PXD000623 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2013-12-18 |
AnnouncementXML | Submission_2014-02-20_06:21:13.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD000623 |
ReviewLevel | Non peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Eduard Sabidó |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; neutral loss: 63.998285; iodoacetamide - site C; iodoacetamide derivatized residue |
Instrument | radial ejection linear ion trap |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: HEK293,Human, primary keratinocyltes, quantification |
Contact List
H. Alexander Ebhardt |
contact attribute | hebhardt@imsb.biol.ethz.ch |
contact affiliation | ETH Zurich |
contact email | hebhardt@imsb.biol.ethz.ch |
Eduard Sabidó |
contact attribute | eduard.sabido@crg.eu |
contact affiliation | CGR Barcelona |
contact email | eduard.sabido@crg.eu |
Full Dataset Link List
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/2013/12/PXD000623 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- 33075
- InstrumentRef: INSTRUMENT_1
- Label: HEK293
- ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
- Name: ERLIC fractionation HEK293
- 33078
- InstrumentRef: INSTRUMENT_1
- Label: F8
- ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
- Name: ERLIC FRACTION 8
- 33080
- InstrumentRef: INSTRUMENT_1
- Label: quant kera
- ModificationList: iodoacetamide derivatized residue, monohydroxylated residue, neutral loss,
- Name: Keratinocytes
- 33073
- InstrumentRef: INSTRUMENT_1
- Label: HEK293
- ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
- Name: ERLIC fractionation HEK293
- 33076
- InstrumentRef: INSTRUMENT_1
- Label: HEK293
- ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
- Name: ERLIC fractionation HEK293
- 33071
- InstrumentRef: INSTRUMENT_1
- Label: HEK293
- ModificationList: monohydroxylated residue, neutral loss, iodoacetamide - site C,
- Name: ERLIC fractionation HEK293
- 33079
- InstrumentRef: INSTRUMENT_1
- Label: F9
- ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
- Name: ERLIC FRACTION 9
- 33077
- InstrumentRef: INSTRUMENT_1
- Label: F7
- ModificationList: monohydroxylated residue, neutral loss, iodoacetamide derivatized residue,
- Name: ERLIC FRACTION 7
- 33072
- InstrumentRef: INSTRUMENT_1
- Label: F10
- ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
- Name: ERLIC FRACTION 10
- 33074
- InstrumentRef: INSTRUMENT_1
- Label: HEK293
- ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss,
- Name: ERLIC fractionation HEK293