PXD000253

PXD000253 is an original dataset announced via ProteomeXchange.

Title	Quantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis
Description	Carbon metabolism in Mycobacterium smegmatis was analysed using reverse-phase chromatography coupled to orbitrap high-resolution mass spectrometer using trypsin digestion. MS/MS files were searched against the Mycobacterium smegmatis strain MC2-155 database Release 1 - July 2010 ) by MaxQuant software (version 1.3.0.5). Mass spectra were searched with an initial mass tolerance of 7 ppm in MS mode and 0.5 Da in MS/MS mode. Up to two missed cleavages were allowed. Carbamidomethylation was set as a fixed modification, whereas oxidation (M), acetylation (Protein N-term) and Phospho (S, T, Y) were considered as variable modifications. Minimum required peptide length was set to seven amino acids and at least two (unique + razor) peptides were required for protein identification. A cut-off was fixed at 1% FDR at the peptide and protein level. Reverse and contaminants sequences were removed and proteins with a Posterior Error Probability (PEP) lower than 0.1 were accepted for further data treatment. Protein quantification was performed with razor and unique peptides, using only unmodified, oxidated (M) and acetylated (Protein N-term) peptides. A minimum of two ratio counts was required to quantify proteins.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_05:20:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Romain Hamelin
SpeciesList	scientific name: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155); NCBI TaxID: 246196;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; phosphorylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2013-05-13 13:50:41	ID requested
1	2014-07-09 02:44:31	announced
⏵ 2	2014-07-24 05:20:15	announced	Updated project metadata.

Chopra T, Hamelin R, Armand F, Chiappe D, Moniatte M, McKinney JD, Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis. Mol Cell Proteomics, 13(11):3014-28(2014) [pubmed]

curator keyword: Biological

submitter keyword: Mycobacterium smegmatis, dimethyl, LC-MS/MS, metabolic pathways, carbon-sources, MaxQuant

Moniatte
contact affiliation	PCF
contact email	marc.moniatte@epfl.ch
lab head
Romain Hamelin
contact affiliation	PCF
contact email	romain.hamelin@epfl.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/07/PXD000253

PRIDE project URI

• PRIDE
  1. PXD000253
     1. Label: PRIDE project
     2. Name: Quantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis