Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation. We describe a composite method of utilizing MS data to assign accurate monoisotopic masses to MS/MS spectra, including those subject to cofragmentation. The method, "multiplexed post-experiment monoisotopic mass refinement" (mPE-MMR), consists of the following: multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra, multiplexing of charge states to assign correct charges to the precursor ions of MS/ MS spectra with no charge information, and mass correction for inaccurate monoisotopic peak picking. When combined with MS-GF+, a database search algorithm based on fragment mass difference, mPE-MMR effectively increases both sensitivity and accuracy in peptide identification from complex high-throughput proteomics data compared to conventional methods.
Bibliographical noteFunding Information:
This work was supported by the Multiomics Research Program (NRF-2012M3A9B9036675), the Brain Research Program (NRF-2014M3C7A1046047), and the International Research and Development Program (NRF-2015K1A3A1A21000273) funded by the Korean Ministry of Science, ICT & Future Planning. Efforts at Pacific Northwest National Laboratory were supported by grants from the National Institute of General Medical Sciences (P41 GM103493) and the U.S. Department of Energy Office of Biological and Environmental Research Genome Sciences Program under the Panomics Program.
© 2016 American Chemical Society.
ASJC Scopus subject areas
- Analytical Chemistry