Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry.
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.
Meng
Fanyu
F
Molecular Profiling Proteomics, Merck Research Laboratories, Merck and Co. Inc., Rahway, New Jersey 07065, USA.
Wiener
Matthew C
MC
Sachs
Jeffrey R
JR
Burns
Chrissina
C
Verma
Priyanka
P
Paweletz
Cloud P
CP
Mazur
Matthew T
MT
Deyanova
Ekaterina G
EG
Yates
Nathan A
NA
Hendrickson
Ronald C
RC
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
D045424:Complex Mixtures; D010455:Peptides; D011506:Proteins