Journal of Proteome Research最新文献

Cardiac rehabilitation (CR) is highly beneficial in postmyocardial infarction (MI) patients; however, its metabolic impact remains underexplored. This study investigated metabolic and lipidomic adaptations to an intensive CR program in 25 nondiabetic male patients (<75 years) following a first uncomplicated ST-elevation MI (STEMI). CR involved 24 ± 3 sessions, with baseline and final clinical assessments, and, in a subgroup of 17 patients, longitudinal dried blood spots (DBS) were collected, and metabolomics/lipidomics analysis was also performed. CR significantly improved clinical outcomes, including the 6 min walk test, B-type natriuretic peptide (BNP), left ventricular ejection fraction (LVEF%), C-reactive protein (CRP), and homocysteine levels. Metabolomic analysis showed sustained metabolic adaptations, notably increased N-acetyl-l-tyrosine (NAT), suggesting a mitohormesis response to exercise-induced mitochondrial stress. The third training session exhibited the highest metabolic adaptation, primarily in energy metabolism pathways like the TCA cycle, indicating enhanced oxidative energy generation and improved exercise performance. The lipidome displayed an acute response to the first training, with upregulation of phosphatidylserines (PS). Predicted increased activity of phosphatidylserine synthase-1 (PSS1), enzymes vital for PS synthesis, underscores PS's protective role in myocardial damage and its contribution to muscle activity. These findings highlight CR's beneficial metabolic adaptations, potentially via mitohormesis, and suggest possible mechanistic targets and candidate biomarkers requiring investigation in future controlled intervention studies.

A COVID-19 booster dose has been found to be effective in our fight against SARS-CoV-2 infection. However, their long-term beneficial or adverse effects among healthy individuals are not fully understood. We investigated the impact of the Pfizer-BioNTech-(BNT162b2) booster dose on plasma proteome profiles of fully vaccinated healthy individuals in a mimic of reinfection to understand the disease mechanisms and to identify novel diagnostic and prognostic biomarkers. In contrast to prebooster, postbooster recipients exhibited a distinct proteomic signature following SARS-CoV-2 spike (S) protein stimulation. The gene ontology (GO) terms of biological processes revealed the five most significant functions enriched in stress and immune responses, especially via complement and blood coagulation systems. Likewise, the Reactome pathway demonstrated significant activation of complement cascade, platelet degranulation, and innate immune systems. Moreover, the protein-protein interaction network exhibited regulation of body fluid levels and acute inflammatory response. In summary, our study identified abundant dysregulated signatures predominantly associated with the complement, the innate immune system, and platelet degranulation. Besides eliciting humoral immunity, our study also found key proteins involved in blood coagulation pathways that could perhaps shed light on individuals exhibiting comorbidities associated with COVID-19 vaccination. Therefore, factors dysregulated following SARS-CoV-2 spike (S) protein stimulation may provide insights into pathways potentially implicated in post-vaccination reactions.

An interconnected loop of messages and counter-messages determine the outcome of host-pathogen interactions. Multihost pathogenicity across plants and animals, particularly nematode, is a major source of new infectious diseases. Fusarium oxysporum, a multihost pathogen, causes vascular wilt in chickpea and fusariosis in worm and humans. To comprehend Fusarium-responsive multihost pathogenicity, we temporally profiled cross-kingdom species, chickpea and worm using SWATH-mass spectrometry. Morphological analyses revealed that increased wilting and intestinal disintegration elicits a disease response in chickpea and worm. Peptide-spectrum library consisted of 5629 and 3138 proteins from Fusarium infected chickpea and worm, respectively. SWATH analysis identified 1573 and 2249 disease-responsive chickpea (CaDRPs) and worm proteins (CeDRPs) linked to diverse organs, organelles, and functionality. Pairwise comparisons; over-representation analysis between time, treatment, and organism; wilt, and fusariosis diseasome revealed common and unique modules. CaDRPs involved in preformed defense, biomolecule synthesis, phytohormone regulation, ser/thr kinase, and ATP signaling have perturbed interactions and functions, majorly in chloroplast. CeDRPs linked to the cuticular support, muscle organization, neuronal information, intestinal metabolism, G-protein, and notch signaling showed a deregulated function, especially in the cytoplasm. Common biological processes, included primary metabolism, ribosome biogenesis, calcium signaling, and proteostasis. Our data provide first evidence of translational plasticity in the Fusarium diseasome providing novel insights into multihost pathogenesis.

Previous studies have shown the link between sedentary behavior and health outcomes. However, self-reported sedentary behavior is less accurate than accelerometer-measured sedentary behavior. Additionally, the proteomic signatures associated with sedentary behavior and their potential impact on biological pathways remain unknown. In this study, we identified proteomic signatures of sedentary behavior using whole-proteome association analysis and LASSO regression based on data from 2921 plasma proteins in 10,848 participants with complete accelerometer measurements from the UK Biobank. Our results indicate that both sedentary behavior and its related proteomic signatures are significantly linked to the risk of developing diabetes, hypertension, and chronic kidney disease. Furthermore, mediation analysis showed that proteomic signatures of sedentary behavior mediate the relationships between sedentary activity and the risk of diabetes and chronic kidney disease. These findings suggest that sedentary behavior and its associated proteomic signatures contribute to increased risks of these diseases. Investigating how sedentary behavior affects diseases through peripheral physiology is essential for public health.

Lipoic acid (LA), an endogenous small molecule, is widely utilized in metabolic regulation and disease intervention. While its mechanism of action has been largely attributed to protein lipoylation, the dynamic chemical properties of its five-membered cyclic disulfide moiety remain underexplored. Here, we designed and synthesized alkyne-functionalized lipoic acid-derived probes, LAN-yne and LAO-yne. Employing a chemoproteomic strategy, we systematically mapped the covalent targets of the LAN-yne across the cellular proteome and assessed their potential biological functions. Quantitative proteomic analysis identified 852 probe-modified proteins and 1,157 corresponding cysteine modification sites. This study demonstrates that LA's endocyclic disulfide bond can be mimicked to mediate specific protein modification via thiol-disulfide exchange, providing novel molecular insights and a technical platform for investigating LA's potential pharmacological mechanisms and structural derivatization efforts beyond lipoylation.

Isobaric labeling is widely used in quantitative proteomics for its multiplexing capabilities, but scaling beyond current limits remains a challenge. Here, we introduce UltraPlex-TMT, a streamlined and scalable workflow that integrates orthogonal protease digestion with hyperplex TMT/TMTpro labeling to effectively double sample throughput. UltraPlex-TMT can be readily implemented without custom chemistry or instrumentation. We benchmarked UltraPlex-TMT using lysine- and arginine-specific protease digests of a two-species proteome labeled with TMT11plex and TMT18plex across four subplexes in a proof-of-concept pseudo-58-plex design. MS2 acquisition quantified ∼6,000-7,000 proteins per subplex and ∼9,000 in total, with ∼50% overlap across all conditions, generating a robust core proteome set with high quantitative reproducibility. RTS-MS3 acquisition showed similar coverage trends, albeit with fewer quantified proteins. Despite reduced depth, MS3 data provided higher quantification accuracy, illustrating a trade-off between proteome depth and precision. Gene set enrichment analysis revealed strong biological concordance between MS2 and MS3 data, and in all conditions tested, the use of orthogonal protease digestion did not introduce systematic quantification bias. UltraPlex-TMT offers a flexible foundation for isobaric labeling-based high-throughput proteomics and is poised to benefit from faster acquisition platforms and extended multiplexing chemistries, supporting future studies exceeding 200-plex scale, potentially equivalent to subminute analysis.

Phosphorylation is a key post-translational modification that can impact the function of a protein and the outcome of cell signaling pathways. Using phosphoproteomics to characterize the phosphorylation changes downstream of trophic factor signaling is important for better understanding the pleiotropic actions of this class of molecules. Insulin-like growth factor-1 (IGF-1) is a trophic factor that can influence cellular growth and differentiation, and IGF-1 signaling in the brain has been linked to cognitive processes. While its main signaling molecules are well characterized, we sought to perform a more in-depth and unbiased analysis of the IGF-1 phosphoproteome in neuronal cells. To obtain insight into the IGF-1 signaling pathway in neuronal cells, we performed a quantitative mass spectrometric phosphoproteomics analysis in rat pheochromocytoma (PC-12) cells. Our results illustrate a diverse phosphoproteome downstream of IGF-1, with insight into novel phosphoprotein sites, such as Plcβ3 (Ser¹¹⁰⁵), that likely influence IGF-1 signaling in neuronal cells. We also identify a robust upregulation of the Rho GTPase cycle and an activation of synaptogenesis signaling downstream of IGF-1. These results pave the way for more targeted studies on specific phosphoprotein sites, which will facilitate a better understanding of how these phosphorylation events impact IGF-1-related signaling outcomes in neuronal cells.

The primary computational challenge in mass spectrometry-based proteomics is determining the peptide sequence responsible for generating each measured tandem mass spectrum. This task is traditionally addressed through sequence database searching as well as alternative approaches such as spectral library searching. ANN-SoLo is a powerful spectral library search engine optimized for open modification searching, enabling the detection of peptides carrying any post-translational modification. Here, we present an enhanced version of ANN-SoLo that combines the strengths of both spectral library searching and sequence database searching by integrating with Prosit to generate predicted spectral libraries from protein sequence databases. Additionally, it provides functionality to generate decoys at both the spectrum and the peptide levels, introduces an optimized internal file structure for large-scale analytics, and improves search accuracy by incorporating complementary ion information into spectrum vector representations. These advancements collectively address challenges associated with missing spectral libraries and enhance peptide identification in large-scale and complex proteomics workflows.

The increasing exposure risks of tetrabromobisphenol A (TBBPA) have drawn much attention, owing to its widely produced and ubiquitous occurrence. Despite the potential toxicities are largely explored in vitro experiments, limited evidence exists about the fact that TBBPA induced the targeting organ effects on the metabolism. Herein, we found that TBBPA exposure for 2 weeks induced oxidative stress and lipometabolism disturbance in the liver of male ICR mice. Using the promising approach combining UHPLC-MS with MALDI imaging, 78 discrepant lipid molecules between the control and TBBPA exposure groups were simultaneously screened and identified, with spatial visualization. After the enrichment analysis, the biosynthesis of glycerophospholipid metabolism was the most distinct in the eight metabolic pathways that were involved with TBBPA in the process of liver injury, which was closely associated with hepatocyte membrane stability and lipid transport functions. Furthermore, the Q-PCR analysis and molecular docking results demonstrated that TBBPA promoted the accumulation of lipids like triglyceride (TG), DG, LPE, and LPC, as well as the deficiency of phosphatidylcholine and PE by inhibiting the key genes LPCAT3 and Pcyt2 involved in glycerophospholipid synthesis, simultaneously enhancing the expression of phosphatidylethanolamine N-methyltransferase and Diacylglyceryl acyltransferase 1, the latter being the crucial gene for TG synthesis. This study affords novel insight into further understanding the potential effect of liver organ by TBBPA exposure.

Mass spectrometers and their attached liquid chromatography (LC) systems, often referred to as LC-MS/MS instrumentation, have become an indispensable tool in biomedical research to identify and quantify proteins, metabolites, and other molecules of interest. However, these sophisticated instruments are very susceptible to malfunction or suboptimal performance, and as a result, quality control (QC) samples are typically acquired at regular intervals to assess their performance. Not surprisingly, several QC software packages have been developed in recent years to analyze and interrogate a variety of QC samples. However, existing QC software predominantly supports proteomic QC samples, with limited options for metabolomic and lipidomic QC samples. In addition, pipelines and workflows that can accommodate both types of QC samples are largely missing. To address this unmet demand, we have developed MaSpeQC, which is a free, easy-to-install, interactive and fully customizable web application to track LC-MS/MS performance across proteomic, metabolomic, and/or lipidomic workflows. MaSpeQC is vendor-agnostic and can handle any commercially available or in-house-generated QC sample from which it extracts relevant metrics. Furthermore, MaSpeQC provides an intuitive web interface for performance monitoring and early detection of issues through customizable email alerts.