods : number of aa mass mods coming from PEFF
- Display full SAAV pattern for each mapped sequence when viewing expanded protein list
- Added new num_prots column, which can be zero if UNMAPPED; links to madcaps for alignment
- Added peptide length column
- fix ptm field name for PTMProphet MASSDIFFMODE analysis.
- extend to visualize PTMProphet MASSDIFF and ADDUCT localizations ... also allow filtering for specific adducts or massdiffs ...
- Add min/max Quantic filter and display additional columns for Quantic
- Add min/max scan filter
- Added Kojak e-value field
- Load inverse reduced ion mobility
- Updated "ions" link for SpectraST results - now displays query and library spectra in butterfly mode in Lorikeet

promast
- Write pepXML output:
  - Update pepXML input file (in place, unless -o flag specifies otherwise)
  - updates main entry with one that has "best" mapping match (max NTT, min SAAVs)
  - Add <alternative_protein> tags in order from best map to worst (max NTT, min SAAVs); including all SAAV info
  - extracts only PName from PEFF instead of entire header for protein_descr
  - preserves mass-mod info
  - Add <analysis_summary> and <analysis_timestamp> tags for database_refresh
  - Only considers hit_rank=1 peptides; skips the rest
  - Uses XML::Twig perl module
- New option to only consider sequences with up to a specified max num of SAAVs
- Added options to "float" or "sink" proteins within indistinguishable groups based on user preference (e.g. list DECOY_ entries last, as a tie-breaker)
- Change meaning of -t option to <max> number of threads to use; will use 1 per 1k sequences up to all available if unset
- For each peptide, count a given mapped protein only once
- Properly count and report number of UNMAPPED sequences
- Store full path to reference FASTA/PEFF file
- Reformat usage statement and certain warning messages for clarity

PTMProphet
- new options EXCLUDEMASSDIFFMIN= EXCLUDEMASSDIFFMAX= to allow PTMProphet in MASSDIFF mode to localize mass differences on sufficient magnitude.
- new Option: STATIC mass difference search option

PeptideProphet
- new model ZACCMASS auto adjust for run-to-run mass difference changes

Quantic
- new feature DIAMODE, uses theoretical isotopic distros (from Mercury8) to correct relative intensities of cleavable linkers.
- protein level analysis and ProteinProphet integration for quantities based on neutral loss of cleavable linker
- new option COUPLED to consider intact peptide coupled neutral losses from the monoisotopic unfragmented precursor peak.
- new features to annotate and quantify based on neutral loss of a cleavable linker
- option ANNOTATE

xinteract
- New -v option to record inverse reduced ion mobility in pepXML
- New -u option to define "unknown to PeptideProphet" decoys
- New option -OT to enable MatchedIons model in PeptideProphet
- new option -OO to enable ONEFVAL for PeptideProphet
- new option -OZ to enable ZACCMASS for PeptideProphet
- new option for using Gaussian model for negatives (EVD is used by default)
- New experimental -PEFF option for mapping sequences to variants in PEFF-index files (using promast instead of RefreshParser)
- user specified enzyme parameters at runtime
- New Behavior: All work and intermediate outputs are placed in the current directory
  - New Option -TEMP enables previous behavior of performing all work in the TEMP directory (made default by Brian Pratt some time ago)
- Only call (decoy) ProphetModels if a decoy tag was specified (otherwise, what's the point?)

decoyFastaGenerator
- option to generate de Bruijn decoys

New Enzyme definition lysarginase
- Further, allow user to specify custom enzyme rules on command-line (xinteract/InteractParser)
Include comet 2021.01.0 and related conf file -- Please read the relevant Comet release notes, as some parameters have changed behavior
Include Kojak 2.0.0 (alpha-1) and related conf file
Include PSI-MOD.obo, which is required for comet+peff mod searches
Update to latest version of calctppstat
Include gnuplot 5.28 (Windows)
Upgrade (strawberry) perl to 5.30.2.1 (Windows)
New Enzyme parameters allow specifying parameters for enzymes not defined already

[edit]

Improvements/Changes/Bug Fixes

comparePeps_Categories.pl
- new option -I for ion mobility

DISCO
- more peptides from boxcar and ion mobility (TIMS-TOF) support
- change MININTENS= option so the filtered intensity is in units of a multiplicative factor on the minimum intensity peak in the spectrum, values 1 and higher ...
- for each target only extract unique mz fragments (don't chase the same fragment.)
- adjust correlation thresholds based on number of points used to compute the correlation ...
- replace SCAN_WINDOW option with MAX_SCAN_WINDOW MIN_SCAN_WINDOW options to define all window sizes to test
- automatically modulate the scan window for calculation of correlations to boost IDs, tweak the correlations of reported peaks to improve pseudo-spectrum quality
- retry readFile up to 100 times if failing because some file systems error out when you ask them for a file only once ...
- get back good performance on Triple TOF by adjust the binarySearchDataForPeak function, also experimental pea similarity..
- correct an inefficient Spectrum allocation exposed when ion mobility bins are set high ...
- apply different background filter in each ion mobility bin for extended dynamic range
- some extra newlines for easier to read progress reporting
- add a version number and a reference in mzML so can be properly formed mzML
- TIMS_TOF related changes
- Greater reliance on mzParser (less use of pwiz)
- Better thread load balancing
- increased sensitivity by averaging
- Correct bug associated with MININTENS= parameter that filters out lower intensity peaks to speed up processing
- correct some bugs associated with low sensitivity for TIMSTOF data ...
- correct a bug with no spectra returned when MININTENS= was enabled on non-TIMS-TOF file...
- BUGFIX correct crash on empty data ...
- BUGFIX don't go past the ends of the run!
- BUGFIX return ability to process irregular DIA files (e.g. ones with different types of MS1 scans)
- BUGFIX wasting time at the end of the run by overrunning counter corrected

fetchDataset.pl
- BUGFIX for data stored on a drive other than C:

iProphet
- Increasing multi-threading ability for iProphet
- NRS minimum value -15 as before ...
- BUGFIX prevent a single thread in iProphet multi-threaded mode from disabling and entire model when it cannot find data ... make sure there is no data in all threads before models are auto-disabled.
- BUGFIX NSM model was not working with THREADS>1

Libra
- Set m_reporterFromMS3=false as default in case parameter is not present in condition file
- Thermo MS3 mode is called SPS, not SRS...
- Plug memory leaks

Lorikeet
- Updated to latest (Dec.19.2019)
- Added masses for TMT-16 tags
- Change default fragment tolerance to 0.25Da
- enable highlighting neutral loss peaks associated with GA-Ac tag 172.075837 on Lysine
- Display % of total MS2 ion current matched/annotated
- Gray-out theoretical fragment ions in table that are outside of the m/z range of acquired peaks
- made it easier to click on checkboxes and radio buttons
- Added stand-alone Lorikeet MS/MS spectrum viewer html/js page (eventually use this instead of cgi-based page)
- Fixed bug whereby we were not always capturing peptide charge
- BUGFIX: Lorikeet was incorrectly calculating the cterm modification masses, this corrects it.
- No longer pass fake [0,0.01] and [2000,0.01] datapoints to set x-axis range; use minDisplayMz and maxDisplayMz instead

Mascot2XML
- Handle decoy_peptides and decoy_summary according to same CONTENTTYPE as non-decoy counterparts

MADCAPS
- Enable single-page view when only one protein is passed (hence, no alignment)
- Provide feedback if no protein entries are retrieved from FASTA/PEFF
- Break out annotation so it is easier to read (esp. PEFF)
- Added show/hide toggle for long (PEFF) fields
- Fix display bug when protein entry has no annotation in database
- Fixed neXtProt NX_ -1 links to PAtlas
- Styling updates

mzIMLTools
- Expanded features to comply with the mzID validator
- updated adding database behavior to better detect duplicate entries with alternate paths

mzParser
- Handle Ion Mobility Data
- Support for inverse reduced ion mobility
- Updated mzML reader to handle latest Numpress settings represented by newer cvParams.
- recognize all types of MSnumpress+zlib binary data arrays.
- Added new behavior where random-access reading of non-ScanNumbered mzML data (i.e. Sciex data) now returns the 1-based index position in the file.
  - replaces old behavior that returned a number indicating it was the Nth spectrum read.
  - Note, if the mzML file does not have an index, then the scan number is always the Nth read, even for random-access.
- when a spectrum contains frame= , don't trust the scan= value...frame= data is DIA data and the scan= information should not be used fro the scan number, using scan index instead.
- Remove crufty scanIndex-based spectrum lookup. Solely use faster implementation of scanNumber lookup.
- Added extra diagnostics to error message of RAMPface:readHeader().
- read precursor info from mzML
- change memory management for multi-threaded speed on windows

Petunia
- Expanded Libra Conditions to 25 channels
  - Added channel defaults for TMT-16
  - Also added defaults for DiLeu-21 tags (no support for isotopic correction factors yet, as these are quite different from current paradigm)
- Only use modified masses when running Static Mod quant!
- Added TPPcel link in File Browser for .tsv files
- Add links to new TPPcel visualizer for json files from ProtXML and DidIScanThat
  - File name is passed to TPPCel via postMessage so that data can be added instead of stomping existing view
- Added link to SpectraST web page a link to PWiz/msconvert page
- Pre-check "Accurate Mass Binning" for PeptideProphet
- Pre-check to disable NSP model in iProphet (to avoid users running it also in ProteinProphet)
- Default StPeter and PTMProphet options to hi-res (not low)
- Automatically scroll to bottom of command output sub-windows (jobs page)
- Added one-fval and neg-gaussian options to xinteract
- Respect choice of Output Directory when processing files individually via xinteract
- Harmonize quant options in iprophet page with those of xinteract
- Allow custom specification for speclibs location
- After downloading PAtlas speclib, link to directory, not specific speclib
- allow auto-refresh with URL parameter so don't have to keep clicking
- enable QuanticProteinParser option for ProteinProphet page
- Enable vertical scrolling of top menu (e.g. when window is small)
- Add button to disable mass model in PeptideProphet
- Allow negative values when validating integer values (e.g. num threads)
- GammaNeg also an option for Comet results
- On the xinteract page allow the user to specify known decoys separately from unknown decoys
- Pre-fill mod AA masses for XPRESS and ASAPRatio by guessing from peeking into pepXML file
- Adjust m/z window values for XPRESS and ASAPRatio to 0.05 (from 0.5)
- Added hints for MS2 mass tolerance for StPeter
- Open/close sections by clicking on header bar; removed checkboxes
- Remove references to mzXML, refer to mzML
- Added option to configure Petunia banner text (and tab title) locally
- Allow 7 PTMs to be specified for PTMProphet (instead of 5)
- Rearrange ASAPRatio options
- Removed unused MALDI (file conversion) option in xinteract page
- Removed Area ratio setting
- Removed all references to long-deprecated raw->mzXML converters (ReAdW, mzWiff, etc)
- Removed long-retired link to runsearch, and put a warning on the RunSequest page
- Remove deprecated and rarely used ProteinProphet options
- Remove never-used options for ICAT models
- Remove WINDOWS option from Disco (no longer required; can still be passed via advanced params)
- Re-ordered a few items in TPPTools menu
  - Create new Databases sub-section; move relevant tools therein
  - Move decoy validation tools under Utilities
- Pin file actions buttons at bottom of viewport to avoid having to scroll to bottom of page
- Change FileChooser background color to white with orange border
- Added warning text to iProphet/NSP model
- Improve validation of options for decoy fasta generator
- Minor text changes for clarity and grammar
- Force windows drive to be lowercase
- zip file large file size support
- Correctly pass multiple user directories to updatePaths (updated to comma-separated)
- Updated links to XTandem API and Percolator
- replace downloadFilesArchive subroutine with one that works ... previous one was corrupting mzML files!
- Bugfix DNA2AA wrong reference page
- BUGFIX switching pipelines was causing crash
- Bugfix: to properly expand filtered Jobs table entries
- Fix not being able to read extra long lines in messages pane

PeptideProphet
- update version and create a separate model for MSFragger so parameters can be tuned for it independently of the Tandem model...required MSFragger to not pretend to be Tandem in pepXML...
- enable expect score model for Magnum and plot full range of values
- New optional matchedIons model, by CHARGE
- New features ONEFVAL, z-score based accurate mass model, NEGGAUSS
  - ONEFVAL option to generate a single f-val mixture model for all charge states
  - option for using Gaussian model for negatives (EVD is used by default).
- option to allow multiple negative distribution types
- allow modelling comet 2020 results which do not have deltacnstar parameter
- Expanded support for Kojak results:
  - Support for expectation scores from Kojak
  - Use combined expect score for Kojak PeptideProphet in EXPECTSCORE mode .. separate models for top and bottom expect score already exist
  - Kojak 2.0 discriminant score and mixture distribution
- adjust mixture model QC function to be more lenient
- KDModel: print observed densities only when we have the fits
- recalculate mean and std dev at each iteration because CLEVEL is set according to having an accurate value here
- optional old-style ACCMASS model as option and new-style z-score ACCMASS model as a separate option
- use all types of decoys for the negative model
- report Accurate Mass model run stats in pepXML search_summary parameter tags "peppro_accmass_runmean" and "peppro_accmass_runstdev" for run-by-run mass difference calibration
- BUGFIX correct a crash on Tandem results modelling
- bugfix PeptideProphet RT model ... also extend MAXRT
- BUGFIX the IsoMassDiff model is separated by charge, so all IsoMassDiff charge models need to be initialized with all search_offset masses available in the search.
- Correct a few issues with noDistr() bad model detection and reporting
- fix runtime crash associated with uninitialized value and need to recompute gridwid when calues can shift between interations (e.g. z-score based accurate mass model)
- bugfixes to allow FORCEDISTR to compute PSM probabilities for Kojak results
- fix bug with all probs being wrongly set to 0.

PepXMLViewer
- Added link to chromatogram for label-free XPRESS analysis ("peak_area")
- Report num_prots as "2" for intra-protein XLs, and "1" for inter-protein ones
- Add separator to expanded protein lists for XL crosslinks
- Do not consider _UNMAPPED entries as part of "unique proteins" count
- Do not add (empty) protein links to _UNMAPPED entries
- Add mouse-over tips to SpectraST and PeptideAtlas links
- Disable Glyco B checkbox if NxS/T box is not checked
- added check for incorrectly specified modification position
- Clean up layout of PTMProphet filters
- Place quant scale in (fixed) header
- Replace "close menu" icon with more obvious red "X"
- Replace messages "!" with a more screen-friendly icon
- Use standard TPP footer
- Pop "Messages" tab only once when file cannot be reached for status check
- Remove filename's potential colon...ouch
- Enable vertical scrolling of top menu (e.g. when window is small)
- Add xlink type to link to models page
- Added test for no peptide sequence: do not add links etc
- Properly trim whitespace in input file name
- Restore spreadsheet link
- Clean up Quantic score code to fix export to ploTPP
- large file support (in expat)
- fix bug where certain saav=0 stats were mis-counted
- BUGFIX correct plotTPP file path bug on Windows
- BUGFIX correct problem with PTMProphet Filter disappearing when new columns are added

ploTPP
- Add support for categories (string) x-axis and stacking data
- Add "Select All" checkbox
- Handle sequences with AA-specific values (probabilities, etc)
- Add many user interactive settings:
  - color chooser with opacity slider
  - log scale rebinning
  - number of bins
  - plot range
  - point size
- Provide more basic stats on data
- Load all .new files in directory (and not just one)
- Added Restore button

ProteoGrapher
- Added file loading status bar and one for final processing of data
- Warning with number of proteins with no GO mappings
- Skip empty records
- more flexibility for parsing out the uniprot ID
- Move reference json files to new ref/ dir
- Update links from Petunia and ProtXMLViewer
- Load JSON from a pure JSON file (not a JSON encoded javascript variable)
- Improved error handling on file loading
- More descriptive error messages
- Update to current TPP L&F

ProteinProphet
- added group weight and list of files as a single input file (requested by Nesvizhskii Lab)
- enable QuanticProteinParser import
- Do not store long PEFF elements in protXML (ModResPsi, ModRes, VariantSimple, VariantComplex)
- better reporting of modified peptides mapped to proteins in IPROPHET
- new option STATICMODS to encode static mods into the modified_peptide string, because searches with different static mods can theoretically be combined at this step.

ProtXMLViewer
- Implement visualization of Quantic protein and peptide quantities from cleavable linker neutral losses when available
- Add support for StPeter dSIn values
  - Also add user option to display NSAF/dNSAF values instead of SIn/dSIn
- display indistinguishable_peptide (charged modified peptides for iProphet) underneath each peptide entry so that now all peptides mapped can be observed...
  - adjust peptide titles to display charge_<modified_peptide> for all related indistinguished peptides.
  - Display quantic values for the indistinguishable_peptides also
- Minor L&F updates
  - default links are now black, orange+underline hover (instead of always blue + underlined)
  - entry and madcaps links are wider and with hover effects to make them more obvious
  - fixed annotation alignment
  - slightly larger font
  - nicer graph legend box
  - Highlight mouse-hovered protein entry
  - Highlight (bold) PEFF fields in annotation view
- Trim PEFF annotations so as not to show values for VariantSimple, VariantComplex, ModRes, ModResPsi, as they potentially take too much space
- Capture organism stats from PEFF \TaxName field
- Display reference database in File Info tab
- Export proper json instead of javascript code snippet; also fixed stpeter export therein
- Warn if reference database file is not found
- Fix link to PAtlas for neXtProt NX_,-1 entries

PTMProphet
- enable analysis on SpectraST pepXML files ...
- More multithreading for speed ...
- Do not include in/output filenames in options string (which only gets written as an a tag attribute in pepXML, which already contains such info
- write intermediate files to current directory instead of WEBSERVER_TMP, which was filling up too often
- use extended SpectraST::Peptide library that allows to define 'user tokens' that would override any definition in the static mass tables and are allowed to have different masses in different instances of the Peptide class (e.g. in different threads of PTMProphet analysis) ...
- support for Magnum adducts, allow evaluating adducts and massdiffs on modified positions, allow evaluating adducts and massdiffs at the same time as variable mods defined in MASSDIFFMODE, exclude mass range feature for MASSDIFFMODE, annotate modifications as massdiff, adduct or param...
- switch mutex to try_lock instead of lock/unlock cycle, which was causing crashes on gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
- Bug fixes: MASSDIFFMODE functional again
- BUGFIX MASSDIFFMODE wrong mod masses being reported...also use the same prior for MASSDIFFMODE as for EM=1 and EM=3 to help EM converge ...
- fix xml formatting issues due to multithreading, implement options OSCOREMODE and QUANTMODE
- fix some bugs related to flat PTM probabilities and EM=1 and EM=3 execution options.
- BUGFIX address bug exposed when multiple variable mods of different types, but occuring on same amino acids, are be present in one peptide.
- BUGFIX correct deadlock issue when msms_run_summary has zero spectrum_query tags ... NEW: threaded updateProbs routine
- correct come issues with multithreading and writing invalid pepXML files ... prepare for adduct masses as annotated my Magnum ...
- BUGFIX add any static mods on the n-terminal to the mass of the n-terminal
- correct some issues related to analyzing files without probabilities ... also correct a bug with ROC curve reporting.
- BUGFIX clear out old tags ...
- BUGFIX correct error with reading NIONS / CIONS user parameter ...
- fix bug dealing with c-terminal modifications.
- Bug Fix: correct combinations to not evaluate more peptides than necessary
- BUGFIX: issue with incorrect masses being reported in MASSDIFFMODE
- try to prevent infinite loop when unclosed msms_run tags exists from incomplete analyses

RefreshParser
- Report number of sequences mapped (along with number of not mapped)
- Alert with an error if zero sequences were mapped
- Eliminate memory leaks

readmzXML
- read Ion Mobility
- Added precursor charge and nativeId to scan header information
- Capture instrument serial number, hi/low mz values
- Add more instruments to cvParams detection (many more needed)
- New -R option to print run and instrument header info

reSpect
- mzParser now works with scan number ... mzParser corrected by Mike exposed reSpect bug
- BUGFIX mainly correct issues with writing mzML files using pwiz ...

RTCatalog
- Removed dependency on pwiz and boost and replaced with identical interface in mzParser that already existed.
  - This removes dependency on pwiz and boost for the core TPP libraries, allowing us to modularly compile our code separately from pwiz code.
  - Tools that use one, the other, or both can then link one, the other, or both as needed, instead of forcing every tiny little script to link everything all the time.
- change uninitialized values from -1 to a much smaller number (iRT values can be negative.)
- only lop off everything past the last '_' when in DISCO mode, in regular mode keep the run names unaltered

SpectraST
- Fix MSP import of new NIST HCD libraries due to different format in mods, fragmentation, etc. HCD collision energy now part of spectrum's identity, so that spectra of same peptide ion but of different CEs will not be considered replicates.
- Fix bug writing create mode indiscriminately to Spec= field

StPeter
- Added new parameter to set minimum probability threshold regardless of FDR.
- Added peptide-level normalized spectral index score (per Henry Lam's request)
- clarifying output to the user.
- Fixed rounding bug when representing modification masses on peptides.

tpp2mzid
- New interface to specify preferred mzID version (for PRIDE compatibility)
- add new content to the mzID output
- Updating software to work with the newer mzIMLTools API
- bugfixes and improvements for PTMProphet to mzID.

tpp models
- Update to new L&F
- Use new common tpp.css (also enables sticky table headers!)
- Added support for multiple PeptideProphet models in same file (e.g. for XL analysis); also added score overlay of massdiff, isomassdiff, ntt, nmc, etc
- Add button to toggle 1% Zoom in MASSD models
- Handle new matchedions model
- Also plot sum of pos+neg models for each charge state
- Display all PTMProphet run options
- Fix bug in parsing certain PTMProphet models; do not capture data points with value = zero; enable auto-tickmarks for MASSDIFF models (which can now be open search)
- Fix PTMProphet sens/err models and table

XPRESS peptide interface:
- Added LabelFree option, which displays (single) chromatogram, fit, and parameters
  - "View" only; no curation yet
- Also added marker at scan number of CID, labeled and label-free
- Updated to new L&F
- Added pop-up messages window
- Adjust link target window names in protein page

XPRESS protein interface:
- New L&F
- Use AJAX call when updating protein ratio
- Update links to point to pepXML models page, viewer, Lorikeet
- Added option to xpress-prophet-update.cgi to return html portion (not entire page)
- Fix link from ProtXMLViewer

HardKlor
- Updated to support Ion Mobility
- use spectrum member variable to boost speed in multi-threaded setting where reallocs add up

MSToolkit
- Updated to support Ion Mobility (TIMS_TOF)
- mzParser deal with Precursors in mzML to store isolation window info
- Improved memory management with fewer reallocations to improve performance in multi-threaded applications

cramp
- fix case where scan number was being used as a scan index

tpp pwiz
- allow pwiz to process more, differently encoded, files

Greatly increase protein header size to handle PEFF headers in various components

[edit]

Miscellaneous

Make usage statements somewhat more readable (esp. xinteract)

Standardize progress bar across various TPP components

New ISB-inspired wait "spinner". Added so far to ASAPRatio, Pep3D, and PPSX

comet params: Place full path to PSI-MOD.obo file, now in TPP distro

PWIZ Updated to compile on newer versions of gcc in msys2 mingw64 with pthreads

More descriptive error messages and feedback in various tools

Fix various memory leaks, and clean up of old/commented out code

Removed antique TPP model rendering utilities, old (pre-Lorikeet) plot-msms.cgi, and all references to them

CPAN perl modules Statistics::R, Statistics::Regression, XML::Twig added/required

[edit]

Known Issues

promast calculates NTT for Trypsin only -- more enzyme support forthcoming
promast does not consider flanking SAAVs when calculating optimal NTT
Need to add more instruments to cvParams detection in mzParser
ASAPRatioCGIDisplay.cgi will crash with seg fault if pepXML index is not in consecutive numeric order

[edit]

Getting the TPP Software

Download the TPP version 6.0.0 native windows installer (TPP_Setup_6.0.0.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 6.0.0 source code .tgz package

Or, check out the code directly from svn:

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

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

[edit]

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.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:6.0.0_Release_Notes"

TPP:6.0.0 Release Notes

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 Trans-Proteomic Pipeline (TPP) software, release 6.0.0 is a '''major''' release of TPP that contains new features, improvements, and fixes to 5.2.0.  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]].
+For installation help, please see [[TPP:5.2_Installation]] (same as for 6.0.0)
 ** Enables interactive examination and interrogation of spectra stored in public repositories (only ''PeptideAtlas'' so far)
 ** Can be displayed standalone or butterfly-style for comparison against currently loaded spectrum
+* Major updates to '''ASAPRatio peptide UI''':
+** Add button to list IDs info in a table and overlay onto chromatogram (calls qsir via AJAX/json)
+*** Added qsir utility to extract all CIDs info within specified scan and m/z ranges
+** Enable mouse drag for selection of scan range and background (with toggle)
+** Simultaneous adjustment of light+heavy scan ranges by holding down <shift> while dragging mouse
+** Highlight input elements that have changes
+** Add toggle to display relative vs absolute y-scale ranges
+** Added 'X' to zero out background
+** Cease using gnuplot/png images and instead use flot.js
+** New L&F
+* Major revamp of '''ASAPRatio protein UI''':
+** New page layout: single table with collapsible peptide sections
+** Added more obvious "accepted" status for peptides, peaks, spectra
+** Added NTT and mapping uniqueness flags to peptide bar
+** Added background color quant scale
+** Added link to MADCAPS
+** Fixed links to PepXMLViewer; Lorikeet; TPP Models
+** Added pop-up messages window
+** Fixed memory overrun when building mods in spectrum links
 ** Can be repositioned via mouse-drag
 ** Uses new cgi to serve directory listing via json
+* New '''RACI''' library (Random Access Compressed Ifstream)
+** This small library (libraci in TPP) can be used in place of pwiz::util::random_access_compressed_ifstream
+** It is actually the same-ish code, but deboosted in favor of STL, and without the need to drag the entire ProteoWizard with it.
+** Simple, lightweight, and you can still read pep.xml.gz files
 * New '''NeoProtXMLParser''' API -- a new C++ API for reading and writing ProtXML files. This is intended to *eventually* replace the libprotxml currently in the TPP.
+* TIMS-TOF support for '''DISCO'''
+* Cleavable linker based neutral loss quantitation with '''Quantic'''
+* '''Quantic''' results integrated with ProteinProphet on protein level
+* multithreaded execution of '''PeptideProphet'''
+* '''PTMProphet''' can localize adducts and massdiffs
 * '''Updated Look and Feel''' for most interfaces and viewers
 * ''PepXMLViewer''
+** 64-bit support for large files
 ** Update to new L&F
 ** Add new js FileBrowser widget to assist in file loading
 ** new options EXCLUDEMASSDIFFMIN= EXCLUDEMASSDIFFMAX= to allow PTMProphet in MASSDIFF mode to localize mass differences on sufficient magnitude.
 ** new Option: STATIC mass difference search option
+* ''PeptideProphet''
+** new model ZACCMASS auto adjust for run-to-run mass difference changes
+* ''Quantic''
+** new feature DIAMODE, uses theoretical isotopic distros (from Mercury8) to correct relative intensities of cleavable linkers.
+** protein level analysis and ProteinProphet integration for quantities based on neutral loss of cleavable linker
+** new option COUPLED to consider intact peptide coupled neutral losses from the monoisotopic unfragmented precursor peak.
+** new features to annotate and quantify based on neutral loss of a cleavable linker
+** option ANNOTATE
+* ''xinteract''
+** New -v option to record inverse reduced ion mobility in pepXML
+** New -u option to define "unknown to PeptideProphet" decoys
+** New option -OT to enable MatchedIons model in PeptideProphet
+** new option -OO to enable ONEFVAL for PeptideProphet
+** new option -OZ to enable ZACCMASS for PeptideProphet
+** new option for using Gaussian model for negatives (EVD is used by default)
+** New experimental -PEFF option for mapping sequences to variants in PEFF-index files (using promast instead of RefreshParser)
+** user specified enzyme parameters at runtime
+** New Behavior: All work and intermediate outputs are placed in the current directory
+***  New Option -TEMP enables previous behavior of performing all work in the TEMP directory (made default by Brian Pratt some time ago)
+** Only call (decoy) ProphetModels if a decoy tag was specified (otherwise, what's the point?)
 * ''decoyFastaGenerator''
 * New Enzyme definition ''lysarginase''
+** Further, allow user to specify custom enzyme rules on command-line (xinteract/InteractParser)
 * Include ''comet 2021.01.0 and related conf file -- '''Please read the relevant Comet release notes, as some parameters have changed behavior'''
 * Include ''Kojak'' 2.0.0 (alpha-1) and related conf file
 * Include ''PSI-MOD.obo'', which is required for comet+peff mod searches
+* Update to latest version of ''calctppstat''
 * Include ''gnuplot 5.28'' (Windows)
 * Upgrade (strawberry) ''perl'' to 5.30.2.1 (Windows)
+* New Enzyme parameters allow specifying parameters for enzymes not defined already
 = Improvements/Changes/Bug Fixes =
+* ''comparePeps_Categories.pl''
+** new option -I for ion mobility
 * ''DISCO''
 ** BUGFIX: Lorikeet was incorrectly calculating the cterm modification masses, this corrects it.
 ** No longer pass fake [0,0.01] and [2000,0.01] datapoints to set x-axis range; use minDisplayMz and maxDisplayMz instead
+* ''Mascot2XML''
+** Handle decoy_peptides and decoy_summary according to same CONTENTTYPE as non-decoy counterparts
 * ''MADCAPS''
 ** Fixed neXtProt NX_ -1 links to PAtlas
 ** Styling updates
+* ''mzIMLTools''
+** Expanded features to comply with the mzID validator
+** updated adding database behavior to better detect duplicate entries with alternate paths
 * ''mzParser''
 ** Improve validation of options for decoy fasta generator
 ** Minor text changes for clarity and grammar
-** Force windows drive to be lowercase.
+** Force windows drive to be lowercase
+** zip file large file size support
 ** Correctly pass multiple user directories to updatePaths (updated to comma-separated)
-** Updated link to XTandem API
+** Updated links to XTandem API and Percolator
 ** replace downloadFilesArchive subroutine with one that works ... previous one was corrupting mzML files!
 ** Bugfix DNA2AA wrong reference page
 *** Kojak 2.0 discriminant score and mixture distribution
 ** adjust mixture model QC function to be more lenient
+** KDModel: print observed densities only when we have the fits
+** recalculate mean and std dev at each iteration because CLEVEL is set according to having an accurate value here
 ** optional old-style ACCMASS model as option and new-style z-score ACCMASS model as a separate option
 ** use all types of decoys for the negative model
 ** Restore spreadsheet link
 ** Clean up Quantic score code to fix export to ploTPP
+** large file support (in expat)
 ** fix bug where certain saav=0 stats were mis-counted
-** BUGFIX correct plotTPP file path bug on Windows (now working!) ...
+** BUGFIX correct plotTPP file path bug on Windows
-** BUGFIX correct problem with PTMProphet Filter disappearing when new columns are added ...
+** BUGFIX correct problem with PTMProphet Filter disappearing when new columns are added
 * ''ploTPP''
 ** Load all .new files in directory (and not just one)
 ** Added Restore button
+* ''ProteoGrapher''
+** Added file loading status bar and one for final processing of data
+** Warning with number of proteins with no GO mappings
+** Skip empty records
+** more flexibility for parsing out the uniprot ID
+** Move reference json files to new ref/ dir
+** Update links from Petunia and ProtXMLViewer
+** Load JSON from a pure JSON file (not a JSON encoded javascript variable)
+** Improved error handling on file loading
+** More descriptive error messages
+** Update to current TPP L&F
 * ''ProteinProphet''
 ** better reporting of modified peptides mapped to proteins in IPROPHET
 ** new option STATICMODS to encode static mods into the modified_peptide string, because searches with different static mods can theoretically be combined at this step.
+* ''ProtXMLViewer''
+** Implement visualization of Quantic protein and peptide quantities from cleavable linker neutral losses when available
+** Add support for StPeter dSIn values
+*** Also add user option to display NSAF/dNSAF values instead of SIn/dSIn
+** display indistinguishable_peptide (charged modified peptides for iProphet) underneath each peptide entry so that now all peptides mapped can be observed...
+*** adjust peptide titles to display charge_<modified_peptide> for all related indistinguished peptides.
+*** Display quantic values for the indistinguishable_peptides also
+** Minor L&F updates
+*** default links are now black, orange+underline hover (instead of always blue + underlined)
+*** entry and madcaps links are wider and with hover effects to make them more obvious
+*** fixed annotation alignment
+*** slightly larger font
+*** nicer graph legend box
+*** Highlight mouse-hovered protein entry
+*** Highlight (bold) PEFF fields in annotation view
+** Trim PEFF annotations so as not to show values for VariantSimple, VariantComplex, ModRes, ModResPsi, as they potentially take too much space
+** Capture organism stats from PEFF \TaxName field
+** Display reference database in File Info tab
+** Export proper json instead of javascript code snippet; also fixed stpeter export therein
+** Warn if reference database file is not found
+** Fix link to PAtlas for neXtProt NX_,-1 entries
 * ''PTMProphet''
 ** Alert with an error if zero sequences were mapped
 ** Eliminate memory leaks
+* ''readmzXML''
+** read Ion Mobility
+** Added precursor charge and nativeId to scan header information
+** Capture instrument serial number, hi/low mz values
+** Add more instruments to cvParams detection  (many more needed)
+** New -R option to print run and instrument header info
 * ''reSpect''
 ** mzParser now works with scan number ... mzParser corrected by Mike exposed reSpect bug
 ** BUGFIX mainly correct issues with writing mzML files using pwiz ...
+* ''RTCatalog''
+** Removed dependency on pwiz and boost and replaced with identical interface in mzParser that already existed.
+***This removes dependency on pwiz and boost for the core TPP libraries, allowing us to modularly compile our code separately from pwiz code.
+*** Tools that use one, the other, or both can then link one, the other, or both as needed, instead of forcing every tiny little script to link everything all the time.
+** change uninitialized values from -1 to a much smaller number (iRT values can be negative.)
+** only lop off everything past the last '_' when in DISCO mode, in regular mode keep the run names unaltered
 * ''SpectraST''
 ** clarifying output to the user.
 ** Fixed rounding bug when representing modification masses on peptides.
+* ''tpp2mzid''
+** New interface to specify preferred mzID version (for PRIDE compatibility)
+** add new content to the mzID output
+** Updating software to work with the newer mzIMLTools API
+** bugfixes and improvements for PTMProphet to mzID.
 * ''tpp models''
 ** Added option to xpress-prophet-update.cgi to return html portion (not entire page)
 ** Fix link from ProtXMLViewer
 * ''HardKlor''
 ** Improved memory management with fewer reallocations to improve performance in multi-threaded applications
+* ''cramp''
+** fix case where scan number was being used as a scan index
+* ''tpp pwiz''
+** allow pwiz to process more, differently encoded, files
+* Greatly increase protein header size to handle PEFF headers in various components
-* Make usage statements somewhat more readable (esp. ''xinteract'')
 = Miscellaneous =
+* Make usage statements somewhat more readable (esp. ''xinteract'')
 * Standardize progress bar across various TPP components
 * CPAN perl modules Statistics::R, Statistics::Regression, XML::Twig added/required
-= Known Issues =
-* None
+= Known Issues =
+* ''promast'' calculates NTT for Trypsin only -- more enzyme support forthcoming
+* ''promast'' does not consider flanking SAAVs when calculating optimal NTT
+* Need to add more instruments to cvParams detection in ''mzParser''
+* ASAPRatioCGIDisplay.cgi will crash with seg fault if pepXML index is not in consecutive numeric order
 = Getting the TPP Software =
 * For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki.
 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.
-= SVN Log =
-The SVN log of all changes since the previous release is available at [[TPP:6.0.0_SVN_Log]].