期刊
JOURNAL OF PROTEOME RESEARCH
卷 8, 期 3, 页码 1347-1357出版社
AMER CHEMICAL SOC
DOI: 10.1021/pr800720d
关键词
Top-down; bottom-up; proteomics; intact proteins; HPLC; tandem MS; mass spectrometry; FTICR; RPLC
资金
- National Center for Research Resources [RR 018522]
- National Institute of Allergy and Infectious Diseases [YI-AI-4894-01]
- National Institute of General Medical Sciences [1101 GM063883]
- U.S. Department of Energy (DOE) Office of Biological and Environmental Research
We present an integrated top-down and bottom-up approach that is facilitated by concurrent liquid chromatography-mass spectrometry (LC-MS) analysis and fraction collection for comprehensive high-throughput intact protein profiling. The approach employs high-resolution, reversed-phase (RP) LC separations coupled on-line with a 12 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer to profile and tentatively identify modified proteins, using detected intact protein masses in conjunction with bare protein identifications from the bottom-up analysis of the corresponding LC fractions. Selected identifications are incorporated into a target ion list for subsequent off-line gas-phase fragmentation that uses an aliquot of the original fraction used for bottom-up analysis. In a proof-of-principle demonstration, this comprehensive strategy was applied to identify protein isoforms arising from various amino acid modifications (e.g., acetylation, phosphorylation) and genetic variants (e.g., single nucleotide polymorphisms, SNPs). This strategy overcomes major limitations of traditional bottom-up (e.g., inability to characterize multiple unexpected protein isoforms and genetic variants) and top-down (e.g., low throughput) approaches.
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