Remodeling nanoDESI Platform with Ion Mobility Spectrometry to Expand Protein Coverage in Cancerous Tissue

Promising mass spectrometry imaging: exploring microscale insights in food

This review focused on mass spectrometry imaging (MSI), a powerful tool in food analysis, covering its ion source schemes and procedures and their applications in food quality, safety, and nutrition to provide detailed insights into these aspects. The review presented a detailed introduction to both commonly used and emerging ionization sources, including nanoparticle laser desorption/ionization (NPs-LDI), air flow-assisted ionization (AFAI), desorption ionization with through-hole alumina membrane (DIUTHAME), plasma-assisted laser desorption ionization (PALDI), and low-temperature plasma (LTP). In the MSI process, particular emphasis was placed on quantitative MSI (QMSI) and super-resolution algorithms. These two aspects synergistically enhanced MSI's analytical capabilities: QMSI enabled accurate relative and absolute quantification, providing reliable data for composition analysis, while super-resolution algorithms improved molecular spatial imaging resolution, facilitating biomarker and trace substance detection. MSI outperformed conventional methods in comprehensively exploring food functional factors, biomarker discovery, and monitoring processing/storage effects by discerning molecular species and their spatial distributions. However, challenges such as immature techniques, complex data processing, non-standardized instruments, and high costs existed. Future trends in instrument enhancement, multispectral integration, and data analysis improvement were expected to deepen our understanding of food chemistry and safety, highlighting MSI's revolutionary potential in food analysis and research.

Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging (nano-DESI MSI): A Tutorial Review

Nanospray desorption electrospray ionization (nano-DESI) is a liquid-based ambient mass spectrometry imaging (MSI) technique that enables visualization of analyte distributions in biological samples down to cellular-level spatial resolution. Since its inception, significant advancements have been made to the nano-DESI experimental platform to facilitate molecular imaging with high throughput, deep molecular coverage, and spatial resolution better than 10 μm. The molecular selectivity of nano-DESI MSI has been enhanced using new data acquisition strategies, the development of separation and online derivatization approaches for isobar separation and isomer-selective imaging, and the optimization of the working solvent composition to improve analyte extraction and ionization efficiency. Furthermore, nano-DESI MSI research has underscored the importance of matrix effects and established normalization methods for accurately measuring concentration gradients in complex biological samples. This tutorial offers a comprehensive guide to nano-DESI experiments, detailing fundamental principles and data acquisition and processing methods and discussing essential operational parameters.

Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

Molecular analysis of the extracellular microenvironment: from form to function

The extracellular matrix (ECM) proteome represents an important component of the tissue microenvironment that controls chemical flux and induces cell signaling through encoded structure. The analysis of the ECM represents an analytical challenge through high levels of post-translational modifications, protease-resistant structures, and crosslinked, insoluble proteins. This review provides a comprehensive overview of the analytical challenges involved in addressing the complexities of spatially profiling the extracellular matrix proteome. A synopsis of the process of synthesizing the ECM structure, detailing inherent chemical complexity, is included to present the scope of the analytical challenge. Current chromatographic and spatial techniques addressing these challenges are detailed. Capabilities for multimodal multiplexing with cellular populations are discussed with a perspective on developing a holistic view of disease processes that includes both the cellular and extracellular microenvironment.

Next-generation pathology practices with mass spectrometry imaging

Mass spectrometry imaging (MSI) is a powerful technique that reveals the spatial distribution of various molecules in biological samples, and it is widely used in pathology-related research. In this review, we summarize common MSI techniques, including matrix-assisted laser desorption/ionization and desorption electrospray ionization MSI, and their applications in pathological research, including disease diagnosis, microbiology, and drug discovery. We also describe the improvements of MSI, focusing on the accumulation of imaging data sets, expansion of chemical coverage, and identification of biological significant molecules, that have prompted the evolution of MSI to meet the requirements of pathology practices. Overall, this review details the applications and improvements of MSI techniques, demonstrating the potential of integrating MSI techniques into next-generation pathology practices.

Recent advances in top-down proteome sample processing ahead of MS analysis

Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.

Surface-sampling mass spectrometry to study proteins and protein complexes

This review aims to summarise the current capabilities of surface mass spectrometry (MS) approaches that offer intact protein analysis, and that of non-covalent complexes. Protein analysis is largely achieved via matrix-assisted laser desorption/ionisation (MALDI), which is in itself a surface analysis approach or solvent-based electrospray ionisation (ESI). Several surface sampling approaches have been developed based on ESI, and those that have been used for intact protein analysis will be discussed below. The extent of protein coverage, top-down elucidation, and probing of protein structure for native proteins and non-covalent complexes will be discussed for each approach. Strategies for improving protein analysis, ranging from sample preparation, and sampling methods to instrument modifications and the inclusion of ion mobility separation in the workflow will also be discussed. The relative benefits and drawbacks of each approach will be summarised, providing an overview of current capabilities.

Matrix Effects Free Imaging of Thin Tissue Sections Using Pneumatically Assisted Nano-DESI MSI

Mass spectrometry imaging has the potential to reveal important molecular interaction in morphological regions in tissue. However, the simultaneous ionization of the continuously altered and complex chemistry in each pixel can introduce artifacts that result in skewed molecular distributions in the compiled ion images. These artifacts are known as matrix effects. Mass spectrometry imaging using nanospray desorption electrospray ionization (nano-DESI MSI) enables the elimination of matrix effects by doping the nano-DESI solvent with internal standards. Carefully selected internal standards ionize similarly and simultaneously with the extracted analytes from thin tissue sections, and the matrix effects are eliminated through a robust data normalization method. Herein we describe the setup and use of pneumatically assisted (PA) nano-DESI MSI with standards doped in the solvent for elimination of matrix effects in ion images.

High-Throughput Intact Protein Analysis for Drug Discovery Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry

Mass spectrometry (MS) is the primary analytical tool used to characterize proteins within the biopharmaceutical industry. Electrospray ionization (ESI) coupled to liquid chromatography (LC) is the current gold standard for intact protein analysis. However, inherent speed limitations of LC/MS prevent analysis of large sample numbers (>1000) in a day. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI-MS), an ambient ionization MS technology, has recently been established as a platform for high-throughput small molecule analysis. Here, we report the applications of such a system for the analysis of intact proteins commonly performed within the drug discovery process. A wide molecular weight range of proteins 10-150 kDa was detected on the system with improved tolerance to salts and buffers compared to ESI. With high concentrations and model proteins, a sample rate of up to 22 Hz was obtained. For proteins at low concentrations and in buffers used in commonly employed assays, robust data at a sample rate of 1.5 Hz were achieved, which is ∼22× faster than current technologies used for high-throughput ESI-MS-based protein assays. In addition, two multiplexed plate-based high-throughput sample cleanup methods were coupled to IR-MALDESI-MS to enable analysis of samples containing excessive amounts of salts and buffers without fully compromising productivity. Example experiments, which leverage the speed of the IR-MALDESI-MS system to monitor NISTmAb reduction, protein autophosphorylation, and compound binding kinetics in near real time, are demonstrated.

Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry

Imaging of proteoforms in human tissues is hindered by low molecular specificity and limited proteome coverage. Here, we introduce proteoform imaging mass spectrometry (PiMS), which increases the size limit for proteoform detection and identification by fourfold compared to reported methods and reveals tissue localization of proteoforms at <80-μm spatial resolution. PiMS advances proteoform imaging by combining ambient nanospray desorption electrospray ionization with ion detection using individual ion mass spectrometry. We demonstrate highly multiplexed proteoform imaging of human kidney, annotating 169 of 400 proteoforms of <70 kDa using top-down MS and a database lookup of ~1000 kidney candidate proteoforms, including dozens of key enzymes in primary metabolism. PiMS images reveal distinct spatial localizations of proteoforms to both anatomical structures and cellular neighborhoods in the vasculature, medulla, and cortex regions of the human kidney. The benefits of PiMS are poised to increase proteome coverage for label-free protein imaging of tissues.

Proteoform-Selective Imaging of Tissues Using Mass Spectrometry

Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform‐specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano‐DESI MSI) for the proteoform‐selective imaging of biological tissues. Nano‐DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof‐of‐concept experiments demonstrate that nano‐DESI MSI combined with on‐tissue top‐down proteomics is ideally suited for the proteoform‐selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain.

Native Ambient Mass Spectrometry Enables Analysis of Intact Endogenous Protein Assemblies up to 145 kDa Directly from Tissue

Untargeted label-free interrogation of proteins in their functional form directly from their physiological environment promises to transform life sciences research by providing unprecedented insight into their transient interactions with other biomolecules and xenobiotics. Native ambient mass spectrometry (NAMS) shows great potential for the structural analysis of endogenous protein assemblies directly from tissues; however, to date, this has been limited to assemblies of low molecular weight (<20 kDa) or very high abundance (hemoglobin tetramer in blood vessels, RidA homotrimer in kidney cortex tissues). The present work constitutes a step change for NAMS of protein assemblies: we demonstrate the detection and identification of a range of intact endogenous protein assemblies with various stoichiometries (dimer, trimer, and tetramer) from a range of tissue types (brain, kidney, liver) by the use of multiple NAMS techniques. Crucially, we demonstrate a greater than twofold increase in accessible molecular weight (up to 145 kDa). In addition, spatial distributions of protein assemblies up to 94 kDa were mapped in brain and kidney by nanospray desorption electrospray ionization (nano-DESI) mass spectrometry imaging.

Ion Mobility Spectrometry of Superheated Macromolecules at Electric Fields up to 500 Td

Since its inception in 1980s, differential or field asymmetric waveform ion mobility spectrometry (FAIMS) has been implemented at or near ambient gas pressure. We recently developed FAIMS at 15-30 Torr with mass spectrometry and utilized it to analyze amino acids, isomeric peptides, and protein conformers. The separations broadly mirrored those at atmospheric pressure, save for larger proteins that (as predicted) exhibited dipole alignment at ambient but not low pressure. Here we reduce the pressure down to 4.7 Torr, allowing normalized electric fields up to 543 Td-double the maximum in prior FAIMS or IMS studies of polyatomic ions. Despite the collisional heating to ∼1000 °C at the waveform peaks, the proteins of size from ubiquitin to albumin survived intact. The dissociation of macromolecules in FAIMS appears governed by the average ion temperature over the waveform cycle, unlike the isomerization controlled by the peak temperature. The global separation trends in this "superhot" regime extend those at moderately low pressures, with distinct conformers and no alignment as theorized. Although the scaling of the compensation voltage with the field fell below cubic at lower fields, the resolving power increased and the resolution of different proteins or charge states substantially improved.

Native Mass Spectrometry Imaging of Proteins and Protein Complexes by Nano-DESI

Previously, we have demonstrated native mass spectrometry imaging (native MSI) in which the spatial distribution of proteins maintained in their native-like, folded conformations was determined using liquid extraction surface analysis (LESA). While providing an excellent testbed for proof of principle, the spatial resolution of LESA is currently limited for imaging primarily by the physical size of the sampling pipette tip. Here, we report the adoption of nanospray-desorption electrospray ionization (nano-DESI) for native MSI, delivering substantial improvements in resolution versus native LESA MSI. In addition, native nano-DESI may be used for location-targeted top–down proteomics analysis directly from tissue. Proteins, including a homodimeric complex not previously detected by native MSI, were identified through a combination of collisional activation, high-resolution MS and proton transfer charge reduction.