scholarly journals Integrating mass spectrometry of intact protein complexes into structural proteomics

PROTEOMICS ◽  
2012 ◽  
Vol 12 (10) ◽  
pp. 1547-1564 ◽  
Author(s):  
Suk-Joon Hyung ◽  
Brandon T. Ruotolo
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Structural Proteomics ◽  
Intact Protein

scholarly journals Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications

2020 ◽  
Vol 48 (5) ◽  
pp. 1953-1966
Author(s):  
Lindsay K. Pino ◽  
Jacob Rose ◽  
Amy O'Broin ◽  
Samah Shah ◽  
Birgit Schilling
Keyword(s):  
Mass Spectrometry ◽  
Human Health ◽  
Protein Complexes ◽  
Protein Quantification ◽  
Intact Protein ◽  
Protein Signaling ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Health And Disease ◽  
Proteomics Research

Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein–protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.

scholarly journals Fixed-Charge Trimethyl Pyrilium Modification for Enabling Enhanced Top-Down Mass Spectrometry Sequencing of Intact Protein Complexes

2018 ◽  
Vol 90 (4) ◽  
pp. 2756-2764 ◽  
Author(s):  
Daniel A. Polasky ◽  
Frederik Lermyte ◽  
Michael Nshanian ◽  
Frank Sobott ◽  
Phillip C. Andrews ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Fixed Charge ◽  
Intact Protein ◽  
Top Down ◽  
Top Down Mass Spectrometry

scholarly journals Mass spectrometry: From plasma proteins to mitochondrial membranes

2019 ◽  
Vol 116 (8) ◽  
pp. 2814-2820 ◽  
Author(s):  
Carol V. Robinson
Keyword(s):  
Mass Spectrometry ◽  
Cell Biology ◽  
Protein Complexes ◽  
Intact Protein ◽  
Exchange Reactions ◽  
Soft Landing ◽  
Mass Spectrometers ◽  
Radical Method ◽  
Key Steps ◽  
Soluble Complexes

In this Inaugural Article, I trace some key steps that have enabled the development of mass spectrometry for the study of intact protein complexes from a variety of cellular environments. Beginning with the preservation of the first soluble complexes from plasma, I describe our early experiments that capitalize on the heterogeneity of subunit composition during assembly and exchange reactions. During these investigations, we observed many assemblies and intermediates with different subunit stoichiometries, and were keen to ascertain whether or not their overall topology was preserved in the mass spectrometer. Adapting ion mobility and soft-landing methodologies, we showed how ring-shaped complexes could survive the phase transition. The next logical progression from soluble complexes was to membrane protein assemblies but this was not straightforward. We encountered many pitfalls along the way, largely due to the use of detergent micelles to protect and stabilize complexes. Further obstacles presented when we attempted to distinguish lipids that copurify from those that are important for function. Developing new experimental protocols, we have subsequently defined lipids that change protein conformation, mediate oligomeric states, and facilitate downstream coupling of G protein-coupled receptors. Very recently, using a radical method—ejecting protein complexes directly from native membranes into mass spectrometers—we provided insights into associations within membranes and mitochondria. Together, these developments suggest the beginnings of mass spectrometry meeting with cell biology.

Subunit Architecture of Intact Protein Complexes from Mass Spectrometry and Homology Modeling†

2008 ◽  
Vol 41 (5) ◽  
pp. 617-627 ◽  
Author(s):  
Thomas Taverner ◽  
Helena Hernández ◽  
Michal Sharon ◽  
Brandon T. Ruotolo ◽  
Dijana Matak-Vinković ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Homology Modeling ◽  
Protein Complexes ◽  
Intact Protein

Mass spectrometric characterization of protein structures and protein complexes in condensed and gas phase

2017 ◽  
Vol 23 (6) ◽  
pp. 445-459 ◽  
Author(s):  
Yelena Yefremova ◽  
Bright D Danquah ◽  
Kwabena FM Opuni ◽  
Reham El-Kased ◽  
Cornelia Koy ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Electrospray Mass Spectrometry ◽  
Protein Complexes ◽  
Protein Structures ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Direct Access ◽  
Intact Protein

Proteins are essential for almost all physiological processes of life. They serve a myriad of functions which are as varied as their unique amino acid sequences and their corresponding three-dimensional structures. To fulfill their tasks, most proteins depend on stable physical associations, in the form of protein complexes that evolved between themselves and other proteins. In solution (condensed phase), proteins and/or protein complexes are in constant energy exchange with the surrounding solvent. Albeit methods to describe in-solution thermodynamic properties of proteins and of protein complexes are well established and broadly applied, they do not provide a broad enough access to life-science experimentalists to study all their proteins' properties at leisure. This leaves great desire to add novel methods to the analytical biochemist's toolbox. The development of electrospray ionization created the opportunity to characterize protein higher order structures and protein complexes rather elegantly by simultaneously lessening the need of sophisticated sample preparation steps. Electrospray mass spectrometry enabled us to translate proteins and protein complexes very efficiently into the gas phase under mild conditions, retaining both, intact protein complexes, and gross protein structures upon phase transition. Moreover, in the environment of the mass spectrometer (gas phase, in vacuo), analyte molecules are free of interactions with surrounding solvent molecules and, therefore, the energy of inter- and intramolecular forces can be studied independently from interference of the solvating environment. Provided that gas phase methods can give information which is relevant for understanding in-solution processes, gas phase protein structure studies and/or investigations on the characterization of protein complexes has rapidly gained more and more attention from the bioanalytical scientific community. Recent reports have shown that electrospray mass spectrometry provides direct access to six prime protein complex properties: stabilities, compositions, binding surfaces (epitopes), disassembly processes, stoichiometries, and thermodynamic parameters.

scholarly journals Investigation of intact protein complexes by mass spectrometry

2004 ◽  
Vol 23 (5) ◽  
pp. 368-389 ◽  
Author(s):  
Albert J. R. Heck ◽  
Robert H. H. van den Heuvel
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Intact Protein

scholarly journals Mass spectrometry of intact protein complexes

2013 ◽  
Vol 10 (1) ◽  
pp. 38-38 ◽  
Author(s):  
Allison Doerr
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Intact Protein

ChemInform Abstract: Subunit Architecture of Intact Protein Complexes from Mass Spectrometry and Homology Modeling

ChemInform ◽  
2008 ◽  
Vol 39 (36) ◽  
Author(s):  
Thomas Taverner ◽  
Helena Hernandez ◽  
Michal Sharon ◽  
Brandon T. Ruotolo ◽  
Dijana Matak-Vinkovic ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Homology Modeling ◽  
Protein Complexes ◽  
Intact Protein
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