Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry

T. S.Keshava Prasad, H. C. Harsha, Shivakumar Keerthikumar, Nirujogi Raja Sekhar, Lakshmi Dhevi N. Selvan, Praveen Kumar, Sneha M. Pinto, Babylakshmi Muthusamy, Yashwanth Subbannayya, Santosh Renuse, Raghothama Chaerkady, Premendu P. Mathur, Raju Ravikumar, Akhilesh Pandey

Research output: Contribution to journalArticle

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 60000 and MS/MS resolution of 7500. On the basis of 32453 unique peptides identified from 118815 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.

Original languageEnglish (US)
Pages (from-to)247-260
Number of pages14
JournalJournal of proteome research
Volume11
Issue number1
DOIs
StatePublished - Jan 1 2012

Keywords

  • Medical mycology
  • candidemia
  • candidiasis
  • clinical proteomics
  • fungal infection
  • genome annotation
  • molecular diagnostics

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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  • Cite this

    Prasad, T. S. K., Harsha, H. C., Keerthikumar, S., Sekhar, N. R., Selvan, L. D. N., Kumar, P., Pinto, S. M., Muthusamy, B., Subbannayya, Y., Renuse, S., Chaerkady, R., Mathur, P. P., Ravikumar, R., & Pandey, A. (2012). Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. Journal of proteome research, 11(1), 247-260. https://doi.org/10.1021/pr200827k