Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.
Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, "integrated post-experiment monoisotopic mass refinement" (iPE-MMR), integrates steps (1) generation of refined MS/MS data by DeconMSn; (2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; and (3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. With the combination of these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data.
Jung
Hee-Jung
HJ
Department of Chemistry, Korea University, 1, 5-ka, Anam-dong, Seongbuk-gu, Seoul 136-701, Republic of Korea.
Purvine
Samuel O
SO
Kim
Hokeun
H
Petyuk
Vladislav A
VA
Hyung
Seok-Won
SW
Monroe
Matthew E
ME
Mun
Dong-Gi
DG
Kim
Kyong-Chul
KC
Park
Jong-Moon
JM
Kim
Su-Jin
SJ
Tolic
Nikola
N
Slysz
Gordon W
GW
Moore
Ronald J
RJ
Zhao
Rui
R
Adkins
Joshua N
JN
Anderson
Gordon A
GA
Lee
Hookeun
H
Camp
David G
DG
Yu
Myeong-Hee
MH
Smith
Richard D
RD
Lee
Sang-Won
SW
D010455:Peptides / Q000032:analysis; D020543:Proteome / Q000032:analysis; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000737:chemistry; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010455:Peptides; D020543:Proteome