TY - JOUR
T1 - Multiplexed post-experimental monoisotopic mass refinement (mPE-MMR) to increase sensitivity and accuracy in peptide identifications from tandem mass spectra of cofragmentation
AU - Madar, Inamul Hasan
AU - Ko, Seung Ik
AU - Kim, Hokeun
AU - Mun, Dong Gi
AU - Kim, Sangtae
AU - Smith, Richard D.
AU - Lee, Sang Won
N1 - Funding 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.
Publisher Copyright:
© 2016 American Chemical Society.
PY - 2017/1/17
Y1 - 2017/1/17
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85035116865&partnerID=8YFLogxK
U2 - 10.1021/acs.analchem.6b03874
DO - 10.1021/acs.analchem.6b03874
M3 - Article
C2 - 27966901
AN - SCOPUS:85035116865
SN - 0003-2700
VL - 89
SP - 1244
EP - 1253
JO - Analytical Chemistry
JF - Analytical Chemistry
IS - 2
ER -