TY - JOUR
T1 - Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry
AU - Prasad, T. S.Keshava
AU - Harsha, H. C.
AU - Keerthikumar, Shivakumar
AU - Sekhar, Nirujogi Raja
AU - Selvan, Lakshmi Dhevi N.
AU - Kumar, Praveen
AU - Pinto, Sneha M.
AU - Muthusamy, Babylakshmi
AU - Subbannayya, Yashwanth
AU - Renuse, Santosh
AU - Chaerkady, Raghothama
AU - Mathur, Premendu P.
AU - Ravikumar, Raju
AU - Pandey, Akhilesh
PY - 2012/1/1
Y1 - 2012/1/1
N2 - 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.
AB - 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.
KW - Medical mycology
KW - candidemia
KW - candidiasis
KW - clinical proteomics
KW - fungal infection
KW - genome annotation
KW - molecular diagnostics
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U2 - 10.1021/pr200827k
DO - 10.1021/pr200827k
M3 - Article
C2 - 22129275
AN - SCOPUS:84855533919
SN - 1535-3893
VL - 11
SP - 247
EP - 260
JO - Journal of Proteome Research
JF - Journal of Proteome Research
IS - 1
ER -