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MSFragger

Ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog

Check spectral files at the beginning.
Add a parameter (write_calibrated_mgf) to write calibrated spectra to MGF files.
Add uncalibrated_precursor_neutral_mass attribute to pepXML file.
Change the default value of allow_multiple_variable_mods_on_residue to 0.
Change the default values of min_fragments_modelling in open search to 2.
Change the default values of min_matched_fragments in open search to 4.
Limit the minimum value of precursor_mass_lower to -150 Da.
Check intensity_transform and remove_precursor_range in parameter optimization step.
Improve parameter optimization algorithm.
Various minor bug fixes and improvements.

Switching from ‘date’ to ‘version number’ in naming released versions. This version is named 2.0 in recognition of the many improvements implemented in MSFragger in the last six months.
Support direct reading from Bruker raw files (.d folder).
Support MGF file converted by Bruker DataAnalysis.
FragPipe now supports running MSFragger with raw Thermo or Bruker files as input within FragPipe (limited functionality).
Pass ion mobility information (if applicable) from the spectral file (mzML, MGF, and .d folder) to the resulting pepXML file.
New option to remove unfragmented precursor peaks from tandem mass spectra (remove_precursor_peak and remove_precursor_range parameters). Recommended option for ETD/EThcD data.
New option to apply sqrt root transform to fragment ion intensities (intensity_transform parameter). Recommended option for ETD/EThcD data.
Support calibrating precursor masses even when there are no MS1 scans in the input spectral file.
Support assigning mass offsets to the localized amino acid sites.
Add a --version flag to print version to console.
Add a --help flag to print help information to console.
Add a --config flag to write three fragger.params templates to current folder.
Limit maximum precursor charge to 7.
Various minor bug fixes and improvements.

Support direct reading from Thermo RAW files through the command line and the ProteomeDiscoverer node. FragPipe will be able to read raw files soon.
Add an excluded_scan_list_file parameter that takes the path of a text file containing scan names. MSFragger would skip those scans if the path is not empty. Comment or delete this parameter name and its value if you do not want to use it.
If there is no spectral file specified, generating pepindex and exiting.

Support mass calibration.
Support optimal parameters finding.
Support additional ion series including a-, b-, c-, x-, y-, and z-ions.
Write localized modifications to .tsv file if localize_delta_mass = 1.
Improve .tsv file’s columns.
Support command line parameters.
Print parameters to the command line.
Write parameters to the pepXML file.
Re-implement alternative protein mapping for efficiency.
Make the MGF file parsing more robust.
Fix a bug about the inaccuracy of the searching speed printed to the command line.
Showing the numbers of unique peptides in the command line.
Various bug fixes and improvement.

Improved error messages for OutOfMemoryError and when too many peptides were generated durning digestion
report_alternative_proteins option added. Turned off by default.
write input file type in msms_pipeline_analysis tag, previously was hardcoded as ".mzXML"
write alternative proteins
If MsAdjuster is used, output precursor intensity in spectrum_query tag
added option to write both TSV and pepXML files. output_format = tsv_pepXML
added precursor_mass_mode option

usage: precursor_mass_mode = isolated / selected / recalculated
default shifted_ions_exclude_ranges to (-1.5, 3.5)

added shifted_ions_exclude_ranges option

example usage: shifted_ions_exclude_ranges = (-1.1033548378, -0.9033548378), (-0.1, 0.1), (0.9033548378, 1.1033548378), (1.9067096756, 2.1067096756), (2.9100645134, 3.1100645134), (15.894915, 16.094915), (42.905814, 43.105814)
added output_location option

\n is used as a newline for all platforms
when in split search mode, output files in the working directory instead of the directory of input files