Proteomics

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Arabidopsis thaliana N-terminal proteome,LC-MS

ABSTRACT: An extended ChaFRADIC workflow was applied to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling, a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme were used, and only 1/3 of each ChaFRADIC-enriched fraction were analyzed by LC-MS. Furthermore, our goal was to gain insights of the Met-excision dogma where initiator Met residues are cleaved posstranslationally if the second residue is small, as well as the N-end rule degradation pathway (NERD) discriminating between stabilizing/destabilizing functions of N-terminal amino acid residues in Arabidopsis. We found bona fide NERD destabilizing residues underrepresented. The list of neo N-termini from wild type samples represents an extremely helpful resource for excluding pseudo-candidates of NERD.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell

SUBMITTER: Fiorella Andrea Solari  

LAB HEAD: René Peiman Zahedi

PROVIDER: PXD001855 | Pride | 2015-07-21

REPOSITORIES: Pride

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Publications

An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events in Arabidopsis thaliana.

Venne A Saskia AS   Solari Fiorella A FA   Faden Frederik F   Paretti Tomasso T   Dissmeyer Nico N   Zahedi René P RP  

Proteomics 20150701 14

We applied an extended charge-based fractional diagonal chromatography (ChaFRADIC) workflow to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling and a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme, and measuring only one third of each ChaFRADIC-enriched fraction by LC-MS, we quantified a total of 2791 unique N-terminal peptides corresponding to 2249 different unique N-termini from 1270 Arabidops  ...[more]

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