Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog
3.1.1 - 2020-10-01
- Fix a bug that does not write calibrated MGF.
- Fix a bug that do not allow labile modifications in mass offset search with
restrict_deltamass_to = all
.
3.1 - 2020-09-30
- New DIA search mode of MSFragger, supporting searching DIA data with parameter
precursor_mass_units = 2/3
. - Precursor isotope error correction with parameter
precursor_mass_mode = corrected
. - Support restricting delta mass (open/mass offset searches) to certain amino acids with parameter
restrict_deltamass_to
. - Support putting localized delta mass to peptides as variable modifications with parameter
mass_diff_to_variable_mod = 0/1/2
. For N-Glyco data, will also put unlocalized glycans to the “N” of the first “N-X-S/T” sequon. - Support pin format output, which is compatible with Percolator.
- Upgrade timsdata library (for Bruker timsTOF data) to 2.7.0.
- Write localization information to pepXML file with tag
ptm_result
. - Added b~ and y~ fragment ions to localization (Glyco mode)
- Reduce the PSMs required for mass calibration from 500 to 250, and increase the expectation threshold from 0.001 to 0.005.
- Improve parameter optimization procedure.
- Add a MS2 resolution check.
- Change “O”’s mass to pyrrolysine’s mass, and print two comments for “O” and “U”.
- Change the default value of
allowed_missed_cleavage
to 2. - Change the default enzyme to stricttrypsin.
- Print more significant digits for masses and other key parameters in the output file.
- Various minor bug fixes and improvements.
3.0 - 2020-06-05
- New Glyco/Labile mode of MSFragger (for N-linked and O-linked glycopeptides; can also be used for other labile modifications).
- Change the default value of
write_calibrated_mgf
to 0. - Add 7 ppm to nonspecific search’s fragment tolerance list (optimization step).
- Various minor bug fixes and improvements.
2.4 - 2020-03-21
- Write original spectral file extension to pepXML after mass calibration.
- Write
native_id
to pepXML give mzML or mzXML file. - Add 5 ppm and 50 ppm to the fragment mass tolerance list.
- Improve printed message.
- Support non-zero mass offsets in first search, mass calibration, and parameter optimization.
- Various minor bug fixes and improvements.
2.3 - 2020-01-30
- Add a MS/MS deisotoping module, with a new input file parameter
deisotope
. Default is set to 1 (use deisotoping). - Support water-loss ions: ion types
b-18
andy-18
. - Add one more column to variable modification setting specifying the maximum allowed number of instances of that particular modification on the peptide.
- Replace
max_variable_mods_per_mod
withmax_variable_mods_per_peptide
that specifies the maximum allowed number of variable
modifications on the peptide. - Print the number of peptide candidates with the number of modifications exceeding
max_variable_mods_combinations
. - Print all decimal points to the tsv file.
- Change the minimum allowed
precursor_mass_lower
to -230 (in open search). - Improvements in the parameter optimization procedure.
- Increase estimated memory usage by including the sizes of spectra and result.
- Various minor bug fixes and improvements.
2.2 - 2019-11-08
- 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
to0
. - Change the default values of
min_fragments_modelling
in open search to2
. - Change the default values of
min_matched_fragments
in open search to4
. - Limit the minimum value of
precursor_mass_lower
to -150 Da. - Check
intensity_transform
andremove_precursor_range
in parameter optimization step. - Improve parameter optimization algorithm.
- Various minor bug fixes and improvements.
2.1 - 2019-09-08
- Fixed bugs.
- In parameter optimization step, improve the top-N peak candidates.
2.0 - 2019-09-05
- 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
andremove_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.
20190628 - 2019-06-28
- 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.
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 iflocalize_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
andpepXML
files.output_format = tsv_pepXML
-
added
precursor_mass_mode
optionusage:
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
optionexample 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)