Proteomics

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Comparison of Targeted MS Methods in Activity-Based Protein Profiling 2: DIA

ABSTRACT: To examine the different mass spectrometry approaches to monitoring kinases after enrichment with desthiobiotinylating probes for activity-based protein profiling (ABPP), two experiments were performed with H1993 lung cancer cells. First, cell lysates were pre-treated with DMSO vehicle, dasatinib, or erlotinib prior to addition of the ATP probe for ABPP to compare the differences in kinase labeling associated with examples of kinase inhibitors that vary in target selectivity. Then, to examine changes in cellular signaling, H1993 cells were treated with vehicle controls, BEX-235 (PI3K inhibitor), or Crizotinib. LC-MS/MS using data dependent acquisition, data-independent acquisition (pSMART), parallel reaction monitoring, and selected reaction monitoring (or multiple reaction monitoring) mass spectrometry were used to detect and relatively quantify the desthiobiotinylated kinase peptides.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

DISEASE(S): Non-small Cell Lung Carcinoma

SUBMITTER: John Koomen  

LAB HEAD: John Koomen, PhD

PROVIDER: PXD006096 | Pride | 2017-11-27

REPOSITORIES: Pride

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100815_MM_ABPP_H1993_BEZ_DIA1.raw Raw
100815_MM_ABPP_H1993_BEZ_DIA1.raw (F003752).pride.mztab.gz Mztab
100815_MM_ABPP_H1993_BEZ_DIA1.rawF003752.mzid.gz Mzid
100815_MM_ABPP_H1993_BEZ_DIA1.rawF003752.mzid_100815_MM_ABPP_H1993_BEZ_DIA1.raw_F003752.MGF Mzid
100815_MM_ABPP_H1993_BEZ_DIA1.raw_F003752.dta Raw
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Publications

Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer.

Hoffman Melissa A MA   Fang Bin B   Haura Eric B EB   Rix Uwe U   Koomen John M JM  

Journal of proteome research 20171122 1

Recent developments in instrumentation and bioinformatics have led to new quantitative mass spectrometry platforms including LC-MS/MS with data-independent acquisition (DIA) and targeted analysis using parallel reaction monitoring mass spectrometry (LC-PRM), which provide alternatives to well-established methods, such as LC-MS/MS with data-dependent acquisition (DDA) and targeted analysis using multiple reaction monitoring mass spectrometry (LC-MRM). These tools have been used to identify signal  ...[more]

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