Native Mass Spectrometry at the Convergence of Structural Biology and Compositional Proteomics

Capillary Electrophoresis-Mass Spectrometry for Top-Down Proteomics

Mass spectrometry (MS)-based top-down proteomics (TDP) characterizes proteoforms in cells, tissues, and biological fluids (e.g., human plasma) to better our understanding of protein function and to discover new protein biomarkers for disease diagnosis and therapeutic development. Separations of proteoforms with high peak capacity are needed due to the high complexity of biological samples. Capillary electrophoresis (CE)-MS has been recognized as a powerful analytical tool for protein analysis since the 1980s owing to its high separation efficiency and sensitivity of CE-MS for proteoforms. Here, we review benefits of CE-MS for advancing TDP, challenges and solutions of the method, and the main research areas in which CE-MS-based TDP can make significant contributions. We provide a brief perspective of CE-MS-based TDP moving forward.

Optimization of Capillary Vibrating Sharp-Edge Spray Ionization for Native Mass Spectrometry of Triplex DNA

Capillary vibrating sharp-edge spray ionization (cVSSI) has been used to study the effects of applied voltage and mass spectrometer heated inlet transfer tube temperature on DNA triplex ion production for native mass spectrometry (MS) samples. Overall, medium applied voltage (-900 to -1000 V) results in better ion production of the desired triplex ions (Tri) (i.e., those without cation adducts such as NH4 +, Na+, and K+); mass spectral peak intensities for the [Tri]8-, [Tri]9-, and [Tri]10- ions increase by ∼70, ∼260, and ∼125 fold, respectively, compared to higher voltages (-1100 to -1500 V). The latter voltages result in increased triplex adduct ion (Tri + ad) formation; for the 8-, 9-, and 10- charge states; the ratios of Tri to Tri+ad ion abundances increase by ∼6 fold for the lower voltage. By capillary inlet temperatures of 300 to 400 °C, Tri ion abundances reach maximum values of 6.1 × 105 ([Tri]8-), 2.9 × 106 ([Tri]9-), and 6.4 × 105 ([Tri]10-). Ion abundances for the respective species decrease by ∼4, ∼14, and ∼190 fold at a heated inlet transfer tube temperature of 450 °C. The abundances for Tri+ad ions species generally follow a similar trend as a function of heated inlet transfer tube temperature with the exception that maximum values are obtained at 250 °C. The abundances for DNA triplex fragment ions (Tri-fr) reach maximum values at 400 °C resulting from excessive, in-source ion activation. From these studies, the optimal capillary MS inlet temperature for production of large oligonucleotides by cVSSI is 300 to 350 °C and the applied voltage should be maintained at ∼ -900 V. These studies lay the foundation for native MS of large oligonucleotide species in negative-ion mode exploiting the sensitivity enhancements of cVSSI.

Native Top-Down Proteomics of Endogenous Protein Complexes Enabled by Online Two-Dimensional Liquid Chromatography

Protein complexes are essential for virtually all biological processes, yet their structural characterization remains a major challenge due to their heterogeneous, dynamic nature and the complexity of the proteome. Native top-down mass spectrometry (nTDMS) has emerged as a powerful tool for comprehensive structural characterization of purified protein complexes, but its application to endogenous protein complexes in the proteome is challenging and typically requires labor-intensive and time-consuming prefractionation. Here, for the first time, we develop a nondenaturing online two-dimensional liquid chromatography (2D-LC) method for native top-down proteomics (nTDP), enabling high-throughput structural analysis of endogenous protein complexes. The automated, online interfacing of size-exclusion and mixed-bed ion-exchange chromatography achieves high coverage of endogenous protein complexes. We further develop a multistage nTDMS approach that enables comprehensive structural characterization within the chromatographic timescale, capturing intact non-covalent complexes, released subunits/cofactors, and backbone fragments. Our analysis detected 133 native proteoforms and endogenous protein complexes (up to 350 kDa) from human heart tissue in less than two hours. Such technological leaps in high-throughput structural characterization of endogenous protein complexes will advance large-scale nTDP studies in health and disease.

Accessing Different Protein Conformer Ensembles with Tunable Capillary Vibrating Sharp-Edge Spray Ionization

Capillary vibrating sharp-edge spray ionization (cVSSI) has been used to control the droplet charging of nebulized microdroplets and monitor effects on protein ion conformation makeup as determined by mass spectrometry (MS). Here it is observed that the application of voltage results in noticeable differences to the charge state distributions (CSDs) of ubiquitin ions. The data can be described most generally in three distinct voltage regions: Under low-voltage conditions (<+200 V, LV regime), low charge states (2+ to 4+ ions) dominate the mass spectra. For midvoltage conditions (+200 to +600 V, MV regime), higher charge states (7+ to 12+ ions) are observed. For high-voltage conditions (>+600 V, HV regime), the "nano-electrospray ionization (nESI)-type distribution" is achieved in which the 6+ and 5+ species are observed as the dominant ions. Analysis of these results suggests that different pathways to progeny nanodroplet production result in the observed ions. For the LV regime, aerodynamic breakup leads to low charge progeny droplets that are selective for the native solution conformation ensemble of ubiquitin (minus multimeric species). In the MV regime, the large droplets persist for longer periods of time, leading to droplet heating and a shift in the conformation ensemble to partially unfolded species. In the HV regime, droplets access progeny nanodroplets faster, leading to native conformation ensemble sampling as indicated by the observed nESI-type CSD. The notable observation of limited multimer formation and adduct ion formation in the LV regime is hypothesized to result from droplet aero breakup resulting in protein and charge carrier partitioning in sampled progeny droplets. The tunable droplet charging afforded by cVSSI presents opportunities to study the effects of the droplet charge, droplet size, and mass spectrometer inlet temperature on the conformer ensemble sampled by the mass spectrometer. Additionally, the approach may provide a tool for rapid comparison of protein stabilities.

Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry

Native proteomics measures endogenous proteoforms and protein complexes under a near physiological condition using native mass spectrometry (nMS) coupled with liquid-phase separations. Native proteomics should provide the most accurate bird's-eye view of proteome dynamics within cells, which is fundamental for understanding almost all biological processes. nMS has been widely employed to characterize well-purified protein complexes. However, there are only very few trials of utilizing nMS to measure proteoforms and protein complexes in a complex sample (i.e., a whole cell lysate). Here, we pioneer the native proteomics measurement of large proteoforms or protein complexes up to 400 kDa from a complex proteome via online coupling of native capillary zone electrophoresis (nCZE) to an ultra-high mass range (UHMR) Orbitrap mass spectrometer. The nCZE-MS technique enabled the measurement of a 115-kDa standard protein complex while consuming only about 0.1 ng of protein material. nCZE-MS analysis of an E.coli cell lysate detected 72 proteoforms or protein complexes in a mass range of 30-400 kDa in a single run while consuming only 50-ng protein material. The mass distribution of detected proteoforms or protein complexes agreed well with that from mass photometry measurement. This work represents a technical breakthrough in native proteomics for measuring complex proteomes.

Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry

Native proteomics measures endogenous proteoforms and protein complexes under a near physiological condition using native mass spectrometry (nMS) coupled with liquid-phase separations. Native proteomics should provide the most accurate bird's-eye view of proteome dynamics within cells, which is fundamental for understanding almost all biological processes. nMS has been widely employed to characterize well-purified protein complexes. However, there are only very few trials of utilizing nMS to measure proteoforms and protein complexes in a complex sample (i.e., a whole cell lysate). Here, we pioneer the native proteomics measurement of large proteoforms or protein complexes up to 400 kDa from a complex proteome via online coupling of native capillary zone electrophoresis (nCZE) to an ultra-high mass range (UHMR) Orbitrap mass spectrometer. The nCZE-MS technique enabled the measurement of a 115-kDa standard protein complex while consuming only about 0.1 ng of protein material. nCZE-MS analysis of an E . coli cell lysate detected 72 proteoforms or protein complexes in a mass range of 30-400 kDa in a single run while consuming only 50-ng protein material. The mass distribution of detected proteoforms or protein complexes agreed well with that from mass photometry measurement. This work represents a technical breakthrough in native proteomics for measuring complex proteomes.

Cyclic Ion Mobility-Mass Spectrometry and Tandem Collision Induced Unfolding for Quantification of Elusive Protein Biomarkers

Sensitive analytical techniques that are capable of detecting and quantifying disease-associated biomolecules are indispensable in our efforts to understand disease mechanisms and guide therapeutic intervention through early detection, accurate diagnosis, and effective monitoring of disease. Parkinson's Disease (PD), for example, is one of the most prominent neurodegenerative disorders in the world, but the diagnosis of PD has primarily been based on the observation of clinical symptoms. The protein α-synuclein (α-syn) has emerged as a promising biomarker candidate for PD, but a lack of analytical methods to measure complex disease-associated variants of α-syn has prevented its widespread use as a biomarker. Antibody-based methods such as immunoassays and mass spectrometry-based approaches have been used to measure a limited number of α-syn forms; however, these methods fail to differentiate variants of α-syn that display subtle differences in only the sequence and structure. In this work, we developed a cyclic ion mobility-mass spectrometry method that combines multiple stages of activation and timed ion selection to quantify α-syn variants using both mass- and structure-based measurements. This method can allow for the quantification of several α-syn variants present at physiological levels in biological fluid. Taken together, this approach can be used to galvanize future efforts aimed at understanding the underlying mechanisms of PD and serves as a starting point for the development of future protein-structure-based diagnostics and therapeutic interventions.

Studying Membrane Protein-Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes

Native mass spectrometry (nMS) has emerged as a key analytical tool to study the organizational states of proteins and their complexes with both endogenous and exogenous ligands. Specifically, for membrane proteins, it provides a key analytical dimension to determine the identity of bound lipids and to decipher their effects on the observed structural assembly. We recently developed an approach to study membrane proteins directly from intact and tunable lipid membranes where both the biophysical properties of the membrane and its lipid compositions can be customized. Extending this, we use our liposome-nMS platform to decipher the lipid specificity of membrane proteins through their multiorganelle trafficking pathways. To demonstrate this, we used VAMP2 and reconstituted it in the endoplasmic reticulum (ER), Golgi, synaptic vesicle (SV), and plasma membrane (PM) mimicking liposomes. By directly studying VAMP2 from these customized liposomes, we show how the same transmembrane protein can bind to different sets of lipids in different organellar-mimicking membranes. Considering that the cellular trafficking pathway of most eukaryotic integral membrane proteins involves residence in multiple organellar membranes, this study highlights how the lipid-specificity of the same integral membrane protein may change depending on the membrane context. Further, leveraging the capability of the platform to study membrane proteins from liposomes with curated biophysical properties, we show how we can disentangle chemical versus biophysical properties, of individual lipids in regulating membrane protein assembly.

ProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data

Native mass spectrometry has recently moved alongside traditional structural biology techniques in its ability to provide clear insights into the composition of protein complexes. However, to date, limited software tools are available for the comprehensive analysis of native mass spectrometry data on protein complexes, particularly for experiments aimed at elucidating the composition of an intact protein complex. Here, we introduce ProSight Native as a start-to-finish informatics platform for analyzing native protein and protein complex data. Combining mass determination via spectral deconvolution with a top-down database search and stoichiometry calculations, ProSight Native can determine the complete composition of protein complexes. To demonstrate its features, we used ProSight Native to successfully determine the composition of the homotetrameric membrane complex Aquaporin Z. We also revisited previously published spectra and were able to decipher the composition of a heterodimer complex bound with two noncovalently associated ligands. In addition to determining complex composition, we developed new tools in the software for validating native mass spectrometry fragment ions and mapping top-down fragmentation data onto three-dimensional protein structures. Taken together, ProSight Native will reduce the informatics burden on the growing field of native mass spectrometry, enabling the technology to further its reach.

MASH Native: a unified solution for native top-down proteomics data processing

MOTIVATION

Native top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking.

RESULTS

We have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a "one-stop shop" for characterizing both native protein complexes and proteoforms.

AVAILABILITY AND IMPLEMENTATION

The MASH Native app, video tutorials, written tutorials, and additional documentation are freely available for download at https://labs.wisc.edu/gelab/MASH_Explorer/MASHSoftware.php. All data files shown in user tutorials are included with the MASH Native software in the download .zip file.

Integrated mass spectrometry strategy for functional protein complex discovery and structural characterization

The discovery of functional protein complex and the interrogation of the complex structure-function relationship (SFR) play crucial roles in the understanding and intervention of biological processes. Affinity purification-mass spectrometry (AP-MS) has been proved as a powerful tool in the discovery of protein complexes. However, validation of these novel protein complexes as well as elucidation of their molecular interaction mechanisms are still challenging. Recently, native top-down MS (nTDMS) is rapidly developed for the structural analysis of protein complexes. In this review, we discuss the integration of AP-MS and nTDMS in the discovery and structural characterization of functional protein complexes. Further, we think the emerging artificial intelligence (AI)-based protein structure prediction is highly complementary to nTDMS and can promote each other. We expect the hybridization of integrated structural MS with AI prediction to be a powerful workflow in the discovery and SFR investigation of functional protein complexes.

A Database of Accurate Electrophoretic Migration Patterns for Human Proteins

Native molecular weight (MW) is one of the defining features of proteins. Denaturing gel electrophoresis (SDS-PAGE) is a very popular technique for separating proteins and determining their MW. Coupled with antibody-based detection, SDS-PAGE is widely applied for protein identification and quantitation. Yet, electrophoresis is poorly reproducible and the MWs obtained are often inaccurate. This hampers antibody validation and negatively impacts the reliability of western blot data, resulting worldwide in a considerable waste of reagents and labour. We argue that, to alleviate these problems there is a need to establish a database of reference MWs measured by SDS-PAGE. Using mass spectrometry as an orthogonal detection method, we acquired electrophoretic migration patterns for approximately 10'000 human proteins in five commonly used cell lines. We applied a robust internal calibration of migration to determine accurate and reproducible molecular weights. This in turn allows merging replicates to increase accuracy, but also enables comparing different cell lines. Mining of the data obtained highlights structural factors that affect migration of distinct classes of proteins. When combined with peptide coverage, the data produced recapitulates known post-translational modifications and differential splicing and can be used to formulate hypotheses on new or poorly known processing events. The full information is freely accessible as a web resource through a user friendly graphical interface (https://pumba.dcsr.unil.ch/). We anticipate that this database will be useful to investigators worldwide for troubleshooting western blot experiments, but could also contribute to the characterization of human proteoforms.

Mass spectrometry of intact membrane proteins: shifting towards a more native-like context

Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.

Seeing the complete picture: proteins in top-down mass spectrometry

Top-down protein mass spectrometry can provide unique insights into protein sequence and structure, including precise proteoform identification and study of protein–ligand and protein–protein interactions. In contrast with the commonly applied bottom-up approach, top-down approaches do not include digestion of the protein of interest into small peptides, but instead rely on the ionization and subsequent fragmentation of intact proteins. As such, it is fundamentally the only way to fully characterize the composition of a proteoform. Here, we provide an overview of how a top-down protein mass spectrometry experiment is performed and point out recent applications from the literature to the reader. While some parts of the top-down workflow are broadly applicable, different research questions are best addressed with specific experimental designs. The most important divide is between studies that prioritize sequence information (i.e., proteoform identification) versus structural information (e.g., conformational studies, or mapping protein–protein or protein–ligand interactions). Another important consideration is whether to work under native or denaturing solution conditions, and the overall complexity of the sample also needs to be taken into account, as it determines whether (chromatographic) separation is required prior to MS analysis. In this review, we aim to provide enough information to support both newcomers and more experienced readers in the decision process of how to answer a potential research question most efficiently and to provide an overview of the methods that exist to answer these questions.