title: Large-scale quantitative clinical proteomics by label-free liquid chromatography and mass spectrometry.
abstract: We previously reported the development of an integrated proteome platform, namely 2-Dimensional Image Converted Analysis of Liquid chromatography and mass spectrometry (2DICAL), for quantitative comparison of large peptide datasets generated by nano-flow liquid chromatography (LC) and mass spectrometry (MS). The key technology of 2DICAL was the precise adjustment of the retention time of LC by dynamic programming. In order to apply 2DICAL to clinical studies that require comparison of a large number of patient samples we further refined the calculation algorithm and increased the accuracy and speed of the peptide peak alignment using a greedy algorithm, which had been used for fast DNA sequence alignment. The peptide peaks of each sample with the same m/z were extracted every 1 m/z and displayed with along the horizontal axis. Here we report a precise comparison of more than 150,000 typtic peptide ion peaks derived from 70 serum samples (40 patients with uterine endometrial cancer and 30 controls). The levels of 49 MS peaks were found to differ significantly between cancer patients and controls (P < 0.01, Welch's t-test and interquartile range [IQR] of >40), and the differential expression and identification of selected three proteins was validated by immunoblotting. 2DICAL was is highly advantageous for large-scale clinical proteomics because of its simple procedure, high throughput, and quantification accuracy.
authors.affiliation: Chemotherapy Division and Cancer Proteomics Project, National Cancer Center Research Institute, Tokyo, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Negishi
authors.forename: Masaya
authors.initials: M
authors.lastname: Ono
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Handa
authors.forename: Hidenori
authors.initials: H
authors.lastname: Kato
authors.forename: Kohki
authors.initials: K
authors.lastname: Yamashita
authors.forename: Kazufumi
authors.initials: K
authors.lastname: Honda
authors.forename: Miki
authors.initials: M
authors.lastname: Shitashige
authors.forename: Reiko
authors.initials: R
authors.lastname: Satow
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Sakuma
authors.forename: Hideya
authors.initials: H
authors.lastname: Kuwabara
authors.forename: Ken
authors.initials: K
authors.lastname: Omura
authors.forename: Setsuo
authors.initials: S
authors.lastname: Hirohashi
authors.forename: Tesshi
authors.initials: T
authors.lastname: Yamada
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000032:analysis*; D002853:Chromatography, Liquid / Q000379:methods*; D004591:Electrophoresis, Polyacrylamide Gel; D016889:Endometrial Neoplasms / Q000378:metabolism*; D005260:Female; D006801:Humans; D015151:Immunoblotting; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods*
chemical_list: D014408:Biomarkers, Tumor