Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii

peer-reviewed · PROTEOMICS · 2006

peer-reviewed · PROTEOMICS · 2006. Jens Allmer et al. A new high-throughput computational strategy was established that improves genomic data mining from MS…
Date 2006-12-01
Type peer-reviewed
Venue PROTEOMICS
Publisher Wiley
Contribution adjacent
DOI 10.1002/pmic.200600208
Citations (OpenAlex) 69

Abstract

A new high-throughput computational strategy was established that improves genomic data mining from MS experiments. The MS/MS data were analyzed by the SEQUEST search algorithm and a combination of de novo amino acid sequencing in conjunction with an error-tolerant database search tool, operating on a 256 processor computer cluster. The error-tolerant search tool, previously established as GenomicPeptideFinder (GPF), enables detection of intron-split and/or alternatively spliced peptides from MS/MS data when deduced from genomic DNA. Isolated thylakoid membranes from the eukaryotic green alga Chlamydomonas reinhardtii were separated by 1-D SDS gel electrophoresis, protein bands were excised from the gel, digested in-gel with trypsin and analyzed by coupling nano-flow LC with MS/MS. The concerted action of SEQUEST and GPF allowed identification of 2622 distinct peptides. In total 448 peptides were identified by GPF analysis alone, including 98 intron-split peptides, resulting in the identification of novel proteins, improved annotation of gene models, and evidence of alternative splicing.

Authors

  1. Jens Allmer · Hochschule Ruhr West, Izmir Institute of Technology, Ruhr West University of Applied Sciences, University of Münster, University of Pennsylvania
  2. Bianca Naumann · University of Münster, University of Pennsylvania
  3. Christine Markert · University of Pennsylvania
  4. Monica Zhang · University of Pennsylvania
  5. Michael Hippler · University of Münster, University of Pennsylvania

Methods and tools

  • Genomic Peptide Finder: Aligns de novo sequenced peptides directly to a genome, tolerating sequencing errors and introns, to provide proteogenomic evidence for gene annotation.

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