PROTEOMICS

ABSTRACT Zoonotic infections caused by influenza A viruses (IAVs) of animal origin are a major public health concern, as they may represent the initial step toward the emergence of a pandemic strain. The host range of IAVs is shaped by species‐specific virus‐host interactions, and several host barriers have been identified that restrict the adaptation of avian viruses to humans. We used a compara…

The acclimation at mild low temperature can improve the ability of cold tolerance and protect tissues from stress-induced injury in many species, but mechanisms triggering the signal transduction of cold acclimation remain largely unknown. Here, we deciphered the early signaling events associated with immediate temperature drops in zebrafish larvae. Early alternations in the phosphoproteome of la…

Sensitivity, robustness, and reproducibility of sample preparation are main determinants of data quality in bottom-up mass spectrometry-based proteomics. To this end, in-gel protein clean-up and digestion has been used for decades and is characterized by its robustness and compatibility with harsh lysis conditions. Single-pot solid-phase-enhanced sample preparation (SP3) has gained substantial po…

It is widely established that the layers of proteins bound to the surface of nanoparticles (NPs), also known as the protein corona, critically influence their behavior in biological environments. Despite numerous proteomics studies performed in different NP-corona systems, the impact of proteomic sample preparation methods on corona profiling remains poorly understood. In this study, we systemati…

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by high metastatic potential, poor prognosis, and limited effective therapeutic options. In this study, we investigated the molecular mechanisms underlying the anticancer effects of the nucleolin (NCL)-targeting DNA aptamer AS1411 using label-free quantitative proteomic profiling. AS1411 treatment signifi…

Mesenchymal stem cells (MSCs) are adult stem cells able to self-renewal or differentiation into different cell types, including chondrocytes. N-Glycans are post-translational modifications of glycoproteins that contribute to vital cell functions. In this work, we examined the cell surface N-glycome of human MSCs isolated from bone marrow to identify biomarkers for chondrogenic differentiation. In…

Extracellular vesicles (EVs) are fundamental intercellular signaling organelles; these lipid-bilayer-enclosed particles are secreted by all cell types and carry a cargo of proteins, lipids, and nucleic acids to facilitate such cell communication and transfer. Advances in the field of single EV analyses, including profiling techniques, capture and detection strategies, digital technologies, multip…

Absence of the endosomal SNAREs vti1a and vti1b results in perinatal death and severe neuronal phenotypes in mice, while lack of one of these proteins results in minor phenotypes. Proteomic differences were investigated to obtain a deeper insight into processes in which vti1a and vti1b are involved. Here we applied a bottom-up shotgun proteomic approach to investigate the differences in wild-type…

Microfluidic affinity-based capture of extracellular vesicles (EVs) holds great promise for disease diagnostics and monitoring therapeutic EV production. However, optimizing microfluidic channel geometries for efficient EV capture remains understudied due to the effort required to experimentally test numerous designs. To overcome this, we developed an automated parallel pattern search (PPS) optim…

Extracellular vesicles (EVs) are membrane-encapsulated nanoparticles with key roles in cell biology and growing importance in biomedicine. However, EVs are challenging to characterize because they are highly heterogeneous. Single EV analysis methods are valuable tools for addressing this challenge. Here, we developed single EV analysis pipeline for assessment of transmission electron microscopy (…

Imaging mass spectrometry has made significant advancements in recent years owing to its ability to study the spatial localization and abundance of proteins, peptides, lipids, glycans, metabolites, and drugs. In this study, we employed an imaging mass spectrometry-based workflow called MALDI-IHC, which uses antibodies conjugated with photocleavable mass-tags, to investigate the detection of estro…

Single-cell omics tools provide unique insights into heterogeneous cell populations and their responses to stimuli. For example, single-cell RNA sequencing has identified several transcriptionally distinct populations of microglia, which are resident immune cells of the central nervous system (CNS) that are responsive to CNS injury, infection, and neurodegeneration. To date, single-cell studies o…

MS-based proteomics offers powerful opportunities for biomarker discovery; nevertheless, it is associated with technical challenges, including missing values and batch effects. Although imputation and batch-correction methods are well established in proteomics, their impact remains incompletely characterized in large-scale clinical proteomics datasets. Here, we examine the practical impact and in…

Fragilariopsis cylindrus is a key diatom in the Southern Ocean, where low iron and manganese availability constrain primary production and biogeochemical activity. The molecular mechanisms used by polar diatoms, including F. cylindrus, to cope with trace metal limitations remain largely unexplored. Here we present phenotypic characterizations and proteomic profiles of F. cylindrus grown under con…

Extracellular vesicles (EVs) represent an important mode of intercellular communication and cell regulation, by selective packaging and transfer of biological information between cells. The advent of quantitative mass spectrometry (MS)-based proteomics, lipidomics, and various other sequencing and profiling technologies, in conjunction with advances in molecular cell biology, imaging, EV purifica…

Cells are comprised of a broad spectrum of structures that compartmentalize biochemical and signaling mechanisms. These structures can be comprised of many biomolecules, but especially lipids, proteins, and nucleic acids. Techniques are limited to quantify or discover new subcellular structures. We explored whether a proteomics approach using chemical crosslinking followed by size-exclusion chrom…

Cobalt is an essential micronutrient but becomes toxic at elevated concentrations, requiring microorganisms to balance acquisition and detoxification. Aeromonas hydrophila, an opportunistic aquatic pathogen, is often encountered in metal-contaminated aquatic environments; however, its adaptive responses to cobalt stress have not been systematically characterized. Here, we applied quantitative pro…

Extracellular vesicles (EVs) are heterogeneous and play important roles in intercellular communication, contributing to physiological and pathological processes. Since few markers currently exist to differentiate subtypes of EVs, this study aimed to determine proteomic and lipidomic differences among four EV subpopulations. Large and small EVs (L-EVs and S-EVs) were isolated from human mast cells…

Proteomics is strengthening research in biology and the diversification of the model organisms studied is very promising for fully understanding the complexity of biological principles. However, the lack of protein sequence databases for many species is a major bottleneck. Existing computational solutions are usually incomplete and/or only usable by bioinformaticians. We have built an open-source…