v0.13.1

Changed

• Internal performance and stability improvements for RT prediction & LDA

v0.13.0

What's Changed

• Added a missing comma by @hbarsnes in #66
• Better error messages by @Elendol in #65
• Overhaul modifications: multiple variable mods, modifications of specific AA at termini by @lazear in #69

This release adds support for multiple variable modifications, and peptide/protein-terminal modifications that are specific to individual amino acids.

The new syntax looks like this:

"variable_mods": {
    "M": [15.9949],
    "^Q": -17.026549,
    "^E": -18.010565,
    "[": 42.010565
},

Either a single floating point number (-18.0) or a list of floating point numbers ([-18.0, -15.2]) can be supplied as modifications.

• "^X": Modification to be applied to amino acid X if it appears at the N-terminus of a peptide
• "$X": Modification to be applied to amino acid X if it appears at the C-terminus of a peptide
• "[X": Modification to be applied to amino acid X if it appears at the N-terminus of a protein
• "]X": Modification to be applied to amino acid X if it appears at the C-terminus of a protein

Modification strings without the "X" will be treated as before - applied to the N/C-terminus of the peptide itself.

Full Changelog: v0.12.0...v0.13.0

v0.12.0

[0.12.0]

Added

• Add wide_window option to configuration file. This option turns off precursor_tol, instead using the isolation window written in the mzML file.

Changed

• Changed internal calculation of precursor tolerances when searching with isotope_errors. The new version should be more accurate. This change also enables a significant boost to search speed for open searches.

v0.11.2

[0.11.2]

Added

• Add rank & charge features to LDA

Changed

• One-hot encode charge state information for percolator .pin files
• Change PSMId -> SpecId for Mokapot compatibility with .pin files

v0.11.1

[0.11.1]

Added

• Support for additional fragment ion types, via the "database.ion_kinds" configuration option. Valid values are "a", "b", "c", "x", "y", "z"

    "database": {
      "enzyme": {
        "missed_cleavages": 1,
        "min_len": 8,
        "max_len": 30,
        "cleave_at": "KR",
        "restrict": "P"
      },
      "ion_kinds": ["b", "y", "c", "z"],
      "static_mods": {
        "C": 57.0214
      },
      "variable_mods": {
        "M": 15.9949,
        "S": 541.0611
      },
    },

Changed

• Sort protein names alphanumerically for each peptide entry. This should enhance stability across runs, and fixes a bug with picked-protein group FDR
• Fix another bug where picked-FDR approaches assume internal decoy generation

Full Changelog: v0.11.0...v0.11.1

v0.11.0

What's Changed

This is the biggest release yet - major overhaul to LFQ, changes to chimeric searching!
Please note that there are some breaking changes to the quant section of the configuration file format

It is possible that the changelog below (and in CHANGELOG.md) are not completely comprehensive, please open an issue if you discover something.

LFQ actually works pretty well now: 🎯 🚀

Added

• Support for percolator output files (--write-pin CLI flag)
• Support for modifying file batch size (--batch-size N CLI flag)
• Add delta_best feature, which reports the delta hyperscore from the best match to current ranked PSM
• Add Sage version to results.json files

Changed

• Rename "file" to "filename" in quant.tsv by @lgatto in #57
• Breaking changes to quant section of the configuration file format
• Rename delta_hyperscore to delta_next
• Altered internal scoring algorithm. Rather than consider all MS2 peaks within a m/z tolerance window to be matches to a theoretical spectrum, consider only the closest peak. This should increase the accuracy of # of matched peaks, and subsequent scores
• Overhaul of chimeric scoring, report_psms can now be used to search for multiple chimeric spectra
• Completely overhauled the LFQ algorithm: added match-between runs, peak scoring using normalized spectral angle relative to theoretical isotopic envelope, target decoy scoring of MS1 integration
• Fixed bug in picked-peptide FDR that could lead to liberal FDR
• Fixed bug in picked-protein FDR that could lead to conservative FDR
• Fixed bug where using variable protein terminal (e.g. protein N-terminal acetylation) modifications could cause some determinism. This also improves the accuracy of peptide => protein assignment. Unfortunately this fix has performance implications, causing creation of the fragment index to take up to ~2x as long.

Removed

• Remove no-parallel CLI flag, and parallel configuration file entry

Full Changelog: v0.10.0...v0.11.0

v0.10.0

Added

• Retention times are now globally aligned across files
• RT prediction is then performed on all files at once (on aligned RTs), rather than one file at a time - previously, there were many instances where some files in a search could not have RTs predicted, decreasing the effectiveness of delta_rt as a feature for LDA.

Changed

• Peptide sequences within a protein are now deduplicated - previously, repeated peptides would be called multiple times for the same protein (e.g. num_proteins > 1 even if the peptide was unique)

Full Changelog: v0.9.4...v0.10.0

• Global retention time alignment by @lazear in #52

v0.9.4

What's changed

• Fix issues with RT prediction (and occasionally LDA) that arise from 0's being present on the diagonals of the covariance matrix

Full Changelog: v0.9.3...v0.9.4

v0.9.3

What's changed

• Internal code for calculating factorials
• Allow users to set minimum number of matched b+y ions for reporting PSMs

Full Changelog: v0.9.2...v0.9.3

v0.9.2

What's Changed

• Added option for TMT signal/noise quantification, if noise values are present in mzML

Full Changelog: v0.9.1...v0.9.2