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base repository: lazear/sage
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base: v0.14.5
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head repository: lazear/sage
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compare: master
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9 contributors

Commits on Dec 6, 2023

  1. Update README.md

    @lazear
    lazear authored Dec 6, 2023
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Commits on Jan 3, 2024

  1. feat: add MGF reader

    @yujinjeong2 @lazear
    yujinjeong2 authored and lazear committed Jan 3, 2024
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  2. chore: lints, formatting, touch up mgf charge regex

    @lazear
    lazear committed Jan 3, 2024
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Commits on Jan 4, 2024

  1. Fix link to Picked group FDR in README.md

    @MatthewThe @lazear
    MatthewThe authored and lazear committed Jan 4, 2024
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Commits on Feb 3, 2024

  1. feat: ion mobility model 

    added mobility to outputs and model details

simplified model

removed redundant logging

changed feature engineering

removed old comments

removed resolved comment
    @jspaezp @lazear
    jspaezp authored and lazear committed Feb 3, 2024
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  2. chore: release v0.14.6 

    - add ion mobility to parquet outputs
- update changelog
- cargo fmt
    @lazear
    lazear committed Feb 3, 2024
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Commits on Feb 7, 2024

  1. fix

    @jspaezp @lazear
    jspaezp authored and lazear committed Feb 7, 2024
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  2. added test

    @jspaezp @lazear
    jspaezp authored and lazear committed Feb 7, 2024
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Commits on Mar 8, 2024

  1. fix: add missing parquet columns (#118)

    @lazear
    lazear committed Mar 8, 2024
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  2. chore: update deps

    @lazear
    lazear committed Mar 8, 2024
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Commits on Mar 15, 2024

  1. fix: mgf paths were being lowercased (#124)

    @lazear
    lazear committed Mar 15, 2024
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  2. chore: release v0.14.7

    @lazear
    lazear committed Mar 15, 2024
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Commits on Apr 15, 2024

  1. Update timsrust; use spectrum index instead of precursor index as spe… 

    …ctrum id
    @RalfG @lazear
    RalfG authored and lazear committed Apr 15, 2024
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Commits on May 1, 2024

  1. fix: don't deisotope reporter ion region if MS2-TMT is used (#82)

    @lazear
    lazear committed May 1, 2024
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Commits on Jul 9, 2024

  1. FEAT: update to timsrust 0.3.0

    @sander-willems-bruker @lazear
    sander-willems-bruker authored and lazear committed Jul 9, 2024
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Commits on Jul 25, 2024

  1. chore: update lock file, fix some lints (#145)

    @lazear
    lazear committed Jul 25, 2024
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  2. fix: improve accuracy of preliminary score estimation 

    - Remove fragment_min/max_mz parameters
- Adjust ppm tolerance during preliminary search to account for charge
    @lazear
    lazear committed Jul 25, 2024
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  3. feat: add link to mzIdentML converter (#130)

    @lazear
    lazear committed Jul 25, 2024
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  4. feat: report non-absoluted precursor mass error (#132)

    @lazear
    lazear committed Jul 25, 2024
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  5. feat: add override_precursor_charge setting (#137)

    @lazear
    lazear committed Jul 25, 2024
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  6. feat: enforce variable modifications as a list of values

    @lazear
    lazear committed Jul 25, 2024
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Commits on Jul 30, 2024

  1. fix: bug in MS1 picked-precursor FDR (#150)

    @lazear
    lazear committed Jul 30, 2024
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Commits on Sep 10, 2024

  1. FEAT: updated to timsrust 0.4.0

    @sander-willems-bruker @lazear
    sander-willems-bruker authored and lazear committed Sep 10, 2024
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  2. CHORE: moved spectrum reader config serialization to timsrust

    @sander-willems-bruker @lazear
    sander-willems-bruker authored and lazear committed Sep 10, 2024
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  3. CHORE: simplified bruker spectrum reader config

    @sander-willems-bruker @lazear
    sander-willems-bruker authored and lazear committed Sep 10, 2024
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Commits on Oct 17, 2024

  1. adding option to choose OpenMSHyperscore instead of SageHyperscore

    @theGreatHerrLebert @lazear
    theGreatHerrLebert authored and lazear committed Oct 17, 2024
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  2. adding hyper score to cmd arguments

    @theGreatHerrLebert @lazear
    theGreatHerrLebert authored and lazear committed Oct 17, 2024
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  3. impl update for feature score type

    @theGreatHerrLebert @lazear
    theGreatHerrLebert authored and lazear committed Oct 17, 2024
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  4. removed match statement from hyperscore cal

    @theGreatHerrLebert @lazear
    theGreatHerrLebert authored and lazear committed Oct 17, 2024
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Commits on Oct 30, 2024

  1. adding reference to i2MassChroQ

    @OlivierLangella @lazear
    OlivierLangella authored and lazear committed Oct 30, 2024
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Commits on Nov 3, 2024

  1. docs: remove mention of deleted parameters

    @jspaezp @lazear
    jspaezp authored and lazear committed Nov 3, 2024
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Commits on Nov 26, 2024

  1. Update README.md 

    Added more tools that support sage
    @douweschulte @lazear
    douweschulte authored and lazear committed Nov 26, 2024
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Commits on Dec 14, 2024

  1. refactor(cli): initial branch commit

    @jspaezp @lazear
    jspaezp authored and lazear committed Dec 14, 2024
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  2. (refactor) moved format reader dispatch

    @jspaezp @lazear
    jspaezp authored and lazear committed Dec 14, 2024
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Commits on Feb 13, 2025

  1. feat: database splitting 

    FEAT: added option to iterate over fasta chunks

FEAT: Added cloning to Search and QuantSettings

CHORE: made reordering of target_decoys a seperate function outside of digest

CHORE: implemented build db from peptide list

FIX: reorder_peptide function return

FIX: ambiguous target/decoy peptides are now always target

FEAT: added fasta chunking params to db

CHORE: refactored process_chunk from runner

FEAT: added defaultto IndexedDatabase

FEAT: added quick_score option to quickly filter peptides

FEAT: added parsing of the prefilter fasta by chunk parameters

FEAT: added extra low memory option

FEAT: using heap to retain best scores in low_mem mode

FIX: merge issues

FEAT: auto calculate prefilter chunk size

chore: linearize history via rebase
    @sander-willems-bruker @lazear
    sander-willems-bruker authored and lazear committed Feb 13, 2025
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  2. fix: unresolved imports

    @lazear
    lazear committed Feb 13, 2025
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23 changes: 22 additions & 1 deletion CHANGELOG.md
View file
Original file line number Diff line number Diff line change
@@ -4,6 +4,27 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [v0.15.0-alpha] (unreleased)
### Added
- Initial support for searching diaPASEF data
- `override_precursor_charge` setting that forces multiple charge states to be searched
### Breaking Changes
- `precursor_ppm` field reports the non-absoluted average mass error, rather than the absoluted average mass error.
- Don't deisotope reporter ion regions if MS2-based TMT/iTRAQ is used
- Removed `fragment_min_mz` and `fragment_max_mz` parameters. These were decreasing the accuracy of preliminary scoring estimation when attempting to annotate multiply-charged, high-m/z ions.

## [v0.14.7]
### Added
- Added columns missing from parquet output: `semi_enzymatic` and `missed_cleavages`
### Changed
- Fixed ion mobility parsing from some mzMLs
- MGF paths were being lowercased prior to parsing

## [v0.14.6]
### Added
- Support for MGF files
- Support for writing ion mobility measurements to output files: `ion_mobility`, `predicted_mobility`, `delta_mobility` added to primary tsv and parquet reports. Ion mobility is predicted in a similar manner to RT, using a linear model trained on the data from the search.

## [v0.14.5]
### Added
- Support for semi-enzymatic digests (`database.enzyme.semi_enzymatic` parameter)
@@ -232,4 +253,4 @@ Either a single floating point number (-18.0) or a list of floating point number
### Added
- Retention time prediction
- Ability to filter low-number b/y-ions for faster preliminary scoring (`database.min_ion_index` option)
- Ability to toggle retention time prediction (`predict_rt`)
- Ability to toggle retention time prediction (`predict_rt`)
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