PXD003370 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | 1D LC-MS/MS proteomic profiling of MCF10A, HeLa, Hep G2, and HEK293 cells using peptide-based immunoaffinity enrichment and 105 commercially available monoclonal antibodies to proteins associated with the DNA damage response (DDR) network |
Description | Immunoaffinity enrichment of peptides coupled to multiple reaction monitoring-mass spectrometry (immuno-MRM) enables highly specific, sensitive, and precise quantification of peptides and post-translational modifications. Major obstacles to developing a large number of immuno-MRM assays are the poor availability of monoclonal antibodies (mAbs) validated for immunoaffinity enrichment of peptides and the cost and lead time of developing the antibodies de novo. Although many thousands of mAbs are commercially offered, few have been tested for application to immunoaffinity enrichment of peptides. In this study we tested the success rate of using commercially available mAbs for peptide immuno-MRM assays. We selected 105 commercial mAbs (76 targeting non-modified “pan” epitopes, 29 targeting phosphorylation) to proteins associated with the DNA damage response network. We found that 8 of the 76 pan (11%) and 5 of the 29 phospho-specific mAbs (17%) captured tryptic peptides (detected by LC-MS/MS) of their protein targets from human cell lysates. Seven of these mAbs were successfully used to configure and analytically characterize immuno-MRM assays. By applying selection criteria, the results indicate a success rate up to 24% is possible, establishing the feasibility of screening a large number of catalog antibodies to provide readily-available assay reagents. |
HostingRepository | PRIDE |
AnnounceDate | 2016-04-13 |
AnnouncementXML | Submission_2016-04-13_02:10:20.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Jacob Kennedy |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | carbamoylated residue; phosphorylated residue |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-12-17 23:42:54 | ID requested | |
⏵ 1 | 2016-04-13 02:10:21 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
ProteomeXchange project tag: CPTAC Consortium |
curator keyword: Biomedical |
submitter keyword: Human, monoclonal antibodies, MCF10A, HeLa, HEK293, Hep G2, IR, LC-MS/MS |
Contact List
Amanda G Paulovich |
contact affiliation | Fred Hutchinson Cancer Research Center |
contact email | apaulovi@fredhutch.org |
lab head | |
Jacob Kennedy |
contact affiliation | Fred Hutchinson Cancer Research Center |
contact email | jkennedy@fhcrc.org |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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- PRIDE
- PXD003370
- Label: PRIDE project
- Name: 1D LC-MS/MS proteomic profiling of MCF10A, HeLa, Hep G2, and HEK293 cells using peptide-based immunoaffinity enrichment and 105 commercially available monoclonal antibodies to proteins associated with the DNA damage response (DDR) network