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Simulated phosphopeptide spectral library for confident site localization

ABSTRACT: We have developed a new workflow to unambiguously localize phosphorylation sites on proteins. We demonstrate that spectral matching of phosphopeptide datasets against a library of the well-simulated spectra provided higher sensitivity for confident site localization than other tested programs. To computationally simulate tandem mass spectra representing all possible singly phosphorylated forms of a peptide, characteristic fragment ions are predicted from ions of their dephosphorylated form generated by beam-type collision-induced dissociation.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Susumu Imanishi

LAB HEAD: Garry L. Corthals

PROVIDER: PXD000474 | Pride | 2015-03-17

REPOSITORIES: Pride

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Confident site localization using a simulated phosphopeptide spectral library.

Suni Veronika V Imanishi Susumu Y SY Maiolica Alessio A Aebersold Ruedi R Corthals Garry L GL

Journal of proteome research 20150327 5

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 ...[more]

PMID: 25774671

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