xcorrrs

Standalone Rust implementation of Comet's XCorr based on

• Eng JK, McCormack AL, Yates JR.
  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
  J Am Soc Mass Spectrom.
  1994;5(11):976-989.
  doi:10.1016/1044-0305(94)80016-2

• Eng JK, Fischer B, Grossmann J, Maccoss MJ.
  A fast SEQUEST cross correlation algorithm.
  J Proteome Res.
  2008;7(10):4598-4602.
  doi:10.1021/pr800420s

This implementation computes an XCorr value closely aligned with the original Comet algorithm. The generation of theoretical fragments relies on the rustyms/rusteomics-mzcore library, enabling full ProForma support. As a result, there may be subtle differences in theoretical fragment calculation compared to Comet's approach, resulting in slightly differences in the Xcorr.

Tests

For each PSM in test_files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.tsv the matched peptide is converted to a Proforma String, including PSMs, and matched against the spectrum from the MS run using the xcorr reimplementation. The root means squared error is than calulated on Comet's reported xcorr and the results of the reimplementation (scaled by the highest Xcorr of both implementations). Accepted is a RMSE below 0.0002.

Test prints

I you want some TSV and correlation plots printed start the test with env VERBOSE=1 cargo test ...

Data

Test data is taken from PXD028735 (LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw), converted to mzML using msconvert (3.0.24155, vendor peak picking) and identified with Comet 2025.01 using the protoeme UP000005640 (including isoforms, downloaded at 2024-05-08, compressed version at test_files/2024-05-08_UP000005640_isoforms.fasta.gz). Comet parameter file was mostly unchanged except for the MS and output paramters (test_files/comet.params).
Due to the size of the mzML and GitHub file limits, the data array of the identified spectra were extracted and saved as parquet files without metadata to be used in tests.

Acknowledgement and thanks

• Jimmy Eng - Provided test data and insight into Comet's Xcorr and helped debugging details