Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add suppot for crosslinking mass spectrometry experiments #28

Open
wants to merge 19 commits into
base: main
Choose a base branch
from
Open

Add suppot for crosslinking mass spectrometry experiments #28

wants to merge 19 commits into from

Conversation

wfondrie
Copy link
Owner

In crosslinking mass spectrometry experiments, we try to detect two peptides that are covalently linked from a single MS2 spectrum. Because the pairs can take various forms (target-target, target-decoy, decoy-decoy), a different approach to estimating FDR is needed.

This PR implements the approach from Walzthoeni et al by adding the CrosslinkPsmDataset and CrosslinkConfidence classes to mokapot!

There's still a bit to do:

  • Finish building out the unit and system tests
  • Update the documentation

@wfondrie
Added CrosslinkPsmDataset
d130153
@wfondrie
Crosslink confidence estimation should work except for protein pairs.
96f7f54
@wfondrie
Picked protein approach for cross-links is almost done.
b4cecbc
@wfondrie
Draft of cross-linked picked protein finished
9c57655
@wfondrie
Fixed SettingWithCopy warning
6f2c66b
@wfondrie
Working on a cursory level. Seems to be some TDC error
b93cb75
@wfondrie
Cross-linking seems to be working
0944571
@wfondrie
Merged in 0.6.0 master
483f660
@wfondrie
Started adding xlms support to the pepXML parser.
2a0525f
@wfondrie
Merged in 0.7.1
ef72738
@wfondrie
Fixed linting
be5c225
@wfondrie
Removed print statements
5af3fd7
@wfondrie
PepXML parser almost ready for CSMs
316862e
@wfondrie
Ready to add tests
4d220d6
@wfondrie
Added crosslink_tdc tests
d2b98ff
@wfondrie
Added tests for crosslinking results to the PepXML parser
171a7ad
@wfondrie
Fixed linting
ac3c515
@wfondrie
Added CrosslinkPsmDataset tests
6cb0226
@wfondrie
Faster q-value calculation
fc486f5
sambenfredj referenced this pull request in msaid-de/mokapot Apr 12, 2023
@sambenfredj
Merge branch 'feature/optimize_peps_and_qvals_calculation' into 'deve…
205479d 
…lop'

Optimize peps and qvals

Closes #31 and #28

See merge request msaid/chimerys/mokapot!28
jspaezp pushed a commit to jspaezp/mokapot that referenced this pull request Jun 21, 2024
@sambenfredj
Fix cli tests: (wfondrie#28)
c5d158a 
- Remove test_cli_pepxml because xml files don't work with streaming
- Replace old output file names
- Add random generator 'rng' variable to confidence since it is required for proteins
- Remove subset_max_train from PluginModel
- Fix bug: convert targets column after reading in chunks
- Fix peptide column name for confidence
- Fix test cli plugins : replace DecisionTreeClassifier with LinearSVC BECAUSE DecisionTreeClassifier return scores as 0 or 1
jspaezp pushed a commit to jspaezp/mokapot that referenced this pull request Jun 21, 2024
@sambenfredj @gessulat
Fix cli tests: (wfondrie#28)
2e1723e 
- Remove test_cli_pepxml because xml files don't work with streaming
- Replace old output file names
- Add random generator 'rng' variable to confidence since it is required for proteins
- Remove subset_max_train from PluginModel
- Fix bug: convert targets column after reading in chunks
- Fix peptide column name for confidence
- Fix test cli plugins : replace DecisionTreeClassifier with LinearSVC BECAUSE DecisionTreeClassifier return scores as 0 or 1
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
1 participant
@wfondrie