Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments.

Bioinformatics
Marc KirchnerHanno Steen

Abstract

Mass spectrometry (MS) has become the method of choice for protein/peptide sequence and modification analysis. The technology employs a two-step approach: ionized peptide precursor masses are detected, selected for fragmentation, and the fragment mass spectra are collected for computational analysis. Current precursor selection schemes are based on data- or information-dependent acquisition (DDA/IDA), where fragmentation mass candidates are selected by intensity and are subsequently included in a dynamic exclusion list to avoid constant refragmentation of highly abundant species. DDA/IDA methods do not exploit valuable information that is contained in the fractional mass of high-accuracy precursor mass measurements delivered by current instrumentation. We extend previous contributions that suggest that fractional mass information allows targeted fragmentation of analytes of interest. We introduce a non-linear Random Forest classification and a discrete mapping approach, which can be trained to discriminate among arbitrary fractional mass patterns for an arbitrary number of classes of analytes. These methods can be used to increase fragmentation efficiency for specific subsets of analytes or to select suitable fragmentation tech...Continue Reading

References

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Citations

Oct 7, 2014·Medical & Biological Engineering & Computing·Mukesh Saraswat, K V Arya
Feb 27, 2013·Molecular & Cellular Proteomics : MCP·John W FroehlichRichard S Lee
Feb 1, 2011·Briefings in Bioinformatics·Torsten Hothorn, Friedrich Leisch
Dec 19, 2013·Evidence-based Complementary and Alternative Medicine : ECAM·Kojo AgyemangXiumei Gao
Jan 1, 2011·Wiley Interdisciplinary Reviews. Data Mining and Knowledge Discovery·Xiang ChenHeping Zhang
Nov 22, 2014·EuPA Open Proteomics·Piotr DittwaldDirk Valkenborg
Nov 3, 2016·Rapid Communications in Mass Spectrometry : RCM·Christian J KoehlerBernd Thiede
Dec 12, 2018·BioMed Research International·Zichuan FanYalan Dai

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