Mass Spectrometry-Cleavable Protein N-Terminal Tagging Strategy for System-Level Protease Activity Profiling

2021 ◽  
Author(s):  
Zixiang Fang ◽  
Maheshika S. K. Wanigasekara ◽  
Akop Yepremyan ◽  
Brandon Lam ◽  
Pawan Thapa ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protease Activity ◽  
System Level ◽  
Activity Profiling

scholarly journals N-Terminomics Strategies for Protease Substrates Profiling

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4699
Author(s):  
Mubashir Mintoo ◽  
Amritangshu Chakravarty ◽  
Ronak Tilvawala
Keyword(s):  
Mass Spectrometry ◽  
Protease Activity ◽  
Viral Infections ◽  
Mass Spectrometry Analysis ◽  
Post Translational Modification ◽  
Spectrometry Analysis ◽  
Physiological Conditions ◽  
Inflammatory Conditions ◽  
Biological Mixtures

Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.

Global Protease Activity Profiling Identifies HER2-Driven Proteolysis in Breast Cancer

2021 ◽  
Author(s):  
Eugenia C. Salcedo ◽  
Michael B. Winter ◽  
Natalia Khuri ◽  
Giselle M. Knudsen ◽  
Andrej Sali ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Protease Activity ◽  
Activity Profiling

scholarly journals Predictive models of protease specificity based on quantitative protease-activity profiling data

2019 ◽  
Vol 1867 (11) ◽  
pp. 140253
Author(s):  
Gennady G. Fedonin ◽  
Alexey Eroshkin ◽  
Piotr Cieplak ◽  
Evgenii V. Matveev ◽  
Gennady V. Ponomarev ◽  
...  
Keyword(s):  
Predictive Models ◽  
Protease Activity ◽  
Activity Profiling ◽  
Protease Specificity

Biological signalling activity measurements using mass spectrometry

2011 ◽  
Vol 434 (2) ◽  
pp. 189-199 ◽  
Author(s):  
Pedro R. Cutillas ◽  
Claus Jørgensen
Keyword(s):  
Mass Spectrometry ◽  
Present Review ◽  
System Level ◽  
Comprehensive Understanding ◽  
Disease Biology ◽  
Activity Measurements

MS (mass spectrometry) techniques are rapidly evolving to high levels of performance and robustness. This is allowing the application of these methods to the interrogation of signalling networks with unprecedented depth and accuracy. In the present review we discuss how MS-based multiplex quantification of kinase activities and phosphoproteomics provide complementary means to assess biological signalling activity. In addition, we discuss how a wider application of these analytical concepts to quantify kinase signalling will result in a more comprehensive understanding of normal and disease biology at the system level.

scholarly journals The podocyte protease web: uncovering the gatekeepers of glomerular disease

2018 ◽  
Vol 315 (6) ◽  
pp. F1812-F1816 ◽  
Author(s):  
Markus M. Rinschen ◽  
Pitter F. Huesgen ◽  
Rachelle E. Koch
Keyword(s):  
Mass Spectrometry ◽  
Diabetic Nephropathy ◽  
Focal Segmental Glomerulosclerosis ◽  
Therapeutic Intervention ◽  
Protease Activity ◽  
Glomerular Disease ◽  
Protein Signaling ◽  
Tissue Heterogeneity ◽  
Glomerular Diseases ◽  
Damage Response

Proteases regulate glomerular physiology. The last decade has revealed a multitude of podocyte proteases that govern the glomerular response to numerous chemical, mechanical, and metabolic cues. These proteases form a protein signaling web that integrates stress stimuli and serves as a key controller of the glomerular microenvironment. Both the extracellular and intracellular proteolytic networks are perturbed in focal segmental glomerulosclerosis, as well as hypertensive and diabetic nephropathy. Accordingly, the highly intertwined podocyte protease web is an integrative part of the podocyte’s damage response. Novel mass spectrometry-based technologies will help to untangle this proteolytic network: functional readouts acquired from deep podocyte proteomics, single glomerular proteomics, and degradomics have exposed unanticipated protease activity in podocytes. Future efforts should characterize the interdependency and upstream regulation of key proteases, along with their role in promoting tissue heterogeneity in glomerular diseases. These efforts will not only illuminate the machinery of podocyte proteostasis but also reveal avenues for therapeutic intervention in the podocyte protease web.

scholarly journals Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials

2018 ◽  
Vol 410 (24) ◽  
pp. 6067-6077 ◽  
Author(s):  
Tong Zhang ◽  
Matthew J. Gaffrey ◽  
Brian D. Thrall ◽  
Wei-Jun Qian
Keyword(s):  
Mass Spectrometry ◽  
Engineered Nanomaterials ◽  
System Level ◽  
Biological Responses

scholarly journals Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Martin Steger ◽  
Vadim Demichev ◽  
Mattias Backman ◽  
Uli Ohmayer ◽  
Phillip Ihmor ◽  
...  
Keyword(s):  
Neural Network ◽  
Mass Spectrometry ◽  
Sample Preparation ◽  
Mode Of Action ◽  
System Level ◽  
High Temporal Resolution ◽  
Time Resolved ◽  
Data Independent Acquisition ◽  
Wide Scale

AbstractMass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with data-independent acquisition (DIA)-MS and neural network-based data processing specifically optimized for ubiquitinomics. Compared to data-dependent acquisition (DDA), our method more than triples identification numbers to 70,000 ubiquitinated peptides in single MS runs, while significantly improving robustness and quantification precision. Upon inhibition of the oncology target USP7, we simultaneously record ubiquitination and consequent changes in abundance of more than 8,000 proteins at high temporal resolution. While ubiquitination of hundreds of proteins increases within minutes of USP7 inhibition, we find that only a small fraction of those are ever degraded, thereby dissecting the scope of USP7 action. Our method enables rapid mode-of-action profiling of candidate drugs targeting DUBs or ubiquitin ligases at high precision and throughput.

Profiling Protease Activity in Laundry Detergents with Peptide Arrays and SAMDI Mass Spectrometry

2019 ◽  
Vol 58 (25) ◽  
pp. 10692-10697 ◽  
Author(s):  
Raymond Dai ◽  
Alexei S. Ten ◽  
Milan Mrksich
Keyword(s):  
Mass Spectrometry ◽  
Protease Activity ◽  
Peptide Arrays ◽  
Laundry Detergents

scholarly journals Protease Activity Profiling via Programmable Phage Display of Comprehensive Proteome-Scale Peptide Libraries

Cell Systems ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 375-381.e4
Author(s):  
Gabriel D. Román-Meléndez ◽  
Thiagarajan Venkataraman ◽  
Daniel R. Monaco ◽  
H. Benjamin Larman
Keyword(s):  
Phage Display ◽  
Protease Activity ◽  
Peptide Libraries ◽  
Activity Profiling
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