MassIVE MSV000081205

Complete Public PXD006843

GeLC-MS/MS of H37Rv and two clinical isolates of Mycobacterium tuberculosis

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Description

Clinical isolates were made available from an extensive longitudinal collection of M. tuberculosis isolates circulating in the Western Cape of South Africa. Clinical isolates SAWC3651 and SAWC3517, belonging to the LAM (lineage 4.3) genotype and IS6110 family 14 and 9, respectively, and M. tuberculosis H37Rv were selected for analysis. Proteins were fractionated by SDS-PAGE, using a 4-12% gradient, 1.0 mm NuPage gel (Invitrogen, Carlsbad, CA, USA). Each gel lane was divided into 10 fractions and each fraction was prepared for analysis by mass spectrometry. The reduced and alkylated proteins were subjected to in-gel trypsin digestion for 17 hours at 37 �C using sequencing grade, modified trypsin (Promega, Madison, USA) in 50 mM ABC. The mass spectrometer was operated in data-dependent mode to automatically switch between Orbitrap-MS and LTQ-MS/MS acquisition. Data were acquired using the Xcalibur software package (Thermo Fisher Scientific, Bremen, Germany). Precursor ion scan MS spectra (m/z 400 - 2000) were acquired in the Orbitrap with resolution R = 60 000 with the number of accumulated ions being 1 x 106. The 20 most intense ions were isolated and fragmented in the linear ion trap (number of accumulated ions 1.5 x 104) using collision induced dissociation (30% normalized collision energy). Each of the three tuberculosis lysates were grown in biological duplicate, and duplicate ten-fraction tandem mass spectrometry experiments were produced from each biological replicate. In total, 120 RAW files resulted. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: GeLC-MS/MS ; Clinical microbiology ; Latin American-Mediterranean

Contact

Principal Investigators:
(in alphabetical order) 		David L. Tabb, Stellenbosch University, South Africa
Submitting User: dtabb73

Publications

Heunis T, Dippenaar A, Warren RM, van Helden PD, van der Merwe RG, Gey van Pittius NC, Pain A, Sampson SL, Tabb DL.
Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates.
J Proteome Res. 2017 Oct 6;16(10):3841-3851. Epub 2017 Sep 11.

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