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Influence of various endogenous and artefact modifications on large-scale proteomics analysis.
MedLine Citation:
PMID:  23280976     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
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. Copyright © 2012 John Wiley & Sons, Ltd.
Authors:
Willy V Bienvenut; David Sumpton; Sergio Lilla; Aude Martinez; Thierry Meinnel; Carmela Giglione
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Rapid communications in mass spectrometry : RCM     Volume:  27     ISSN:  1097-0231     ISO Abbreviation:  Rapid Commun. Mass Spectrom.     Publication Date:  2013 Feb 
Date Detail:
Created Date:  2013-01-02     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8802365     Medline TA:  Rapid Commun Mass Spectrom     Country:  England    
Other Details:
Languages:  eng     Pagination:  443-50     Citation Subset:  IM    
Copyright Information:
Copyright © 2012 John Wiley & Sons, Ltd.
Affiliation:
CNRS, ISV, UPR2355, Bâtiment 23A, 1 avenue de la Terrasse, F-91198, Gif-sur-Yvette Cedex, France; Beatson Institute for Cancer Research, Proteomics and Mass Spectrometry, Garscube Estate, Switchback Road, Glasgow, G61 6BD, UK. willy.bienvenut@isv.cnrs-gif.fr.
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