PXD005579-2

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.
3	2024-10-22 04:35:12	announced	2024-10-22: Updated project metadata.

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