PXD000328

PXD000328 is an original dataset announced via ProteomeXchange.

Title	Protein synthesis rate is the predominant regulator of protein expression during differentiation
Description	The protein expression changes was measured at five time points (Exp1: 0, 12, 24 h; Exp2: 6, 12, 48 h) in differentiating THP-1 cell (human) cells and at three time points(0, 12, 24 h) in differentiating C2C12 cells(mouse), using two triple, or one triple Stable isotope labeling by amino acids in cell culture (SILAC) experiment, respectively. These measurements were compared to the relative synthesis and degradation rates in both proliferating and differentiating cells. All measurements were performed in biological triplicates. Sample processing: The lysate was boiled in 1 % deoxycholate, before being separated by SDS-PAGE and/or in-solution digested to peptides and separated by isoelectric focusing (IEF). Finally we measured the synthesis and degradation rates of macromolecular sub-complexes as they eluted from a size exclusion chromatography (SEC) column. Here the cells were lysed by douncing, macromolecular complexes concentrated on a 100 kDa molecular weight cut-off filter, before being fractionated by HPLC-SEC into 48 fractions. The fractions were subsequently individually in solution-digested and analyzed by LC-MS/MS. As a general rule it seems that protein expression is largely controlled by changes in the relative synthesis rate, whereas the relative degradation rate of the majority of proteins stays constant. In these data, we also observe that the proteins in defined sub-structures of larger protein complexes tend to have highly correlated synthesis and degradation rates but that this does not necessarily extend to the holo-complex. Data analysis: Raw MS files from an LTQ-Orbitrap or LTQ-Orbitrap-Velos were analyzed by MaxQuant, MS/MS spectra were searched against Uniprot (proteomes) human 21/6/2011 or mouse 20/4/2012 by the Andromeda search engine. For identification, the false discovery rate (FDR) was set to 0.01 on the protein and on the peptide levels.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:17:47.688.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anders Kristensen
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-08 03:05:51	ID requested
1	2013-09-10 08:24:04	announced
1	2014-07-25 01:21:15	announced
⏵ 2	2024-10-22 04:17:48	announced	2024-10-22: Updated project metadata.

Kristensen AR, Gsponer J, Foster LJ, Protein synthesis rate is the predominant regulator of protein expression during differentiation. Mol Syst Biol, 9():689(2013) [pubmed]

10.1038/msb.2013.47;

submitter keyword: Differentiation, proteins synthesis,Proteomics, SILAC, protein degradation

Anders Kristensen
contact affiliation	Biochemistry and Molecular Biology
contact email	anderskr@interchange.ubc.ca
lab head
Anders Kristensen
contact affiliation	Biochemistry and Molecular Biology
contact email	anderskr@interchange.ubc.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000328
     1. Label: PRIDE project
     2. Name: Protein synthesis rate is the predominant regulator of protein expression during differentiation