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Title: Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation

Abstract

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.

Authors:
 [1];  [1];  [1];  [1];  [2];  [2]; ORCiD logo [1]
  1. Laboratory of Gaseous Ion Chemistry, Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea
  2. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1406696
Report Number(s):
PNNL-SA-129635
Journal ID: ISSN 0003-2700; 49531; 453040220
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 89; Journal Issue: 2; Journal ID: ISSN 0003-2700
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Madar, Inamul Hasan, Ko, Seung-Ik, Kim, Hokeun, Mun, Dong-Gi, Kim, Sangtae, Smith, Richard D., and Lee, Sang-Won. Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation. United States: N. p., 2016. Web. doi:10.1021/acs.analchem.6b03874.
Madar, Inamul Hasan, Ko, Seung-Ik, Kim, Hokeun, Mun, Dong-Gi, Kim, Sangtae, Smith, Richard D., & Lee, Sang-Won. Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation. United States. https://doi.org/10.1021/acs.analchem.6b03874
Madar, Inamul Hasan, Ko, Seung-Ik, Kim, Hokeun, Mun, Dong-Gi, Kim, Sangtae, Smith, Richard D., and Lee, Sang-Won. Thu . "Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation". United States. https://doi.org/10.1021/acs.analchem.6b03874.
@article{osti_1406696,
title = {Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation},
author = {Madar, Inamul Hasan and Ko, Seung-Ik and Kim, Hokeun and Mun, Dong-Gi and Kim, Sangtae and Smith, Richard D. and Lee, Sang-Won},
abstractNote = {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.},
doi = {10.1021/acs.analchem.6b03874},
url = {https://www.osti.gov/biblio/1406696}, journal = {Analytical Chemistry},
issn = {0003-2700},
number = 2,
volume = 89,
place = {United States},
year = {2016},
month = {12}
}