Changelog

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

The format is based on Keep a Changelog

20190628 - 2019-06-28

• Supporting 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 don’t want to use it.
• If there is no spectral file specified, generating pepindex and exiting.

20190530 - 2019-05-30

• 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.

20190222 - 2019-02-22

• 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)

20181110 - 2018-11-10

• update MSFTBX dependency

20180924 - 2018-09-24

• 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

20180924 - 2018-09-24

• \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

20180912 - 2018-09-12

• fragment matching is based on neutral masses, memory usage reduced
• restrictions on digested peptide size relaxed
• read in Corrector input if present
• directory for temporary files can be specified with temp_location
• non zero exit codes when terminating with error

20180316 - 2018-03-16

• Fix display issue with static terminal modifications.
• Open search times are reduced by about a quarter.
• Fixed bug with peptide mass calculation less termini.

20180224-RC1 - 2018-02-25

• MSFTBX upgraded to version 1.8.2.

20180223-RC1 - 2018-02-23 (public release)

• Java 9 compatible JAR
• Protein names are escaped to produce valid pepXML

20180215 - 2018-02-15

• Added support for mass offsets (enabling multi-notch searches)