PXD000141

PXD000141 is an original dataset announced via ProteomeXchange.

Title	Mycobacterium tuberculosis ATP-binding Proteome
Description	Mtb was grown as either an actively growing normal culture or as a hypoxia-induced dormant culture. Whole cell lysates of live bacteria were obtained by mechanical disruption with silica beads. ATP-binding proteins were covalently labeled with desthiobiotin-tagged ATP (ActivX, Thermo Pierce). This chemoproteomic approach profiled the ATP-binding proteins present in either metabolic state. Labeled proteins were enriched via streptavidin affinity chromatography, digested with trypsin and subjected to tandem mass spectrometry (LC-MS/MS) for the identification of proteins containing a desthiobiotin modification of lysine (K +196 Da). Differential abundance of nucleotide binding proteins between the two growth conditions were quantified using label-free spectral counting and normalized spectral abundance factors (NSAF). DATABASE SEARCHING: Tandem mass spectra were extracted, charge state deconvoluted and deisotoped by Xcalibur version 2.2 SP1. All MS/MS samples were analyzed using Mascot (Matrix Science, London, UK; version 2.3.02) and SEQUEST (Thermo Fisher Scientific, San Jose, CA, USA; version v.27, rev. 11). Mascot and SEQUEST were set up to search the MtbReverse041712 database (7992 entries) assuming the digestion enzyme Trypsin. Parameters for both search engines were set to a fragment ion mass tolerance of 1.0 Da and a parent ion tolerance of 2.5 Da.  Oxidation of methionine, iodoacetamide derivative of cysteine and the desthiobiotin modification of lysine were specified in Mascot and SEQUEST as variable modifications. PROTEIN IDENTIFICATION AND LABEL-FREE QUANTITATION-- Scaffold (version Scaffold_3.6.1, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. Peptide identifications were accepted if they exceeded specific database search engine thresholds. Mascot identifications required ion scores to be greater than the associated identity scores and 50, 65, 65 and 65 for singly, doubly, triply and quadruply charged peptides. SEQUEST identifications required deltaCn scores of greater than 0.2 and XCorr scores of greater than 1.8, 2.0, 3.0 and 4.0 for singly, doubly, triply and quadruply charged peptides. Proteins identifications were accepted if they contained at least one identified peptide in at least two biological replicates. Peptide spectra meeting the most minimum requirement were manually inspected for quality. Quantification of proteins was performed on normalized spectral abundance factors for each protein (NSAF). BLAST-BASED SEQUENCE DESCRIPTION:  The most relevant description for each of the sequences was acquired based on the significant BLAST results.  The homologs for the sequences were retrieved using the Blastp algorithm and the nonredundant database of NCBI. The Blast2GO suite was used. GENE ONTOLOGY ANNOTATION:  The Pfam domains were mapped to Gene Ontology (GO) terms using the lookup table provided by Pfam2go (http://www.geneontology.org/external2go/pfam2go).  An in-house script was written to retrieve GO annotations based on the root term as "molecular function" and their distance from the root term. PFAM DOMAIN-BASED ANNOTATION:  The InterPro and Pfam IDs corresponding to the GO term "ATP binding" (GO ID:0005524) were retrieved using the QuickGO (www.ebi.ac.uk/QuickGO/) and InterPro BioMart web services (http://www.ebi.ac.uk/interpro/biomart/martview). The ATP-binding associated domains were queried against the ATP-binding proteome data sets according to spectral quality (high, medium, low confidence). Their Pfam and InterPro descriptions, were identified using the InterProscan Web service, which was accessed via the Pipeline Pilot (Accelrys) implementation in the sequence analysis collection.
HostingRepository	PRIDE
AnnounceDate	2013-04-08
AnnouncementXML	Submission_2013-04-08_06:44:04.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karen Dobos
SpeciesList	scientific name: Mycobacterium tuberculosis H37Rv; NCBI TaxID: 83332;
ModificationList	iodoacetamide derivatized residue; monohydroxylated residue; N6-crotonyl-L-lysine
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2013-02-07 02:25:55	ID requested
1	2013-04-08 06:34:33	announced
1	2014-07-25 00:52:21	announced
⏵ 2	2013-04-08 06:44:04	announced	Add reference

Wolfe LM, Veeraraghavan U, Idicula-Thomas S, Sch, ü, rer S, Wennerberg K, Reynolds R, Besra GS, Dobos KM, A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. Mol Cell Proteomics, 12(6):1644-60(2013) [pubmed]

submitter keyword: M. tuberculosis, LC-MS/MS, ABPP, ATP

Karen Dobos
contact affiliation	Microbiology, Immunology, and Pathology
contact email	kdobos@colostate.edu

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