Systems and methods for identifying peptides by sampling and filtering

A system for identifying a peptide for a query spectrum, the system comprising a non-transitory computer readable medium and a processor, the processor operable to:

• generate the query spectrum with a mass spectrometer;
• receive one or more parameters of a query spectrum;
• generate one or more candidate peptide sequences based on the one or more parameters of the query spectrum;
• generate a plurality of samples of the query spectrum;
• select at least one sample from the plurality of samples for comparison with the one or more candidate peptide sequences;
• determine a likelihood indicator for each of the one or more candidate peptide sequences based on a comparison with the at least one sample;
• apply a signal to noise filter to the one or more candidate peptide sequences, wherein the signal to noise filter is configured to:
• (i) determine an observation frequency of each candidate peptide sequence in real data;
• (ii) determine an expected observation frequency of each candidate peptide sequence in noise or random MS/MS spectra;
• and
• (iii) apply a Chi Square test to compare the observation frequency in the real data to the expected frequency in noise or random spectra, and filter the candidate peptide sequences based on the result of the Chi Square test;
• wherein the candidate peptide sequences are selected from a library of known peptide sequences;
• and
• select at least one candidate peptide sequence as a proposed peptide sequence for the query spectrum based on the filtered candidate peptide sequences.