PXD000157

PXD000157 is an original dataset announced via ProteomeXchange.

Title	Proteome analysis of U2OS whole cell lysates
Description	LC-MS analysis of 18 OGE fractions optained from normally grown U2OS cell lysates. The generation of mathematical models of biological processes, the simulation of these processes under different conditions, and the comparison and integration of multiple data sets are explicit goals of systems biology that require the knowledge of the absolute quantity of the system’s components. To date, systematic estimates of cellular protein concentrations have been exceptionally scarce. Here, we provide a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis. We show that these human cultured cells express at least 10000 proteins and that the quantified proteins span a concentration range of seven orders of magnitude up to 20000000 copies per cell. We discuss how protein abundance is linked to function and evolution. Regarding the bioinformatics pipeline employed: the acquired raw files were converted to the centroid mxxml and mgf-format using MassMatrix mass spectrometric data file conversion tools (version 3.9, http://www.massmatrix.org) and searched using MASCOT (version 2.4) against a decoy database of the predicted proteome from homo sapiens extracted from the UniProt/SwissProt database (downloaded on 16/05/2012) and including known contaminants such as keratins/trypsin. The search criteria were set as follows: full tryptic specificity was required (cleavage after lysine or arginine residues); 3 missed cleavages were allowed; carbamidomethylation (C) was set as fixed modification; oxidation (M) as variable modification. The mass tolerance was set to 15 ppm for precursor ions and 0.5 Da for fragment ions.
HostingRepository	PRIDE
AnnounceDate	2013-02-22
AnnouncementXML	Submission_2013-02-22_07:54:15.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000157
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue; monohydroxylated residue; neutral loss: 63.998285
Instrument	radial ejection linear ion trap

Revision	Datetime	Status	ChangeLog Entry
0	2013-02-22 02:25:13	ID requested
1	2013-02-22 07:30:56	announced
1	2014-07-28 00:30:16	announced
⏵ 2	2013-02-22 07:54:15	announced	Add reference

Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R, The quantitative proteome of a human cell line. Mol Syst Biol, 7():549(2011) [pubmed]

submitter keyword: Human, U2OS

Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch

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• PRIDE
  1. 28645
     1. InstrumentRef: INSTRUMENT_1
     2. Label: U2OS human cell
     3. ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
     4. Name: OGE fractions of control sample
     5. PublicationRef: PMID22068332