crux diameter [options] <tide spectra file> <tide database>


DIAmeter detects peptides from data-independent acquisition mass spectrometry data without requiring a spectral library. The input includes centroided DIA data and a proteome FASTA database. DIAmeter then searches the DIA data using Tide, allowing multiple peptide-spectrum matches (PSMs) per DIA spectrum. A subset of these PSMs are selected for further analysis, using a greedy bipartite graph matching algorithm. Finally, PSMs are augmented and filtered with auxiliary features describing various types of evidence supporting the detection of the associated peptide. The PSM feature vectors, the output of DIAmeter, should be processed subsequently by Percolator to induce a ranking on peptides. Percolator will assign each peptide a statistical confidence estimate, where highly ranked peptides are detected in the DIA data with stronger confidence. Further details are provided here:

YY Lu, J Bilmes, RA Rodriguez-Mias, J Villen, and WS Noble. "DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data". Bioinformatics. 37(Supplement_1):i434–i442, 2021.

DIAmeter performs several intermediate steps, as follows:

  1. If a FASTA file was provided, convert it to an index using tide-index. Otherwise, use the given Tide index.
  2. Convert the given fragmentation spectra to a binary format.
  3. Search the spectra against the database and extract the auxiliary features.
  4. Store the results in Percolator input (PIN) format.
  5. Run the PIN file through Percolator.



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: