title: Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-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.affiliation: Laboratory of Gaseous Ion Chemistry, Department of Chemistry, Research Institute for Natural Sciences, Korea University , Seoul 136-701, South Korea.
authors.forename: Inamul Hasan
authors.initials: IH
authors.lastname: Madar
authors.affiliation: Laboratory of Gaseous Ion Chemistry, Department of Chemistry, Research Institute for Natural Sciences, Korea University , Seoul 136-701, South Korea.
authors.forename: Seung-Ik
authors.initials: SI
authors.lastname: Ko
authors.affiliation: Laboratory of Gaseous Ion Chemistry, Department of Chemistry, Research Institute for Natural Sciences, Korea University , Seoul 136-701, South Korea.
authors.forename: Hokeun
authors.initials: H
authors.lastname: Kim
authors.affiliation: Laboratory of Gaseous Ion Chemistry, Department of Chemistry, Research Institute for Natural Sciences, Korea University , Seoul 136-701, South Korea.
authors.forename: Dong-Gi
authors.initials: DG
authors.lastname: Mun
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington, United States.
authors.forename: Sangtae
authors.initials: S
authors.lastname: Kim
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington, United States.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: Laboratory of Gaseous Ion Chemistry, Department of Chemistry, Research Institute for Natural Sciences, Korea University , Seoul 136-701, South Korea.
authors.forename: Sang-Won
authors.identifier: 0000-0002-5042-0084
authors.initials: SW
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D010455:Peptides / Q000032:analysis*; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D020543:Proteome