Methods for determining protein and peptide terminal sequences
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Abstract
Methods and apparatuses for deriving the sequence of an oligomer. In one exemplary method for deriving the sequence of a polypeptide, a predetermined set of mass/charge values for amino acid sequences is stored. An abundance value from mass spectrum data for each mass/charge value in the predetermined set is determined to produce a plurality of abundance values. A first ranking, based on the plurality of abundance values, is calculated for each sequence of a set of amino acid sequences having a first number of amino acids. A second ranking, based on the plurality of abundance values, for each sequence of a set of amino acid sequences having a second number of amino acids is calculated. A cumulative ranking, based on the first ranking and the second ranking, is calculated for each sequence of a set of amino acid sequences having at least the second number of amino acids.
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Citations
136 Claims
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1-114. -114. (canceled)
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115. A machine implemented method for deriving a relative ranking for a subject peptide sequence of length i, said method comprising the steps of:
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(i) generating a mass spectrum data of a protein or protein fragment;
(ii) calculating a first set of m/z values for a first peptide sequence of length i and storing said first set of m/z values in a memory system of the machine;
(iii) determining a first abundance value for said first peptide sequence using said first set of m/z values and said mass spectrum data, and erasing said first set of m/z values in said memory system;
(iv) calculating a second set of m/z values for a second peptide sequence of length i and storing said second set of m/z values in said memory system;
(v) determining a second abundance value for said second peptide sequence using the second set of m/z values and said mass spectrum data;
(vi) mathematically combining the first abundance value and the second abundance value thereby forming an abundance combination for said first and second peptide sequences, and erasing said second set of m/z values in said memory system;
(vii) iterating steps (iv) to (vi) for a plurality of peptide sequences of length i thereby accumulating an abundance combination for a plurality of peptide sequences of length i;
(viii) calculating a normalization parameter based on said abundance combination for said plurality of peptide sequences of length i;
(ix) calculating a subject set of m/z values for a subject peptide sequence of length i and storing said subject set of m/z values in said memory system;
(x) deriving a relative ranking for said subject peptide sequence based on the normalization parameter from step (viii), said subject set of m/z values, and said mass spectrum data, and erasing said subject set of m/z values in said memory system. - View Dependent Claims (116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136)
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Specification