v0.14.7

What's Changed

[v0.14.7]

Added

• Added columns missing from parquet output: semi_enzymatic and missed_cleavages

Changed

• Fix to #117 by @jspaezp in #119

• MGF paths were being lowercased prior to parsing

Full Changelog: v0.14.6...v0.14.7

v0.14.6

What's Changed

• feat: add MGF reader by @yujinjeong2 in #109
• Fix link to Picked group FDR in README.md by @MatthewThe in #111
• Feature: ims model by @jspaezp in #98

New Contributors

• @yujinjeong2 made their first contribution in #109
• @MatthewThe made their first contribution in #111

Full Changelog: v0.14.5...v0.14.6

v0.14.5

[v0.14.5]

Added

• Support for semi-enzymatic digests (database.enzyme.semi_enzymatic parameter) by @FriedLabJHU in #94
• Ability to directly export matched fragment ions (e.g. for spectral library or rescoring) with the --annotate-matches CLI option. This is compatible with the --parquet CLI option as well. Annotations will be written to matched_fragments.sage.tsv or matched_fragments.sage.parquet. by @grosenberger-bruker in #101
• Sage sends basic telemetry data (version of Sage, run time, OS, # of CPU cores, # of peptides in database, whether LFQ is used) to a remote database. No information about your actual data is sent - e.g. identifications, quantities, organism, or modifications, etc are NOT tracked or reported. This data will be used to help focus efforts on improving Sage and figuring which features are most used. Please take a look at crates/sage-cli/src/telemetry.rs to see exactly what is sent! You can disable sending telemetry data by using the --disable-telemetry-i-dont-want-to-improve-sage CLI flag.

Changed

• Modified visibility on some crate internals to support the sagepy project by @theGreatHerrLebert in #103
• Added psm_id field to various output files to match the new --annotate-matches option.

Removed

• Removed the ms1_intensity field from CSV output, since it is essentially useless

New Contributors

• @FriedLabJHU made their first contribution in #94
• @theGreatHerrLebert made their first contribution in #103
• @grosenberger-bruker made their first contribution in #101

Full Changelog: v0.14.4...v0.14.5

v0.14.4

Added

• Unstable feature: Preliminary support for reading Bruker .d folders (ddaPASEF; no MS1/LFQ support yet)

Changed

• Retention times are converted to minutes

Fixed

• Fixed bug where charge state 1 would never be searched

Full Changelog: v0.14.3...v0.14.4

v0.14.3

Added

• quant.lfq_settings.combine_charge_state boolean option. By default this is set to true, and LFQ is performed on the peptide-level, where all charge states are treated as the same precursor. Setting this to false performs LFQ on the peptide-charge-level, where each charge state will be treated separately.

Changed

• Percolator output format now contains the integer-valued charge state encoded in the z=other column, if the charge state is outside the range 2-6 (e.g. a value of 7 will appear in the z=other column, rather than it being one-hot encoded)
• LFQ uses the the charge state range from the precursor_charge configuration option for tracing MS1 peaks

v0.14.1

Added

• Added additional output showing search progress if SAGE_LOG=trace environment variable is set
• Added additional warnings about precursor tolerances
• Added configuration option precursor_charge to make it explicit what charge states are being searched in the case where the mzML does not contain charge state information, or where wide_window is turned on.

Changed

• Added a warning message if variable modifications are specified as single values (e.g. 15.9949) instead of lists of values (e.g. [15.9949]). By v0.15 this will become a hard error and will not parse, to simplify some of the internal logic.

v0.14.0

Added

• Support for parquet file format output. Search results and reporter ion quantification will be written to one file (results.sage.parquet) and label-free quant will be written to another (lfq.parquet). Parquet files tend to be significantly smaller than TSV files, faster to parse, and are compatible with a variety of distributed SQL engines.

Changed

• Implement heapselect algorithm for faster sorting of candidate matches (#80). This is a backwards-incompatible change with respect to output - small changes in PSM ranks will be present between v0.13.4 and v0.14.0

Full Changelog: v0.13.4...v0.14.0

v0.13.4

Fixed

• Bug in mzML parser, where some older specification-compliant mzMLs would not parse. If your mzMLs previously parsed, then there will be no change in behavior. Added a test case

v0.13.3

Fixed

• Bug in database.enzyme.restrict parameter, where null values were being overriden with "P" (causing Trypsin/P to behave like Trypsin)

v0.13.2

[v0.13.2]

Changed

• Subtle change to TMT integration tolerance, and selection of which ion to quantify (most intense). As a result, TMT integration should be more in agreement (if not 100% so) with ProteomeDiscover/FragPipe/etc
• Remove delta_mass (precursor ppm) LDA feature - instead, build a delta mass (or ppm) profile using KDE/posterior error calculation code, and use the P(decoy) as a feature for LDA.