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

Bienvenut, W.V., Sumpton, D., Lilla, S., Martinez, A., Meinnel, T. and Giglione, C. (2013) Influence of various endogenous and artefact modifications on large-scale proteomics analysis. Rapid Communications in Mass Spectrometry, 27(3), pp. 443-450. (doi: 10.1002/rcm.6474)

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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.


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.


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.


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.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Bienvenut, Dr Willy and Sumpton, Mr David and Lilla, Dr Sergio
Authors: Bienvenut, W.V., Sumpton, D., Lilla, S., Martinez, A., Meinnel, T., and Giglione, C.
College/School:College of Medical Veterinary and Life Sciences > Institute of Cancer Sciences
Journal Name:Rapid Communications in Mass Spectrometry
ISSN (Online):1097-0231
Published Online:26 December 2012

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