PXD005579

PXD005579 is an original dataset announced via ProteomeXchange.

Title	A Unique Ribosome Signature Reveals bacterium Translation Initiation Sites
Description	Overnight stationary cultures of wild type S. Typhimurium (Salmonella enterica serovar Thyphimurium - strain SL1344) grown in LB media at 37°C with agitation (200 rpm) were diluted at 1:200 in LB and grown until they reached and OD600 of 0.5 (i.e., logarithmic (Log) phase grown cells). Bacterial cells were collected by centrifugation (6000 × g, 5 min) at 4°C, flash frozen in liquid nitrogen and cryogenically pulverized using liquid nitrogen cooled pestle and mortar. The frozen pellet of a 50 ml culture was re-suspended and thawed in 1 ml ice-cold lysis buffer (50 mm NH4HCO3 (pH 7.9) supplemented with a complete protease inhibitor cocktail tablet (Roche Diagnostics GmbH, Mannheim, Germany) and subjected to mechanical disruption by two repetitive freeze-thaw and sonication cycles (i.e. 2 minutes of sonication on ice for 20-s bursts at output level 4 with a 40% duty cycle (Branson Sonifier 250; Ultrasonic Convertor)). The lysate was cleared by centrifugation for 15 min at 16,000 × g and the protein concentration measured using the protein assay kit (Bio-Rad) according to the manufacturer's instructions. The lysate was added Gu.HCl (4M f.c.) and subjected to N-terminal COFRADIC analysis. Free amines were blocked at the protein level making use of an N-hydroxysuccinimide ester of (stable isotopic encoded) acetate (i.e. NHS esters of 13C2D3 acetate), which allows distinguishing in vivo and in vitro blocked N-terminal peptides. The modified protein sample was digested overnight with sequencing-grade modified trypsin (1/100 (w/w trypsin /substrate)) at 37°C and subsequent steps of the N-terminal COFRADIC procedure were performed.
HostingRepository	PRIDE
AnnounceDate	2017-08-09
AnnouncementXML	Submission_2017-09-11_00:50:29.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005579
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Petra Van Damme
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; NCBI TaxID: 216597;
ModificationList	Oxidation
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-12-16 01:27:35	ID requested
1	2017-08-09 01:40:55	announced
⏵ 2	2017-09-11 00:50:30	announced	Updated publication reference for PubMed record(s): 28854918.

Giess A, Jonckheere V, Ndah E, Chy, ż, y, ń, ska K, Van Damme P, Valen E, Ribosome signatures aid bacterial translation initiation site identification. BMC Biol, 15(1):76(2017) [pubmed]

curator keyword: Biological

submitter keyword: N-terminal COFRADIC, Salmonella T. str SL1344, LTQ Orbitrap Velos, Ribosome profiling

Petra Van Damme
contact affiliation	Department of Biochemistry, Ghent University, Belgium
contact email	petra.vandamme@ugent.be
lab head
Petra Van Damme
contact affiliation	University of Ghent
contact email	petra.vandamme@ugent.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005579
     1. Label: PRIDE project
     2. Name: A Unique Ribosome Signature Reveals bacterium Translation Initiation Sites