Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii
peer-reviewed · PROTEOMICS · 2006
| Date | 2006-12-01 |
| Type | peer-reviewed |
| Venue | PROTEOMICS |
| Publisher | Wiley |
| Contribution | adjacent |
| DOI | 10.1002/pmic.200600208 |
| Citations (OpenAlex) | 71 |
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.
Methods and tools
- GenomicPeptideFinder de novo genomic mining: Pairs de novo amino acid sequencing with the error-tolerant GenomicPeptideFinder search of genomic DNA to find intron-split and alternatively spliced peptides, applied to Chlamydomonas thylakoids.