Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways inChlamydomonas reinhardtii
Autor: | Bianca Naumann, Monica Zhang, Michael Hippler, Jens Allmer, Christine Markert |
---|---|
Rok vydání: | 2006 |
Předmět: |
Molecular Sequence Data
Protozoan Proteins Chlamydomonas reinhardtii Computational biology Bioinformatics Proteomics Tandem mass spectrometry Biochemistry Peptide mass fingerprinting Tandem Mass Spectrometry Animals Database search engine Amino Acid Sequence Databases Protein Molecular Biology Peptide sequence biology Alternative splicing Computational Biology biology.organism_classification Alternative Splicing genomic DNA Electrophoresis Polyacrylamide Gel Energy Metabolism Algorithms |
Zdroj: | PROTEOMICS. 6:6207-6220 |
ISSN: | 1615-9861 1615-9853 |
Popis: | 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. |
Databáze: | OpenAIRE |
Externí odkaz: |