Ahrends Lab - Signaling targeted proteomics

A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells

  • Organism: Homo sapiens
  • Instrument: Q Exactive HF,Orbitrap Fusion Lumos
  • SpikeIn: Yes
  • Keywords: PRM, high resolution, low abundant proteins, UPR, signalling proteins
  • Lab head: Robert Ahrends
Many cellular events are driven by changes in protein expression, measurable by mass spectrometry or antibody-based assays. However, using conventional technology, the analysis of transcription factor or membrane receptor expression is often limited by an insufficient sensitivity and specificity. To overcome this limitation, we have developed a high-resolution targeted proteomics strategy, which allows quantification down to the lower attomol range in a straightforward way without any prior enrichment or fractionation approaches. The method applies isotope-labeled peptide standards for quantification of the protein of interest. As proof of principle, we applied the improved workflow to proteins of the unfolded protein response (UPR), a signaling pathway of great clinical importance, and could for the first time detect and quantify all major UPR receptors, transducers and effectors that are not readily detectable via antibody-based-, SRM- or conventional PRM assays. As transcription and translation is central to the regulation of UPR, quantification and determination of protein copy numbers in the cell is important for our understanding of the signaling process as well as how pharmacologic modulation of these pathways impacts on the signaling. These questions can be answered using our newly established workflow as exemplified in an experiment using UPR perturbation in a glioblastoma cell lines.
Created on 1/10/19, 11:34 AM
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20180801_UPR_paper_celllines.zip2019-01-10 11:32:46819381369
20180406_180307CN1_Heavy&Light_paper_QExHF02_calcurve3.zip2019-01-10 11:32:468214214427
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20180329_180307CN1_Heavy&Light_paper_QExHF02_24hr.zip2019-01-10 11:32:45821421569
20180327_180307CN1_Heavy&Light_paper_QExHF03_60k.zip2019-01-10 11:32:45821421789
20180327_180307CN1_Heavy&Light_paper_QExHF03_30k.zip2019-01-10 11:32:45821421803
20180327_180307CN1_Heavy&Light_paper_QExHF03_240k.zip2019-01-10 11:32:45821421709
20180327_180307CN1_Heavy&Light_paper_QExHF03_15k.zip2019-01-10 11:32:45821421649
20180327_180307CN1_Heavy&Light_paper_QExHF03_120k.zip2019-01-10 11:32:45821421803
20180406_180307CN1_Heavy&Light_paper_QExHF02_calcurve2.zip2019-01-10 11:32:458214215427
20180614_180307CN1_Heavy&Light_paper_QExHF03_240_filltime.zip2019-01-10 11:32:458214218215
20180417_180307CN1_Heavy&Light_paper_QExHF01_6hr.zip2019-01-10 11:32:45821421549
20180415_180307CN1_Heavy&Light_paper_QExHF01_16hr.zip2019-01-10 11:32:458214215012
20180508_UPR_U87_H&L_paper_Lumos.zip2019-01-10 11:32:45821421469
20180507_UPR_LN1_T98_H&L_paper_Lumos.zip2019-01-10 11:32:458214214618
20180430_UPR_A1_LN2_H&L_paper_Lumos.zip2019-01-10 11:32:458214214618
20180502_UPR_SNB_H&L_paper_Lumos.zip2019-01-10 11:32:44821421469