PXD000494-3

PXD000494 is an original dataset announced via ProteomeXchange.

Title	Lactococcus lactis protein turnover
Description	Triplicate chemostat cultivations were carried out with L. lactis subsp. lactis IL1403 at specific growth rates 0.1 and 0.5 h-1 on a chemically defined medium, where both, glucose and lysin (Lys) were jointly limiting the growth. After reaching the steady physiological state, medium was switched to heavy Lys (13C615N2-Lys) containing medium and incorporation of heavy amino acid into biomass was observed over the time course. Samples were collected before the medium switch (0 h) and 0.5; 1.5; 5; and 10 h after the medium switch. Cells were lysed in SDS lysis buffer and digested with trypsin according to Filter Aided Sample Preparation protocol (FASP). LC-MS/MS analysis were performed on Agilent 1200 series nanoflow system connected to a LTQ Orbitrap mass-spectrometer equipped with a nanoelectrospray ion source. Raw data files were analyzed with the MaxQuant software package (version 1.2.7.4). Generated peak lists were searched using the Andromeda search engine (built into MaxQuant) against L. lactis database (downloaded 28.06.2012 from http://www.genome.jp/kegg/genes.html). MaxQuant searches were performed with full tryptic specificity, a maximum of two missed cleavages and a mass tolerance of 0.5 Da for fragment ions. Carbamidomethylation of cysteine was set as a fixed modification and methionine oxidation and protein N-terminal acetylation were set as variable modification. The required false discovery rate (FDR) was set to 1% both for peptide and protein levels and the minimum required peptide length was set to six amino acids. In addition, "Match between runs" option with a time window of 1.5 min was allowed.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:15:24.578.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liisa Arike
SpeciesList	scientific name: Lactococcus lactis subsp. lactis Il1403; NCBI TaxID: 272623;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-04 02:01:22	ID requested
1	2014-01-28 03:53:28	announced
2	2014-07-25 01:40:48	announced	Updated project metadata.
⏵ 3	2024-10-22 04:15:25	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: LC-MSMS,Lactococcus lactis, protein turnover

Liisa Arike
contact affiliation	Competence Center for Food and Fermentation Technologies
contact email	liisa@tftak.eu
lab head
Liisa Arike
contact affiliation	Competence Center for Food and Fermentation Technologies
contact email	liisa@tftak.eu
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/2014/01/PXD000494

PRIDE project URI

• PRIDE
  1. PXD000494
     1. Label: PRIDE project
     2. Name: Lactococcus lactis protein turnover