specollate 1.0.0

Spectra collation and search utilities (SpeCollate)

SpeCollate: MS/MS Database Search Pipeline

Install:

pip install specollate

Quick usage:

from specollate import SpeCollateSearch

searcher = SpeCollateSearch(device='cuda')  # or 'cpu'
results = searcher.search(
    mgf_dir='path/to/mgf_dir',
    peptide_db='path/to/peptide_db',
    output_dir='./specollate_output'
)

print('Target PIN:', results['target_pin'])
print('Decoy PIN:', results['decoy_pin'])

Sample search:

from specollate import SpeCollateSearch

searcher = SpeCollateSearch(device='cuda')  # or 'cpu'
results = searcher.search_with_sample_data(output_dir='./specollate_output')

print('Target PIN:', results['target_pin'])
print('Decoy PIN:', results['decoy_pin'])

Citation:

Tariq MU, Saeed F. SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions. PLoS One. 2021 Oct 29;16(10):e0259349. doi: 10.1371/journal.pone.0259349. PMID: 34714871; PMCID: PMC8555789.