Computational protocol: Leucine-rich alpha-2-glycoprotein-1 is upregulated in sera and tumors of ovarian cancer patients

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Protocol publication

[…] MS/MS samples were analyzed using SEQUEST (ThermoFinnigan, San Jose, CA) and X! Tandem http://www.thegpm.org. The search was done using an NCBI reference sequence of the Homo sapiens database (Oct, 2007; 33029 entries including known contaminants). The search parameters were carbamidomethyl-cysteine and oxidized methionine with 2 trypsin miscleavages. Scaffold (version Scaffold-01_05_14, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identification. Protein probabilities were assigned by the Protein Prophet algorithm []. Proteins of interest with fewer than three peptides for ID were verified using manual inspection of product ion spectra in relation to candidate peptide sequences. Peptide candidates were judged as correct if a continuous series of a minimum of four b-or y-type product ions were present, if all product ion peaks were at least 3 times the intensity of background and if all experimental fragment ions could be matched to theoretical fragment ions. […]

Pipeline specifications

Software tools Comet, X! Tandem
Application MS-based untargeted proteomics
Organisms Homo sapiens
Diseases Ovarian Neoplasms