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Article Dans Une Revue Rapid Communications in Mass Spectrometry Année : 2013

Influence of various endogenous and artefact modifications on large-scale proteomics analysis.

Willy V Bienvenut
David Sumpton
  • Fonction : Auteur
Sergio Lilla
  • Fonction : Auteur
Thierry Meinnel
Carmela Giglione

Résumé

RATIONALE: Some large-scale proteomics studies in which strong cation exchange chromatography has been applied are used to determine proteomes and post-translational modification dynamics. Although such datasets favour the characterisation of thousands of modified peptides, e.g., phosphorylated and N-α-acetylated, a large fraction of the acquired spectra remain unexplained by standard proteomics approaches. Thus, advanced data processing allows characterisation of a significant part of these unassigned spectra. METHODS: Our recent investigation of the N-α-acetylation status of plant proteins gave a dataset of choice to investigate further the in-depth characterisation of peptide modifications using Mascot tools associated with relevant validation processes. Such an approach allows to target frequently occurring modifications such as methionine oxidation, phosphorylation or N-α-acetylation, but also the less usual peptide cationisation. Finally, this dataset offers the unique opportunity to determine the overall influence of some of these modifications on the identification score. RESULTS: Although methionine oxidation has no influence and tends to favour the characterisation of protein N-terminal peptides, peptide alkalinisation shows an adverse effect on peptide average score. Nevertheless, peptide cationisation appears to favour the characterisation of protein C-terminal peptides with a limited to no direct influence on the identification score. Unexpectedly, our investigation reveals the unfortunate combination of the molecular weight of N-α-acetylation and potassium cation that mimics the mass increment of a phosphorylation group. CONCLUSIONS: Since these characterisations rely upon computational treatment associated with statistical validation approaches such as 'False discovery rates' calculation or post-translational modification position validation, our investigation highlights the limitation of such treatment which is biased by the initial searched hypotheses.

Dates et versions

hal-00851368 , version 1 (13-08-2013)

Identifiants

Citer

Willy V Bienvenut, David Sumpton, Sergio Lilla, Aude Martinez, Thierry Meinnel, et al.. Influence of various endogenous and artefact modifications on large-scale proteomics analysis.. Rapid Communications in Mass Spectrometry, 2013, 27 (3), pp.443-50. ⟨10.1002/rcm.6474⟩. ⟨hal-00851368⟩
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