Precursor-ion mass re-estimation improves peptide identification on hybrid instruments.

Journal of Proteome Research
Roland LuethyParag Mallick

Abstract

Mass spectrometry-based proteomics experiments have become an important tool for studying biological systems. Identifying the proteins in complex mixtures by assigning peptide fragmentation spectra to peptide sequences is an important step in the proteomics process. The 1-2 ppm mass-accuracy of hybrid instruments, like the LTQ-FT, has been cited as a key factor in their ability to identify a larger number of peptides with greater confidence than competing instruments. However, in replicate experiments of an 18-protein mixture, we note parent masses deviate 171 ppm, on average, for ion-trap data directed identifications and 8 ppm, on average, for preview Fourier transform (FT) data directed identifications. These deviations are neither caused by poor calibration nor by excessive ion-loading and are most likely due to errors in parent mass estimation. To improve these deviations, we introduce msPrefix, a program to re-estimate a peptide's parent mass from an associated high-accuracy full-scan survey spectrum. In 18-protein mixture experiments, msPrefix parent mass estimates deviate only 1 ppm, on average, from the identified peptides. In a cell lysate experiment searched with a tolerance of 50 ppm, 2295 peptides were confidently ...Continue Reading

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Citations

Jul 20, 2012·Analytical and Bioanalytical Chemistry·Scott J GeromanosJames I Langridge
Mar 5, 2009·Journal of Proteome Research·Michael R HoopmannMichael J MacCoss
Nov 27, 2009·Journal of Proteome Research·Edward J HsiehMichael J MacCoss
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May 11, 2010·Journal of Proteome Research·Kevin BlackburnMichael B Goshe
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Oct 30, 2020·Journal of the American Society for Mass Spectrometry·Elizaveta M SolovyevaMikhail V Gorshkov
Nov 2, 2021·Analytical Chemistry·Taran DriverVitali Averbukh

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