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Open AccessArticle

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

1
Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA
2
Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
3
Adeptrix Corporation, Beverly, MA 01915, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(6), 2016; https://doi.org/10.3390/ijms21062016
Received: 9 February 2020 / Revised: 10 March 2020 / Accepted: 13 March 2020 / Published: 16 March 2020
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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. View Full-Text
Keywords: targeted proteomics; PTMs; BAMS; bead assisted mass spectrometry; MALDI MS; multiplex assays targeted proteomics; PTMs; BAMS; bead assisted mass spectrometry; MALDI MS; multiplex assays
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MDPI and ACS Style

Hamza, G.M.; Bergo, V.B.; Mamaev, S.; Wojchowski, D.M.; Toran, P.; Worsfold, C.R.; Castaldi, M.P.; Silva, J.C. Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics. Int. J. Mol. Sci. 2020, 21, 2016. https://doi.org/10.3390/ijms21062016

AMA Style

Hamza GM, Bergo VB, Mamaev S, Wojchowski DM, Toran P, Worsfold CR, Castaldi MP, Silva JC. Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics. International Journal of Molecular Sciences. 2020; 21(6):2016. https://doi.org/10.3390/ijms21062016

Chicago/Turabian Style

Hamza, Ghaith M.; Bergo, Vladislav B.; Mamaev, Sergey; Wojchowski, Don M.; Toran, Paul; Worsfold, Camilla R.; Castaldi, M. P.; Silva, Jeffrey C. 2020. "Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics" Int. J. Mol. Sci. 21, no. 6: 2016. https://doi.org/10.3390/ijms21062016

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