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  • Added extended unit tests.
  • Added code for quicker FDR calculation.
  • Updated urls to xerces and google test
  • Switched compiler to c++11
  • Added basic pepXML support.
  • Improved testing in Github actions:
    • Made separate stages for unit and system tests for Ubuntu
    • Introduced a test build for centos
    • Moved unit and system tests to release code.
    • Changed the dependency structure to gtest
  • Added command-line argument to switch off reporting to analytics
  • Added possibility to include spectrum file name in tab-delimited input, that is carried over to tab-delimited output.
  • Added possibility to include retention time in tab-delimited input.
  • Discontinued support of the Elude model
  • Removed all retention time modeling and all other DOC features
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  • Fixed problem with Elude model reading on windows (#249)
  • Better error messages for converters (#251)
  • Fixed several build errors (#188, #250)
  • Parallel nested CV SVM training using a single OMP threadpool. Percolator can now handle up to 27 parallel threads to significantly speed up processing and uses parallel STL algorithms on linux (#254)
  • Fixed TabReader error handling (#255)
  • Continuous integration with GitHub Actions with nightly releases for Windows, OSX and Ubuntu (
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  • Added full support for static models (#247)
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  • Added check for inf or nan valued features (#177)
  • Added option to add expMass to PSMid in converters (#232)
  • Added check for protein length < decoy prefix length in picked protein (#242)
  • Added support for N- and C-term modifications formatted as M.n[37]A[16]AERc[16].G
  • Fixes for DOC feature option
  • Fixed tandem2pin incorrect decoy label bug (#238)
  • Fixed tandem2pin duplicate entries for shared peptides
  • Fixed CMake XSD package detection (#234)
  • Fixed quickvalidation issue with resetting of score vector (#235)
  • Fixed rounding error for experimental mass in msgf2pin (#223)
  • Added missing #include for (#225)
  • Fixed duplicate peptide identifications in protein output (#222)
  • Added OSX vagrant build
  • Updated XercesC version
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  • Fixed protein digestion issues due to trypsin/p (#191)
  • Skip XSD schema loading when -s flag is set
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  • Changed FDR calculation for initial direction selection to the more liberal decoys/targets (#208)
  • Added parameter file option instead of only command line specification (#149)
  • Allow training only on best PSM per peak group or spectrum (#207)
  • Include spectral counts for lists of protein inferences (#202)
  • Allow separate control of FDR threshold for initial iteration (#190)
  • Added check of deltaMass and retentionTime columns with DOC features (#167)
  • Added check if output files are writable before training SVM (#185)
  • Fixed tandem BioML input check for tandem2pin (#180)
  • Fixed discrepancy between windows and linux results (#203)
  • Fixed fido protein grouping (#201)
  • Fixed zlib DLL issue on windows (#197)
  • Fixed/clarified several log and help messages (#199, #205, #179)
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  • Fixes empty output on xxx2pin converters on MacOS (#178).

NOTE: for all other platforms besides macOS, the 3.1 release below is still the latest release.

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  • Fixes macOS installer problems with macOS 10.11+ (#193)

NOTE: for all other platforms besides macOS, the 3.1 release below is still the latest release.

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  • Changed all FDR calculations to the more conservative: (decoys+1)/targets
  • Added -o/-no-terminate flag to allow overriding of fatal errors:
    • No default direction can be found: set to the first feature (#135)
    • Separation between target and decoy PSMs/proteins is too great: continue with this direction anyway
    • No target PSMs present: return empty result list
    • No decoy PSMs present: give all target PSMs a q-value of 1/numPSMs
    • No features present: create a single pseudo feature which is always zero
    • Too many values in default direction vector: trim default direction vector to number of features
  • Added mix-max method for FDR and PEP calculation, which replaces target-decoy competition as the default method. The advantage is that this will report all input PSMs in the PSM output and also corrects for incorrect native spectra in qvality (#152)
  • Automatic detection of search input as coming from a concatenated search or from separate target and decoy searches. For a concatenated search, the mix-max method will be skipped. For separate target and decoy searches the user can choose to use the mix-max method (default) or target-decoy competition (-Y flag)
  • Updated and improved stderr output to be more informative
  • Fixed fasta in-silico digestion for protein grouping which mistook N-methionine cleavage for a non-enzymatic cleavage site (#148)
  • Fixed retention time NaN predictions by setting them to 0 instead (#150)
  • Fixed protein group representation for picked-protein in the case that protein names contain a comma, by replacing these by semicolons (#153)
  • Fixed tandem2pin issue that labeled all PSMs as decoy when providing separate target and decoy input files (#154)
  • Added OpenMP runtime library to be included in windows installer (#158)
  • Fixed msgf2pin converter issue with C-terminal modifications (#161)
  • Fixed tandem2pin to parse PTMs (#132)
  • Fixed install location on windows 64-bit from "Program Files (x86)" to "Program Files" (#144)
  • Several fixes for OSX build script (#159, #162, #165)
  • Fixed mass difference calculation in certain converters (#166)
  • Fixed several build issues on several platforms (#79, #113, #133)
  • Build scripts are now changed and tested under CentOS 7.2 and Fedora 23, the precompiled binaries below are generated on those systems as well.
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  • Added protein-level FDRs using best-scoring peptide approach
  • Added support for training on subsets of PSMs to speed up analysis for large data sets
  • Fixed msgf2pin issue with huge ScoreRatio feature (#142)
  • Fixed tandem2pin issue with incorrect decoy label assigment for shared peptides (#143)
  • Added error message when no decoys are provided (#145)
  • Fixed reporting of XML parsing errors for converters (#146)