PXD000573-2

PXD000573 is an original dataset announced via ProteomeXchange.

Title	2D-LC/MS/MS analysis of Escherichia coli during exposure to an abrupt temperature downshift
Description	2D-LC/MS/MS analysis was used to examine time-dependent changes in proteome of E. coli O157:H7 strain Sakai upon an abrupt downshift in temperature (i.e., from 35??C to 14??C). Cell cultures were harvested at 30, 90, 160, and 330 min post-temperature downshift. It also should be noted that these time points were chosen with the aims to characterize the physiology of E. coli during dynamic changes in growth kinetics induced by an abrupt temperature downshift. Specifically, the samples taken at time 30 and 90 min were obtained during adaptation period, whereas the samples at time 160 and 330 min reflected the physiological state of E. coli during growth after the shift. MS/MS data obtained from each protein sample were processed by the Computational Proteomics Analysis System (CPAS), a web-based system built on the LabKey Server (v9.1, released 02.04.2009). The experimental mass spectra produced were subjected to a semi-tryptic search against the combined databases of E. coli O157:H7 Sakai (5,318 entries in total) downloaded from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/, downloaded 25.11.2008) using X!Tandem v2007.07.01. These databases included the E. coli O157:H7 Sakai database (5230 entries, NC_002695.fasta) and two E. coli O157:H7 Sakai plasmid databases, plasmid pO157 (85 entries, NC_002128.fasta) and plasmid pOSAK1 (three entries, NC_002127.fasta). The parameters for the database search were as follows: mass tolerance for precursor and fragment ions: 10 ppm and 0.5 Da, respectively; fixed modification: cysteine cabamidomethylation (+57 Da); and no variable modifications. The search results were then analyzed using the PeptideProphet and ProteinProphet algorithms from the Trans Proteomic Pipeline v3.4.2. All peptide and protein identifications were accepted at PeptideProphet and ProteinProphet of ???0.9, corresponding to a theoretical error rate of ???2%.
HostingRepository	PRIDE
AnnounceDate	2019-11-26
AnnouncementXML	Submission_2019-11-26_05:12:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chawalit Kocharunchitt
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-11-08 03:56:32	ID requested
1	2019-11-25 04:48:39	announced
⏵ 2	2019-11-26 05:12:48	announced	2019-11-26: Updated project metadata.
3	2024-10-22 04:17:59	announced	2024-10-22: Updated project metadata.

King T, Kocharunchitt C, Gobius K, Bowman JP, Ross T, H7 Sakai during dynamic changes in growth kinetics induced by an abrupt temperature downshift. PLoS One, 9(6):e99627(2014) [pubmed]

curator keyword: Biological

submitter keyword: E. coli, 2D-LC/MS/MS, physiology, stress response, cold stress

Tom Ross
contact affiliation	Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
contact email	Tom.Ross@utas.edu.au
lab head
Chawalit Kocharunchitt
contact affiliation	Food Safety Centre
contact email	chawalit.kocharunchitt@utas.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000573
     1. Label: PRIDE project
     2. Name: 2D-LC/MS/MS analysis of Escherichia coli during exposure to an abrupt temperature downshift