PXD000623

PXD000623 is an original dataset announced via ProteomeXchange.

Title	Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell general and cell type-specific signaling proteins
Description	Relating protein concentration to cell-type-specific responses is one of the remaining challenges for obtaining a quantitative systems level understanding of mammalian signaling. Here we used mass-spectrometry (MS)- and antibody-based quantitative proteomic approaches to measure protein abundances for 75% of a hand-curated reconstructed ErbB network of 198 proteins, in two established cell types (HEK293 and MCF-7) and in primary keratinocyte cells. Comparison with other quantitative studies allowed building a set of ErbB network proteins expressed in all cells and another which are cell-specific and could impart specific properties to the network. As a proof-of-concept of the importance of protein concentration, we generated a small simplified mathematical model encompassing ligand binding, followed by receptor dimerization, activation, and degradation. The model predicts ErbB phosphorylation in HEK293, MCF-7, and keratinocyte cells simply by incorporating cell-type-specific ErbB1, ErbB2, and caveolin-1 abundances but otherwise contains similar rate constants. Altogether, the data provide a resource for protein abundances and localization to be included in larger mathematical models, enabling the generation of cell-type-specific computational models. Shotgun MS/MS analysis was conducted on HEK293 cells and on primary keratinocytes and SRM was used for all 3 cell types. Acquired data were analyzed using the Proteome Discoverer software suite (v1.3.0.339, Thermo Fisher Scientific), and the Mascot search engine (v2.3, Matrix Science) was used for peptide identification. Data were searched against an in-house generated database containing all proteins corresponding to human in the Swissprot human database (as of 3/2013) with 600 added common contaminants, as previously described, with a total number of 37 694 sequences in the database. A precursor ion mass tolerance of 7 ppm at the MS1 level was used, and up to three miscleavages for trypsin were allowed. The fragment ion mass tolerance was set to 0.5 Da. Oxidation of methionine and protein acetylation at the N-terminal was defined as variable modification. Carbamidomethylation on cysteines was set as a fix modification. The identified peptides were filtered using a FDR < 5%.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:51:38.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000623
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	H. Alexander Ebhardt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; iodoacetamide - site C
Instrument	LTQ Orbitrap; instrument model: LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-12-05 15:52:06	ID requested
1	2013-12-18 07:25:18	announced
2	2014-02-20 06:21:14	announced	Adding reference.
⏵ 3	2014-07-28 00:51:39	announced	Updated project metadata.

Kiel C, Ebhardt HA, Burnier J, Portugal C, Sabid, ó E, Zimmermann T, Aebersold R, Serrano L, Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. J Proteome Res, 13(1):300-13(2014) [pubmed]

submitter keyword: HEK293,Human, primary keratinocyltes, quantification

H. Alexander Ebhardt
contact affiliation	D_BIOL
contact email	ebhardt@imsb.biol.ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000623
     1. Label: PRIDE project
     2. Name: Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell general and cell type-specific signaling proteins