Global discovery of protein kinases and other nucleotide‐binding proteins by mass spectrometry

Xiao, Yongsheng; Wang, Yinsheng

doi:10.1002/mas.21447

Cited by 25 publications

(29 citation statements)

References 119 publications

(199 reference statements)

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“…LC-MS/MS can additionally require relatively large amounts of starting sample material to identify and accurately quantify low abundant protein variants (e.g., specific sites of phosphorylation, acetylation, methylation, point mutations). Furthermore, sample preparation workflows can require multi-dimensional separation strategies and/or targeted depletions [18][19][20][21], while subsequent bioinformatic analysis can require deconstruction of chimeric spectra [22] to effectively quantify specific proteins of interest.…”

Section: Introductionmentioning

confidence: 99%

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Hamza

Bergo

Mamaev

et al. 2020

IJMS

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The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed “Affinity-Bead Assisted Mass Spectrometry” (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.

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Section: Introductionmentioning

confidence: 99%

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Hamza

Bergo

Mamaev

et al. 2020

IJMS

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“…The regulation of metabolic adaptation and reprogramming is highly pleiotropic, coordinating regulation of kinases, transcription factors, and other proteins across multiple signaling pathways (Brooks Robey et al , 2015). Kinases are key transducers of signaling pathways, often clinically actionable, and can be unbiasedly profiled by ABPP (Duncan et al , 2012; Xiao & Wang, 2016). Since GSEA indicated that MAPKs were uniquely upregulated in SKLMS1 cells upon arginine starvation (Fig.…”

Section: Resultsmentioning

confidence: 99%

Systems level profiling of arginine starvation reveals MYC and ERK adaptive metabolic reprogramming

Brashears

Rathore

Schultze

et al. 2020

Preprint

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22Arginine auxotrophy due to the silencing of argininosuccinate synthetase 1 (ASS1) occurs in many 23 cancers, especially sarcomas. Arginine deiminase (ADI-PEG20) therapy exploits this metabolic 24 vulnerability by depleting extracellular arginine, causing arginine starvation. ASS1-negative cells 25 develop resistance to ADI-PEG20 through a metabolic adaptation that includes re-expressing 26 ASS1. As arginine-based multiagent therapies are being developed, further characterization of 27 the changes induced by arginine starvation is needed. In order to develop a systems-level 28 understanding of these changes, activity-based proteomic profiling (ABPP) and 29 phosphoproteomic profiling were performed before and after ADI-PEG20 treatment in ADI-30 PEG20-sensitive and resistant sarcoma cells. When integrated with previous metabolomic 31 profiling (Kremer et al, 2017a), this multi-omic analysis reveals that cellular response to arginine 32 starvation is mediated by adaptive ERK signaling, driving a Myc-Max transcriptional network. 33Concomitantly, these data elucidate proteomic changes that facilitate oxaloacetate production by 34 enhancing glutamine and pyruvate anaplerosis, and altering lipid metabolism to recycle citrate for 35 oxidative glutaminolysis. Based on the complexity of metabolic and cellular signaling interactions, 36 these multi-omic approaches could provide valuable tools for evaluating response to metabolically 37 targeted therapies. 65invariably contribute to ABPP as well (Wolfe et al, 2013; Piazza et al, 2018a; Veyel et al, 2018). 66Ultimately, ABPP integrates multiple informative proteomic parameters and provides a broad view 67 of proteomic regulation. For example, ABPP can identify adaptive kinomic changes based on 68 either altered kinase expression or activity (Duncan et al, 2012). 69The mechanisms of developing resistance to arginine starvation in sarcomas have been 70 partially defined, and include stabilization of nuclear cMyc (Prudner et al, 2019b), and increased 71 glutamine anaplerosis in order to produce aspartate (Kremer et al, 2017a). In addition, others 72 have examined mechanisms of ASS1 re-expression (Tsai et al, 2017; Long et al, 2017) and 73Deptor regulation (Ohshima et al, 2017). However, the underlying proteomic changes that initiate 74 these events and coordinate metabolic reprogramming remain unknown. We pursued systems 75 biology profiling to understand resistance to arginine starvation, as these approaches have proven 76 effective in delineating the adaptive changes involved in highly pleiotropic phenotypes such as 77 drug resistance (Zecena et al, 2018; Galluzzi et al, 2014), Myc activation, and various metabolic 78 changes (Tomita & Kami, 2012; Schaub et al, 2018). 79To understand ADI-PEG20-resistance of ASS1-negative sarcomas at a systems level, we 80 performed multi-omic profiling using phosphoproteomics and activity-based proteomics, and 81 coupled these data with existing metabolomic analyses (Kremer et al, 2017a). ADI-PEG20-82 senstive leiomyosarcoma cells (SKLMS1) h...

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“…All these affinity matrices were based on the 3 most complementary probes (19,15 and 1) which, in combination as the first matrix, were predicted to enrich 315 kinases ( Figure 3B). One or two more good probes among probe 5, 7, 18 and 20b were added to this core matrix to generate seven other matrices.…”

Section: Kinome Purification Using Mixed Probe Matricesmentioning

confidence: 99%

“…The chemical proteomics concept intends to circumvent the choice of kinases to include in a panel and the limitations of the recombinant proteins assays by covering the native kinome in, ideally unbiased, pull-down experiments. [17][18][19] Examples for such ideas are drug-centric profiling, [20][21][22] the KiNativ technology and other covalent acyl nucleotide probes, 23,24 the Kinobeads technology 25,26 or other multiplexed kinase inhibitors beads. 27,28 Today, these experiments are typically analyzed using quantitative mass spectrometry as an assay readout.…”

Section: Introductionmentioning

confidence: 99%

Optimized Chemical Proteomics Assay for Kinase Inhibitor Profiling

et al. 2015

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Solid supported probes have proven to be an efficient tool for chemical proteomics. The kinobeads technology features kinase inhibitors covalently attached to Sepharose for affinity enrichment of kinomes from cell or tissue lysates. This technology, combined with quantitative mass spectrometry, is of particular interest for the profiling of kinase inhibitors. It often leads to the identification of new targets for medicinal chemistry campaigns where it allows a two-in-one binding and selectivity assay. The assay can also uncover resistance mechanisms and molecular sources of toxicity. Here we report on the optimization of the kinobead assay resulting in the combination of five chemical probes and four cell lines to cover half the human kinome in a single assay (∼ 260 kinases). We show the utility and large-scale applicability of the new version of kinobeads by reprofiling the small molecule kinase inhibitors Alvocidib, Crizotinib, Dasatinib, Fasudil, Hydroxyfasudil, Nilotinib, Ibrutinib, Imatinib, and Sunitinib.

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Global discovery of protein kinases and other nucleotide‐binding proteins by mass spectrometry

Cited by 25 publications

References 119 publications

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Systems level profiling of arginine starvation reveals MYC and ERK adaptive metabolic reprogramming

Optimized Chemical Proteomics Assay for Kinase Inhibitor Profiling

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