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Extend support for timsTOF instruments #122

Merged
merged 71 commits into from
Mar 22, 2024
Merged

Extend support for timsTOF instruments #122

merged 71 commits into from
Mar 22, 2024

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RalfG
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@RalfG RalfG commented Feb 21, 2024 •
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Added

  • New feature generator: IM2Deep modification-aware CCS prediction

Changed

  • Improved parsing from RT and IM from spectrum file if needed (moved out of feature generators)
  • Pass PSMList directly to DeepLC instead of using PEPREC DataFrame.
  • Use indexed mzML and MGF implementations from Pyteomics for faster parsing of RT and IM
  • Log warning if not sufficient PSMs were found for DeepLC retraining
  • Improve procedure for getting calibration PSMs (currently for DeepLC and IM2Deep)

Fixed

  • Also try parsing IM from mzML from precursorList > precursor > selectedIonList > selectedIon > inverse reduced ion mobility (previously only scanList > scan > reverse ion mobility)

ArthurDeclercq and others added 30 commits November 22, 2023 14:04
@ArthurDeclercq
parsing from spectrum id
50aff5e
@ArthurDeclercq
change regex function used
dcfcc00
@ArthurDeclercq
fix unboundLocalError
25aa0ea
@ArthurDeclercq
add regex patterns for im and rt parsing from spectrum id
0e2b192
@rodvrees
im2deep
b45007f
@ArthurDeclercq
add debug statement for im, rt parsing
112860c
@rodvrees
Merge remote-tracking branch 'origin/timsRescore' into timsRescore
0330096
@rodvrees
models + debug
f6c9564
@rodvrees
fix
7585d51
@rodvrees
add models
a0f792f
@rodvrees
fixes in im2deep.py
b4660fd
@rodvrees
fixes in im2deep.py
1a18a42
@rodvrees
im2deep implementation
b93df98
@ArthurDeclercq
remove peprec implementation deeplc
8749ddf
@rodvrees
CCS shift calculation fix
782c7a0
@rodvrees
models + plot
7604153
@ArthurDeclercq
add inverse reduced ion mobility key to mzml parsing
b2d65eb
@ArthurDeclercq
Merge branch 'compomics:timsRescore' into timsRescore
aa9cde0
@ArthurDeclercq
remove print statements
230753c
@ArthurDeclercq
updated inverse reduced ion mobility
d9f9feb
@ArthurDeclercq
Merge branch 'compomics:timsRescore' into timsRescore
6ccb429
@ArthurDeclercq
add unused argument
00d6704
@ArthurDeclercq
skip ms1 scans in mzml
50a01e9
@ArthurDeclercq
Merge branch 'compomics:timsRescore' into timsRescore
2645378
@rodvrees
IM2Deep plot correct labels
a99b492
@rodvrees
calibrate per charge option
1f6e973
@rodvrees
Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into tim…
301d632 
…sRescore
@rodvrees
new models and reference
dd8bd18
@rodvrees
correct format reference
ad0f3d7
@rodvrees
fix model name in IM2Deep
3a5b1ab
rodvrees and others added 23 commits February 2, 2024 13:43
@rodvrees
Implement IM2Deep package
65f134c
@rodvrees
Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into tim…
e1f0ddf 
…sRescore
@ArthurDeclercq
GUI changes im2deep
a9fc45f
@ArthurDeclercq
add im2deep to pyproject
fa97517
@ArthurDeclercq
change dockerfile
a4fd01a
@ArthurDeclercq
optimise spectrum parsing
721cd08
@ArthurDeclercq
update toml file
ceed348
@ArthurDeclercq
added debug logging
fcd393c
@ArthurDeclercq
requested changes
3fc994f
@ArthurDeclercq
change numpy version upper limit
42debd8
@ArthurDeclercq
fix bug
c0713ed
@RalfG
Use newer setup-python action; revert numpy upper limit
fcf579d
@RalfG
Fix numpy version for py311
48fae0e
@RalfG
Update pyproject.toml
9063a84 
Use semi-colon instead of comma's in dependencies
@ArthurDeclercq
requested changes
7ede2f8
@RalfG
Update ms2rescore/feature_generators/im2deep.py
b2a126a
@ArthurDeclercq @rodvrees @RalfG
Add IM2Deep feature generator (#121)
667822e 
* im2deep

* models + debug

* fix

* add models

* fixes in im2deep.py

* fixes in im2deep.py

* im2deep implementation

* CCS shift calculation fix

* models + plot

* add unused argument

* IM2Deep plot correct labels

* calibrate per charge option

* new models and reference

* correct format reference

* fix model name in IM2Deep

* change use of reference dataset

* IM2Deep calibrate correctly

* Implement IM2Deep package

* GUI changes im2deep

* add im2deep to pyproject

* change dockerfile

* optimise spectrum parsing

* update toml file

* added debug logging

* requested changes

* change numpy version upper limit

* fix bug

* Use newer setup-python action; revert numpy upper limit

* Fix numpy version for py311

* Update pyproject.toml

Use semi-colon instead of comma's in dependencies

* requested changes

* Update ms2rescore/feature_generators/im2deep.py

---------

Co-authored-by: rodvrees <[email protected]>
Co-authored-by: rodvrees <[email protected]>
Co-authored-by: rodvrees <[email protected]>
Co-authored-by: RalfG <[email protected]>
@RalfG
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore …
ee36b09 
…into timsRescore
@RalfG
Remove unused code; import im2ccs from im2deep package; use im2ccs ve…
e5b7b87 
…ctorized
@RalfG
Remove unused code and imports; Replace pandas apply with vectorized …
82e7789 
…usage;
@RalfG
Formatting
d158a86
@RalfG
Fix config descriptions for psm_id_im_pattern and psm_id_rt_pattern
a4f198a
@RalfG
Check with Ruff on test (also disallow print statements)
86363ee
@ArthurDeclercq ArthurDeclercq merged commit ff81bd9 into main Mar 22, 2024
5 checks passed
@RalfG RalfG added this to the v3.1.0 milestone Sep 19, 2024
This was referenced Sep 19, 2024
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@RalfG @ArthurDeclercq @rodvrees