Expression data from human HEK293 cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE35084 | GEO | 2012/01/14
SECONDARY ACCESSION(S): PRJNA150915
REPOSITORIES: GEO
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For phosphoproteomic analyses cells were treated with LPA, antagonists or solvent at least in triplicate as described above and lysed in 100 mM Tris pH 7.6, 4% SDS, PhosSTOP (Roche, #4906845001), Protease Inhibitor Cocktail (Sigma, P8340). Analysis of OCMI91s lysates were performed as described [PMID: 19029910]. The protocol was modified to use 12 ug of peptide per channel for TMT labeling, resulting in 500 ug multiplexed samples. LC-MS2 analysis was performed on 50% of the corresponding sample material rehydrated in 0.1% formic acid as published [PMID: 19029910]. Detailed information on instrumentation parametrization was extracted and summarized using MARMoSET [PMID: 310976732] and is included in the repository-deposited data set.
Peptide/spectrum matching as well as TMT quantitation was performed using the MaxQuant suit of algorithms (versions 1.6.8.0, [PMID: 19029910]) against the human canonical and isoforms Uniprot database (downloaded 20190819, 173199 entries). Mass spectrometric raw data along with documentation of instrumentation parameters governing its acquisition as well as MaxQuant parameters employed are deposited. Data were filtered for rows containing no zero values, and analyzed by paired Student's t-test (blocking on replicate set / phosphoproteome analysis chip). Thresholds were set according to the dynamic range of the assay to FC >1.2x or <0.83x and p <0.1.
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