Skip to content

Keep track of spectrum nativeIDs, rather than scan number #28

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
Merged
merged 10 commits into from
Nov 2, 2022
Merged

Keep track of spectrum nativeIDs, rather than scan number #28

merged 10 commits into from
Nov 2, 2022

Conversation

@lazear
Copy link
Owner

@lazear lazear commented Oct 31, 2022

This is a more correct thing to do - mzML files are not guaranteed to have a "scan=(\d)" part in the spectrum id field

Breaking changes:

  • Add a rank column to output file
  • Rename discriminant_score to sage_discriminant_score
  • Use base proforma notation for peptide mods, i.e. "[+304.2071]-PEPTIDEM[+15.9949]AAC[+57.0214]H"
  • Replace scannr with nativeID, i.e. "controllerType=0 controllerNumber=1 scan=30069"

@lazear
Copy link
Owner Author

lazear commented Nov 1, 2022

Breaking changes:

  • Change decoy_prefix to decoy_tag, which can occur anywhere inside the accession, e.g. "sp|P01234_REVERSED|HUMAN"
  • Add a database.generate_decoys parameter, which turns off internal decoy generation - allows the use of SearchGui/PeptideShaker databases

@lazear
Copy link
Owner Author

lazear commented Nov 1, 2022

Breaking changes:

  • Rename results.pin to results.sage.tsv
  • Rename quant.csv to quant.tsv
  • Rename "pin_paths" to "output_paths" in results.json

lazear added 9 commits November 1, 2022 17:06
@lazear
Use spectrum id instead of extracting scan number
3ed8012
@lazear
Write psm Rank column
2eb7af8
@lazear
Rename discriminant_score column to sage_discriminant_score (#27)
576af22
@lazear
Use base proforma notation for peptide mods
b67703f
@lazear
Clippy lints, remove commented out scan number regex
0b5f578
@lazear
Breaking changes to decoy configuration parameters
f91c629 
- Change `decoy_prefix` to `decoy_tag`, which can occur anywhere inside the accession, e.g. "sp|P01234_REVERSED|HUMAN"
- Add a `database.generate_decoys` parameter, which turns off internal decoy generation - allows the use of SearchGui/PeptideShaker databases
@lazear
Update README.md with information about decoys
ae67898
@lazear
Rename output files, paths
0eecee4 
**Breaking changes**:

- Rename results.pin to results.sage.tsv
- Rename quant.csv to quant.tsv
- Rename "pin_paths" to "output_paths" in results.json
@lazear
Add changelog
db6886b
@lazear lazear merged commit 308364f into master Nov 2, 2022
@lazear lazear deleted the spectrum_id branch November 2, 2022 02:27
grosenberger-bruker pushed a commit to grosenberger-bruker/sage that referenced this pull request May 9, 2025
@vijay-gnanasambandan-bruker
Merge pull request lazear#28 from BrukerLSMS/public_master
2b60af9 
Public sage master sync
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.

2 participants

@lazear