ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and protein sequence databases has been developed. This algorithm uses a three tier scoring scheme. First, a binomial probability is used as a preliminary scoring scheme to select candidate peptides. The binomial probability scores generated by ProLuCID minimize molecular weight bias and are independent of database size. A modified cross-correlation score is calculated for each candidate peptide identified by the binomial probability. This cross-correlation scoring function models the isotopic distributions of fragment ions of candidate peptides which ultimately results in higher sensitivity and specificity than that obtained…

• NI
  National Institutes of Health

  Awards: R01 MH067880, 5R01 HL079442-04, 5U01 DE016267-04, P41 GM103533
• NH
  National Heart, Lung, and Blood Institute

  Award: HHSN268201000035C