title: Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry.
abstract: Label-free LC-MS profiling is a powerful quantitative proteomic method to study relative peptide abundances between two or more biological samples. Here we demonstrate the use of a previously described comparative LC-MS method, differential mass spectrometry (dMS), to analyze high-resolution Fourier transform mass spectrometry (FTMS) data for detection and quantification of known peptide differences between two sets of complex mixtures. Six standard peptides were spiked into a processed plasma background at fixed ratios from 1.25:1 to 4:1 to make two sets of samples. The resulting mixtures were analyzed by microcapillary LC-FTMS and dMS. dMS successfully identified five out of the six peptides as statistically significant differences (p <or= 0.005). In this experiment, the smallest fold change reliably detected by our method was 1.5:1, and the errors of estimated ratios of concentrations were less than 20% for peptides spiked at 1.5:1 to 4:1. We conclude that LC-FTMS coupled with dMS is a useful label-free quantitative MS method that can be used to detect subtle yet statistically significant peptide differences in complex protein mixtures, including plasma samples.
authors.affiliation: Molecular Profiling Proteomics, Merck Research Laboratories, Merck and Co. Inc., Rahway, New Jersey 07065, USA.
authors.forename: Fanyu
authors.initials: F
authors.lastname: Meng
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Wiener
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Sachs
authors.forename: Chrissina
authors.initials: C
authors.lastname: Burns
authors.forename: Priyanka
authors.initials: P
authors.lastname: Verma
authors.forename: Cloud P
authors.initials: CP
authors.lastname: Paweletz
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Mazur
authors.forename: Ekaterina G
authors.initials: EG
authors.lastname: Deyanova
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Yates
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Hendrickson
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D002851:Chromatography, High Pressure Liquid; D045424:Complex Mixtures / Q000737:chemistry*; D006801:Humans; D008969:Molecular Sequence Data; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D051381:Rats; D015203:Reproducibility of Results; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D045424:Complex Mixtures; D010455:Peptides; D011506:Proteins