Confident site localization using a simulated phosphopeptide spectral library

Journal of Proteome Research
Veronika SuniGarry L Corthals

Abstract

We have investigated if phosphopeptide identification and simultaneous site localization can be achieved by spectral library searching. This allows taking advantage of comparison of specific spectral features, which would lead to improved discrimination of differential localizations. For building a library, we propose a spectral simulation strategy where all possible single phosphorylations can be simply and accurately (re)constructed on enzymatically dephosphorylated peptides, by predicting the diagnostic fragmentation events produced in beam-type CID. To demonstrate the performance of our approach, enriched HeLa phosphopeptides were dephosphorylated with alkaline phosphatase and analyzed with higher energy collisional dissociation (HCD), which were then used for creating a spectral library of simulated phosphopeptides. Spectral library searching using SpectraST was performed on data sets of synthetic phosphopeptides and the HeLa phosphopeptides, and subsequently compared to Mascot and Sequest database searching followed by phosphoRS and Ascore afforded localization, respectively. Our approach successfully led to accurate localization, and it outperformed other methods, when phosphopeptides were covered by the library. These r...Continue Reading

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Citations

Nov 6, 2015·Analytical Chemistry·Nicholas M Riley, Joshua J Coon
Jan 6, 2016·Mass Spectrometry Reviews·Han HuJoseph Zaia
Dec 1, 2015·Proteomics·Johannes Griss
May 20, 2016·Rapid Communications in Mass Spectrometry : RCM·Fan YuZhixin Tian
Mar 30, 2018·Bioinformatics·Veronika SuniGarry L Corthals
Sep 29, 2020·Journal of Proteome Research·Yi YangLiang Qiao
Jan 25, 2020·Journal of Proteome Research·Marie Locard-PauletLars J Jensen
Nov 21, 2018·Analytical Chemistry·Clement M PotelAlbert J R Heck
Nov 16, 2017·Analytica Chimica Acta·Kaijie XiaoZhixin Tian

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