PXD006843-1

PXD006843 is an original dataset announced via ProteomeXchange.

Title	GeLC-MS/MS of H37Rv and two clinical isolates of Mycobacterium tuberculosis
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.
HostingRepository	MassIVE
AnnounceDate	2017-07-02
AnnouncementXML	Submission_2017-07-02_23:54:29.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	David L. Tabb
SpeciesList	scientific name: Mycobacterium tuberculosis; NCBI TaxID: 1773;
ModificationList	Carbamidomethyl; Oxidation
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-30 01:59:25	ID requested
⏵ 1	2017-07-02 23:54:29	announced

no publication

submitter keyword: GeLC-MS/MS, Clinical microbiology, Latin American-Mediterranean

David L. Tabb
contact affiliation	Stellenbosch University
contact email	dtabb@sun.ac.za
lab head
David L. Tabb
contact affiliation	Vanderbilt University Medical Center
contact email	david.l.tabb@vanderbilt.edu
dataset submitter

MassIVE dataset URI

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