Open AccessQuantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry
Author(s) -
Fanyu Meng,
Matthew C. Wiener,
Jeffrey R. Sachs,
Chrissina Burns,
Priyanka Verma,
Cloud P. Paweletz,
Matthew T. Mazur,
Ekaterina G. Deyanova,
Nathan A. Yates,
Ronald C. Hendrickson
Publication year - 2007
Publication title -
journal of the american society for mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.961
H-Index - 127
eISSN - 1879-1123
pISSN - 1044-0305
DOI - 10.1016/j.jasms.2006.09.014
Subject(s) - chemistry , mass spectrometry , chromatography , peptide , analytical chemistry (journal) , resolution (logic) , fourier transform ion cyclotron resonance , quantitative analysis (chemistry) , tandem mass spectrometry , biochemistry , artificial intelligence , computer science
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.