title: Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry.
abstract: Candida glabrata is a common opportunistic human pathogen leading to significant mortality in immunosuppressed and immunodeficient individuals. We carried out proteomic analysis of C. glabrata using high resolution Fourier transform mass spectrometry with MS resolution of 60,000 and MS/MS resolution of 7500. On the basis of 32,453 unique peptides identified from 118,815 peptide-spectrum matches, we validated 4421 of the 5283 predicted protein-coding genes (83%) in the C. glabrata genome. Further, searching the tandem mass spectra against a six frame translated genome database of C. glabrata resulted in identification of 11 novel protein coding genes and correction of gene boundaries for 14 predicted gene models. A subset of novel protein-coding genes and corrected gene models were validated at the transcript level by RT-PCR and sequencing. Our study illustrates how proteogenomic analysis enabled by high resolution mass spectrometry can enrich genome annotation and should be an integral part of ongoing genome sequencing and annotation efforts.
authors: Institute of Bioinformatics, International Technology Park, Bangalore-560 066, India. keshav@ibioinformatics.org
authors: T S Keshava
authors: TS
authors: Prasad
authors: H C
authors: HC
authors: Harsha
authors: Shivakumar
authors: S
authors: Keerthikumar
authors: Nirujogi Raja
authors: NR
authors: Sekhar
authors: Lakshmi Dhevi N
authors: LD
authors: Selvan
authors: Praveen
authors: P
authors: Kumar
authors: Sneha M
authors: SM
authors: Pinto
authors: Babylakshmi
authors: B
authors: Muthusamy
authors: Yashwanth
authors: Y
authors: Subbannayya
authors: Santosh
authors: S
authors: Renuse
authors: Raghothama
authors: R
authors: Chaerkady
authors: Premendu P
authors: PP
authors: Mathur
authors: Raju
authors: R
authors: Ravikumar
authors: Akhilesh
authors: A
authors: Pandey
mesh_terms: D000595:Amino Acid Sequence; D041221:Candida glabrata / Q000235:genetics / Q000378:metabolism*; D018387:Codon, Initiator; D005583:Fourier Analysis; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015870:Gene Expression; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D010449:Peptide Mapping; D020543:Proteome / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D053719:Tandem Mass Spectrometry
chemical_list: D018387:Codon, Initiator; D005656:Fungal Proteins; D010446:Peptide Fragments; D020543:Proteome