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DKFZ Krijgsveld Lab - QuaNPA

Targeted MS Experiment

 
Label-free Parallel Reaction Monitoring (PRM) analysis of selected novel potential targets of IFNg stimulation in Hela cells.
Permanent Link: https://panoramaweb.org/9BBjQ6.url Share
Borteçen T, Müller T, Krijgsveld J. An integrated workflow for quantitative analysis of the newly synthesized proteome. bioRxiv [Internet]. 2023 Jan 1;2023.03.03.530942. Available from: http://biorxiv.org/content/early/2023/03/03/2023.03.03.530942.abstract
Data License: CC BY 4.0 | ProteomeXchange: PXD043967 | doi: https://doi.org/10.6069/xmzz-y959
  • Organism: Homo sapiens
  • Instrument: Q Exactive HF
  • SpikeIn: No
  • Keywords: QuaNPA, IFNg, PRM
  • Lab head: Jeroen Krijgsveld Submitter: Toman Borteçen
Abstract
In order to validate the changes in protein expression, measured via a newly developed semi-automated workflow for quantitative analysis of the newly synthesized proteome (https://www.biorxiv.org/content/10.1101/2023.03.03.530942v1.full), targeted proteomic analysis was carried out.
Experiment Description
Hela cells were treated with either 0.5% (w/v) BSA or 10 ng/mL recombinant IFNg for either 4h or 24h. Samples for PRM analysis were prepared using SP3 (https://www.embopress.org/doi/full/10.15252/msb.20145625). Quantitative measurements of tryptic peptides, was carried out using an EASY-nLC 1200 system coupled to a Q Exactive HF mass spectrometer.
Sample Description
Hela cells were treated with either 0.5% (w/v) BSA or 10 ng/mL recombinant IFNg for either 4h or 24h. Samples for PRM analysis were prepared using SP3 (https://www.embopress.org/doi/full/10.15252/msb.20145625).
Created on 7/20/23, 5:13 PM

Mass Spec Search

 

Targeted MS Runs

 
Clustergrammer Heatmap
 
Download
01_refined_TB_IFNg_target_PRM_2023-07-19_23-14-08.sky.zip
109 MB 
2023-07-20 17:13:5511525282112

QuaNPA - Supplementry Figure 9

 

Supplementary Figure 9

Overview of the TIC normalized peak areas of the targeted peptides, analysed in Hela cells treated with 10 ng/mL IFNg or 0.5% BSA for 4 h and 24 h, using PRM measurements. Data are based on 3 experimental replicates.

Prosit Spectral Libraries

 

The spectral library, which was used in the analysis, was generated using Prosit (https://www.nature.com/articles/s41592-019-0426-7). More specifically the Prosit_intensity_hcd_2020 and Prosit_2019_irt intensity and retention time prediction models were used.

A list of peptide targets, with defined charge states and normalized collision energies was used as input for the prediction.

 

  Attached Files  
   
 Prosit_input.csv