Sequencing data-encoded peptides from tandem mass spectra

A computer-implemented method for sequencing a data-encoded peptide from an experimental spectrum, raw data of the experimental spectrum being data of a histogram of intensity versus mass/charge ratio as originally obtained in analyzing the data-encoded peptide by mass spectrometry, the method comprising:

• preprocessing the raw data for removing uninterpretable peaks to yield preprocessed data;
• identifying, from a spectrum graph, a first set of one or more candidate sequences contending for a peptide sequence of the peptide, wherein the spectrum graph is formed according to the preprocessed data rather than the raw data for generating a fewer number of candidate sequences to thereby reduce a time cost in sequencing;
• processing the first candidate-sequence set to estimate the peptide sequence;
• after a set of one or more estimates of the peptide sequence is obtained, verifying whether an individual peptide-sequence estimate is invalid;
• and
• purging the set of one or more estimates of the peptide sequence to remove any peptide-sequence estimate found to be invalid;
• wherein the preprocessing of the raw data to yield the preprocessed data comprises:
• dividing a set of mass/charge ratios of the raw data into a plurality of subsets such that an individual subset consists of mass/charge ratios of isotopes of a fragment of the data-encoded peptide, an individual mass/charge ratio having a signal peak in the experimental spectrum, the isotopes of the fragment having a same charge of positive integer value;
• computing a monoisotopic mass of the fragment for the individual subset;
• computing an intensity of the fragment according to the raw data and the mass/charge ratios in the individual subset;
• and
• generating the preprocessed data, wherein:
• the preprocessed data includes a plurality of masses and a plurality of intensities, wherein the plurality of masses is formed with the monoisotopic mass of the fragment for the individual subset, and wherein an individual mass is associated with a corresponding intensity;
• and
• the preprocessed data further includes a first mass set of putative b-ions and a second mass set of putative y-ions for the experimental spectrum, wherein the first and second mass sets are generated by distributing respective masses in the plurality of masses into the first and second mass sets;
• and
• wherein the identifying of the first candidate-sequence set from the spectrum graph comprises the steps of:
• (a) sorting the plurality of masses in a descending order of corresponding intensities of respective masses to thereby form an ordered sequence of masses, wherein the ordered sequence of masses ranks the plurality of masses with a highest-ranking mass being associated with a highest corresponding intensity;
• (b) given a selected mass and a selected number of higher-ranking masses in the ordered sequence of masses, identifying one or more highest-intensity-based tags in the spectrum graph, wherein an individual highest-intensity-based tag is a partial sequence consisting of a first amino acid having the selected mass and a plurality of remaining amino acids each having a mass selected from the selected number of higher-ranking masses;
• (c) processing the one or more highest-intensity-based tags, wherein processing the individual highest-intensity-based tag comprises:
• determining a prefix and a suffix for the individual highest-intensity-based tag;
• if the prefix and suffix are successfully determined, then combining the prefix, the individual highest-intensity-based tag and the suffix to form a new candidate sequence;
• and
• allocating the new candidate sequence to the first candidate-sequence set;
• (d) sequentially using successive values in a strictly decreasing sequence of values as the selected number of higher-ranking masses to repeat the steps (b) and (c) until the first candidate-sequence set is not empty or the strictly decreasing sequence is exhausted;
• and
• (e) starting from the highest-ranking mass, sequentially using successive masses in the ordered sequence of masses as the selected mass to repeat the steps (b)-(d) until the first candidate-sequence set is not empty or a preselected number of higher-ranking masses in the ordered sequence of masses is reached.