TPP:5.1.0 Release Notes

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Trans-Proteomic Pipeline (TPP) software, release 5.1.0 is a major release of TPP that contains new features, improvements, and fixes to 5.0.0. 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:5.1_Installation.

Previous release notes are available at TPP:5.0.0_Release_Notes

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

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Major Changes

New visualization tool MADCAPS: Multiple Alignment, Digestion, Coverage, and Annotations of Protein Sequences
- Uses ClustalOmega (included) to perform sequence alignment
- Linked from ProtXMLViewer, but can be used stand-alone
- Shows potential digestion peptide products
- Indicates if peptide sequences are differentiable and/or unique

New tool ploTPP for simple interactive visualization, including overplotting of values from different sources
- Support for histograms and scatterplots
- Linked from PepXMLViewer and ProtXMLViewer
- Works with numerical values only at the moment; future support for text/categories

New tool fetchDataset for downloading and unpacking public proteomics datasets
- Supports Minids and BDBags; planned support of PASS and PXD identifiers
- Extracts files and can create a TPP/Petunia session file for ease of (re-)analysis and data exploration
- Integrated into Petunia, where one can view current installed version and capabilities, as well as perform updates of the tool
- Requires Python and optional 3rd party packages (separate install required)

New mzIMLTools interface to enable reading and writing of mzIdentML
- Includes usage example/demo

Added basic integration of Novor de-novo engine into TPP
- Added new converter from novor.csv to pepXML, novor2xml

Added basic integration of ProteinPilot results into TPP

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New Features

PeptideProphet
- MASSWIDTH= option for open mass searches
- Support for search engine SIPROS

Petunia
- Implemented simple visualization of tsv files
- Added new Disco input: select Hardklor params; add support for editing said params
- Added support for Novor de novo search engine:
  - Added Novor to available engines
  - Added page to launch Novor; checks for novor.sh/.bat and warns user if not found
  - Added Novor "home" page with analysis steps currently supported in TPP
  - Novor params edit already supported by current code
  - Added page to launch conversion from Novor .csv to pepXML
- Added Database file chooser for Kojak; usage is optional, it will replace entry within selected Kojak.conf
- Added new -c and -n options for randomized decoy generator
- Added 'no centroiding' option to Libra conditions and made it the default
- Added link to new ploTPP.html for relevant .data files

PepXMLViewer
- Show quantitation ratios with a gradient background color (blue->white->red)
- Add color annotated color scale for quant values
- Initial support for Novor search results:
  - New novor_peptide field shows sequence with aaScore as a colored bar above each AA. (similar to ptm_peptide)
  - Added Novor score filter
- Added support for PEFF modifications and substitutions
- Implemented mouse-over description text for column headers
- Enable export of single (histogram) or a pair (scatterplot) of columns for visualization in new ploTPP utility
- Link to view results only opens in new window unless window already present; it auto-refreshes otherwise
- Added link from MASSDIFF column to Unimod search with +/- 1 mass window
- Allow to filter based on (absolute) massdiff
- Handle and display terminal mods and probabilities from PTMProphet
- Support for new speclib search engine Calibr

ProtXMLViewer
- Added background color gradient to pvalue and libra values (text mode)
- Added color annotated color scale for libra and pvalue quant values
- Display and export protein length, when present in protXML
- Enable export of single (histogram) or pairs (scatterplot) of columns for visualization in new PloTPP utility
- Implemented command-line invocation, mostly suited for exporting .tsv and .data files. See usage statement for more info and instructions.
- Add links to new sequence alignment and digestion tool, MADCAPS

DISCO
- Implemented multiple threads
- Multi-thread hardklor; use external hardklor parameters
- DIAUmpire support improved with native format reading
- MS1 Peak integration for quantitation

StPeter
- Added distributed NSAF option (use shared peptides in quant)

compareProts
- Allow to compare proteins based on precursor intensities

Include comet 2017.01.1 and related conf file -- Please read the relevant Comet release notes, as some parameters have changed behavior
Include Kojak 1.5.5 and related conf file
Include ProteoWizard tools v3.0.10141 (3.0.11537 on Windows)
Updated versions of Hardklor, MSToolkit, Lorikeet,...

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Improvements/Changes

ProteinProphet
- MAXPPMDIFF option for open mass searches
- Report accurate exit codes

SpectraST
- Increase accuracy of primary Immonium ion masses
- OpenMod search, allow the tolerance to be specified and passed to allow mass differences bigger than 300 amu.

PTMProphet
- Change pepXML reporting of terminal probabilities as per new schema

Disco
- Change the way isolation windows are specified (now requires flag WINDOWS=<file>)
- Use HardKlor to ID unfragged MS1 precursor features for DISCO extraction

decoyFastaGenerator
- New option to specify cut / no cut sites when creating decoy peptides from target proteins
- Strip out Linux and Windows EOL chars

XPRESS
- Add long overdue support for isotope peaks to XPRESS cgi: When C13 isotope peaks are used in the quantitation, the cgi XPressPeptideUpdateParser.cgi is now aware of them and will display the same ratio,taking into account the data in the C13 isotope peaks
- Streamline XPRESS metabolic labeling support. XPRESS will now automatically determine if peptide is C13 or N15 light/heavy labeled based on modification state of peptide

Petunia
- Directly link to SpectraST output file if only one input file was used (otherwise keep directory as job output)
- Remove leading and trailing spaces in xtandem params (it chokes otherwise!); also ensure only one space after a comma
- Dim/highlight refinement-related xtandem params when value of 'refine' is set to/not to 'yes'
- Show smooth job status transition when udpating to a new status
- Rearranged Libra normalization options so that 'not recommended' values are sorted/displayed last
- Add neutral losses and MS1 tolerance PTMProphet options to xinteract page
- Display statuses in status bar alpha-ordered for consistency
- Flag filenames that contain spaces when listing files; do not allow to select these for input
- Allow choosing pepXML and protXML files as input to idConvert
- Added link to GPM/Tandem from tandem search page
- Removed "terms" from link to ProteoGrapher
- Added tool name to top nav bar, as per new design
- Added 'X' link to remove current filter
- Replaced "format used by xinteract" to "format used by TPP"
- Minor rearrangement of XPRESS interfaces: clarify metabolic options
- Add two more potential modified residues for a total of five for XPRESS
- Update for new Disco command invocation

PepXMLViewer
- Use database used by RefreshParser, if present; otherwise default to using db used in original search
- Do not generate protein link for '_UNMAPPED' entries
- Show normalized Libra ratios by default (formerly: show absolute values)
- Changed alternate row color from light blue to light green
- Align xl cross-link peptides and show xl location with a bar connecting them
- Default to show 100 rows (old: 50)
- Allow filtering by xlink_type if column is being displayed (or search engine is Kojak|PLink)
- Minor L&F revamp to mimic recent changes to other TPP interfaces:
  - Establish fixed header, footer, and menus
  - New toolbar with menus to open/close sections for filtering, displaying , messages, etc.
  - Added tool name to background of menu for easier identification
  - Small color updates
- General cleanup of html template
  - Moved Comet expect filter to top of section
  - <bold> selected display options and filters in respective summary texts
  - Add <label> tags to most radio and checkbox inputs for easier user interaction
  - Compact several form fields
  - Removed XPRESS min area filter
  - Extended Pick Columns widget to 15 items (previous:10)
  - Minor grammar/typo corrections
- Close menu if clicked upon
- Changed menu background color to better differentiate from data table
- Changed mouse-over color for filter/display options
- Slightly compress and simplify ASAPRatio and XPRESS filters
- Added more html labels to ASAP/XPRESS filter options
- Enabled ions link to Lorikeet for SpectraST results
- Added SpectraST and Kojak scores to possible columns when viewing iProphet results

ProtXMLViewer
- Added ability to sort and filter by Libra number of peptides
- Added min/max filtering for each Libra channel
- Enable sorting and filtering by number of spectra used by Xpress, ASAPRatio
- Removed heatmap display option from asap/xpress/stpeter
- Provide legend when displaying graphical peptide view
- Clarify in headings that quant ratios are Heavy/Light
- Keep showing Protein Group headers when filtering only by probability

Spectrum Viewer
- Shade precursor selection window in MS1 scan (mzML files only)
- Label neutral losses of the (unfragmented) precursor peak
- Added C-linked hexose (from W) and CH3SOH (from M[ox]) as auto-detectable custom neutral losses
- Allow and label more than one neutral loss on any fragment
- Updated to new L&F

xinteract
- Update usage statement for XPRESS metabolic labeling

Pep3D
- Break down CIDs by charge state
- Tweaks to match current TPP L&F (html title and header)

tpp_models
- Update L&F to match latest template (darker blue, similar tabs, footer, add tool name to top nav bar, etc)
- Place labels on x-axes for most models
- Scale secondary models to +/- 100% for easier comparison
- Clean up x-tickmarks

ProteoGrapher
- Classify the GO terms in all three categories: Biol.Proc., Mol.Func., Cel.Comp.
- Now works with Firefox

StPeter
- Added biotin as a modification mass

RTCatalog
- PEPSBYRUN= file to match peptide to appropriate run for reporting in RTCatalog
- MINPTMPROB= use minimum PTMProphet probability for reporting peptides

Lib2HTML
- Pass correct cgi url from Petunia
- Open spectra in separate window

subsetdb
- Added option to specify line length for sequences (default=80, as per previous behavior)

digestdb
- Allow long protein accessions (100 chars vs previous 50)

readmzXML
- Added precursor charge to the "-h" text output file

mzParser
- Better handle precursors, especially multiple precursors (MSX mode)
- Updated MSNumpress
- Improved parsing of predicted vs selected precursor ion m/z
- Added selected ion window parsing
- Improved reading of chromatograms from mzML
- Additional header information reading from mzML
- Minor code visualization updates
- Adding back an unused buffer and some legacy functions for Tandem support
- Use the byte offset index to access the header info more quickly

pepXML schema v1.22
- Added 'type' attribute (for XL analysis)
- Added support for aminoacid substitution searches (e.g. via a PEFF database)
  - New optional aminoacid_substitution tag
  - New optional attributes static, variable, and id of mod_aminoacid_mass
- Added support for terminal mod probabilities from PTMProphet
- Changed type for massdiff and calc_pI attributes from string to double
- Belated addition of decoy analysis tags
- Expanded list of possible aa- and term- modification symbols

Windows Installer
- Do not auto-install/run tpptray
- Add link to TPP log files from Programs menu

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Bug Fixes

InteractParser
- Place dataset_derivation tag AFTER the analysis_summaries
- Do not crash if NMC > 9 (double digits)
- Do not attempt to correct start/end scan numbers and charge if already present in file (fixes instances where the index=NN within spectrumNativeID was being used, sometimes incorrectly, causing bad files to be produced)
- Only show "success" message if file and/or extension were actually corrected

PeptideProphet
- Correctly name RT Mixture Model

RTCalculator
- Correct header comment
- Don't print the peptide by peptide rt info in non-verbose mode

iProphet
- NRS model edge condition corrected (missing '-')
- Fix a bug with small sized runs

PTMProphet
- Use Gaussian to approx Poisson when mu is high to prevent some gsl crashes
- Correct crashes when immonium table contains null for some amino acid tokens (e.g. 'Z')
- Correct issues with massdiffmode and unknown modifications (e.g. incorrectly reported n-terminal acetylation)
- Exit with error message when encountering unspecified mod
- Fix bug not allowing PTMProphet to run when only one modification was being specified for localization
- Fix bug associated with reporting peptides with a terminal mod
- Fix EM iteration convergence testing
- Fix tripping over windows full paths

reSpect
- Fix problem with neutral losses

XPRESS
- Fix terminal mod handling (was comparing 'n' vs 'N', etc)

LibraPeptide
- Print error and exit if scan has no peaks (instead of segfault)

ASAPRatioPValue, ASAPRatioProteinRatio, LibraProtein, Pep3D, Tandem2XML
- Fixed numerous memory leaks and other errors, some potentially reporting incorrect results

Mascot2XML
- Fixed XML encoding of alternative protein descriptions (reported and contributed by J. Eckels)

Petunia
- Fix chdir when in Windows (one must also execute change drive!)
- Do not crash on non-existent directory; return empty file list instead
- Added js check for 'alljobs' element before operating on it
- Do not submit form if user presses 'Enter' in filter box

PepXMLViewer
- Fixed index file bug: asapratio_mean was being duplicated which caused issues with sorting in certain cases
- Fixed "require consistent xpress/asap ratios" filter
- Fixed web link to xml and models files that kept causing access problems mainly in Linux
- Correctly display "unavailable" libra values
- Fixed glyc and ASAP labels
- Fixed modified peptide display (for n-terminus)
- Fixed tab-delimited export of ptm_peptide field: get rid of leading comma that showed up in certain conditions
- Fixed text/excel export of loop xlink peptides
- Provide better error report when encountering bad modified peptide
- Plug memory leaks and fix uninitialized variable
- Use correct spelling for "accessIble"

ProtXMLViewer
- Fixed alignment/width of protein annotation span
- Fixed link to XPress CGI
- Fixed FF/Chrome vertical alignment quirks

Spectrum Viewer
- Fixed calculation of PhosphoLossMass_avg

DISCO
- Fixed some memory issues for DIAUmp targets
- Fixed issues preventing DISCO from running to completion in certain edge cases
- Relaxed requirements for having isolation window offset parameters which are absent in current ABSciex mzML files

plotspectrast
- Fixed path issue that resulted in a broken image link

decoyModels
- Removed non-compliant id attribute from analysis_summary
- Added an extra test for <dataset_derivation> tag when looking for place to insert <decoy> analysis tags, for robustness

comet-fastadb
- Encode protein description as XML (and HTML) friendly

tpp_models
- Exit and report error (as opposed to continuing and failing later) when an msms_run_summary open tag is found while inside another msms_run_summary.

ProteoGrapher
- Fixed incorrect paths
- Fixed JSON object loading error

subsetdb
- Fixed crashes under Windows

Enzymes
- Fixed and harmonized specificity rules for chymotrypsin
- Fixed memory leaks

tpplib_perl
- When looking for tpp_hostname executable, first try under TPP_HOME/bin

mzParser
- Only attempt to open a file if there is an actual filename, which avoids potential memory errors
- Include file name in error when unable to open

Apache/conf
- Need to add explicit grant access in case TPP_DATADIR is not under INSTALL_DIR

Updated README/build notes

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Miscellaneous

Compilation/build
- Changes to make sure we can still compile under windows mingw64 using msys2
- Removed reduntant -lpthread linking (already included in BOOST_LDFLAGS)
- Perform path replacement using sed instead of perl due to Windows build oddities
- Strip leading and trailing spaces from user-specified build settings, as they may cause errors
- Break out text and image files -- the latter of which should not go through sed, as it potentially corrupts these files
- Updated packages required for CentOS install

mzParser: Initialize scanHeader.scanType

PepXMLViewer
- Use <!DOCTYPE html> for html5
- Simplified row highlight mechanism: use css :hover (removed mouse-over/out code)

ProtXMLViewer
- Avoid calling Wobniar (colors) repeatedly when displaying graphical peptide view
- Tweak css for missing/empty protein annotations
- Add full file path to footer
- Add tool name to top nav bar, as per new design

Removed some old (commented out) debug code and deprecated Cygwin code blocks
Removed a few old, deprecated programs

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Known Issues

PTMProphet may sometimes report the same mod with different rounding precision
The preview zoom window in MADCAPS may be misaligned in some web browsers

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Getting the TPP Software

Download the TPP version 5.1.0 native windows installer (TPP_Setup_5.1.0.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 5.1.0 source code .tgz package

Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-1-0

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

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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.

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