A magnetic immunoenrichment strategy for N-terminal-oriented proteogenomics applied to the marine bacterium Roseobacter denitrificans

ABSTRACT: Proteogenomics is the alliance of proteomics and genomics with the aim of better annotating structural genes based on protein experimental pieces of evidence established by tandem mass spectrometry. While on average more than one tenth of N-termini of proteins are incorrectly annotated, there is a crucial need for methodological approaches to systematically establish translational starts of polypeptides and their maturations such as N-terminal methionine processing and peptide signal excision. Here, we describe a straightforward strategy to specifically label protein N-termini with a positively charged TMPP label, selectively capture these entities with in-house developed anti-TMPP antibodies coupled to magnetic beads, and analyze them by nanoLC-MS/MS. While most N-terminomics-oriented approaches are based on depletion of internal peptides to retrieve N-terminal peptides, this enrichment approach is fast and results highly specific for improved ionizable TMPP-labeled peptides. The whole proteome of the model marine bacterium Roseobacter denitrificans was analyzed.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Roseobacter Denitrificans (strain Atcc 33942 / Och 114) (erythrobacter Sp. (strain Och 114)) (roseobacter Denitrificans)

SUBMITTER: Jean ARMENGAUD  

PROVIDER: PXD000364 | Pride | 2014-07-16

REPOSITORIES: Pride