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Straightforward and de novo peptide sequencing by MALDI-MS/MS using a Lys-N metalloendopeptidase.

ABSTRACT: In this work, we explore the potential of the metalloendopeptidase Lys-N for MALDI-MS/MS proteomics applications. Initially we digested a HEK293 cellular lysate with Lys-N and, for comparison, in parallel with the protease Lys-C. The resulting peptides were separated by strong cation exchange to enrich and isolate peptides containing a single N-terminal lysine. MALDI-MS/MS analysis of these peptides yielded CID spectra with clear and often complete sequence ladders of b-ions. To test the applicability for de novo sequencing we next separated an ostrich muscle tissue protein lysate by one-dimensional SDS-PAGE. A protein band at 42 kDa was in-gel digested with Lys-N. Relatively straightforward sequencing resulted in the de novo identification of the two ostrich proteins creatine kinase and actin. We therefore conclude that this method that combines Lys-N, strong cation exchange enrichment, and MALDI-MS/MS analysis provides a valuable alternative proteomics strategy.

SUBMITTER: Boersema PJ 

PROVIDER: S-EPMC2667348 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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Straightforward and de novo peptide sequencing by MALDI-MS/MS using a Lys-N metalloendopeptidase.

Boersema Paul J PJ   Taouatas Nadia N   Altelaar A F Maarten AF   Gouw Joost W JW   Ross Philip L PL   Pappin Darryl J DJ   Heck Albert J R AJ   Mohammed Shabaz S  

Molecular & cellular proteomics : MCP 20081129 4

In this work, we explore the potential of the metalloendopeptidase Lys-N for MALDI-MS/MS proteomics applications. Initially we digested a HEK293 cellular lysate with Lys-N and, for comparison, in parallel with the protease Lys-C. The resulting peptides were separated by strong cation exchange to enrich and isolate peptides containing a single N-terminal lysine. MALDI-MS/MS analysis of these peptides yielded CID spectra with clear and often complete sequence ladders of b-ions. To test the applica  ...[more]

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