Metabolomics, a burgeoning field within systems biology, focuses on the comprehensive study of small molecules present in biological systems. Mass spectrometry (MS) has emerged as a powerful tool for metabolomic analysis due to its high sensitivity, resolution, and ability to characterize a wide range of metabolites thus offering deep insights into the metabolic profiles of living systems.

The risk of cardiovascular disease (CVD) in patients with rheumatoid arthritis (RA) is much higher than that in the general population. As its etiology is not fully understood, we performed a pilot study using a shotgun proteomic approach to investigate whether the plasma signature in RA patients with CVD might show an altered profile. Subjects with RA were compared to a group of RA patients with a previous cardiovascular event (CVE). The cohort consisted of an RA control group (n = 10) and a group (n = 10) of RA patients with a history of CVD. Samples were collected at least 6 months before the CVE and 3-6 months after the CVE. All subjects were matched to controls for age, sex, and medication use. Plasma depletion of the 14 most abundant proteins was followed by bottom-up shotgun proteomics analysis (LC‒MS/MS). Relative changes in protein/peptide abundance were investigated using classical statistical analyses with Perseus and XG-Boost machine learning to compare between groups and to determine the relative importance of identified proteins, respectively. Principal component analysis (PCA) revealed no difference in the global protein and peptide signatures between the control and CVE groups. A total of 150, 239 and 74 protein ID's showed in comparison between Post Event vs. controls, Event vs. no Event and Pre event vs. Post Event respectively a statistically difference in relative abundance (p < 0.05). Remarkedly a total of 236 proteins ID's showed a statistical significant difference in relative abundance in the PRE-Event group compared to the control group which could also be confirmed by XGboost machine learning. Here, we demonstrated potential differences in the plasma proteome signature of rheumatic patients with cardiovascular events. Interestingly, this signature may be present prior to CVE's. However the conclusions must be drawn with caution, since this is a pilot study and further investigation with larger cohorts is warranted to identify potential risk markers that may predict the relative risk of CVEs in rheumatic diseases.

Lysine crotonylation (Kcr) is a novel post-translational modification that is important in functional studies. However, our understanding of Kcr in the developing human fetus brain, heart, kidney, liver, and lung remains restricted. In this study, we used high-resolution LC-MS/MS and high-sensitivity immunoaffinity purification to analyze Kcr in the brain, heart, kidney, liver, and lung of 17-week fetus. A total of 24,947 Kcr modification sites were identified in 5,102 proteins, resulting in the most diverse Kcr proteome of fetus organs ever reported. We investigated the universality and specificity of Kcr during the development of several organs in 17-week fetus using bioinformatics analysis. Kcr proteins were found to be closely associated with the synthesis, transcription and translation of genetic material, energy production and metabolic processes. Importantly, the expression of Kcr proteins in each organ was closely related to the organs' developmental functions. Furthermore, several highly modified Kcr proteins may be important targets during fetus organ development. This discovery advances our understanding of fetus organ development and establishes the groundwork for future research into the regulatory mechanisms of crotonylation in fetus organ development.

Tuberculosis drug resistance contributes to the spread of tuberculosis. Immunotherapy is an effective strategy for treating tuberculosis, with the regulation of macrophage-mediated anti-tuberculosis immunity being crucial. Norcantharidin (NCTD), a drug used in tumor immunotherapy, has significant immunomodulatory effects. Thus, NCTD may have an anti-tuberculosis role by regulating immunity. Understanding how NCTD affects the proteome of Mtb-infected macrophages can provide valuable insights into potential treatments. This study aimed to investigate the impact of NCTD (10 μg/mL) on the proteome of macrophages infected with Mtb H37Ra using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. A total of 69 differentially regulated proteins (DRPs) were identified, with 28 up-regulated and 41 down-regulated in the NCTD-treated group. Validation of six DRPs (CLTCL1, VAV1, SP1, TRIM24, MYO1G, and WDR70) by Western blot analysis confirmed the accuracy of the LC-MS/MS method used in this study. NCTD modulates various protein expressions involved in chromatin-modifying enzymes, RHO GTPases activating PAKs, Fc gamma R-mediated phagocytosis, T cell receptor signaling pathway, and antigen processing and presentation. Overall, the research provides new insights into the effects of NCTD on the proteome of Mtb-infected macrophages. The identified changes highlight potential targets for future therapeutic interventions aimed at enhancing host immunity against Mtb infection or developing new anti-TB drugs based on these findings.

Diabetic nephropathy affects a significant proportion of individuals with diabetes, and its progression often leads to cardiovascular disease and infections before the need for renal replacement therapy arises. Empagliflozin has been shown to have various protective effects in cardiovascular disease studies, such as improving diabetic myocardial structure and function, and reducing myocardial oxidative stress. However, the impact of empagliflozin on cardiac protein expression and signaling pathways has not been comprehensively analyzed. To address this gap, we conducted proteome analysis to identify specific protein markers in cardiac tissue from the diabetes model group, including Myh7, Wdr37, Eif3k, Acot1, Acot2, Cat, and Scp2, in cardiac tissue from the diabetes model group. In our drug model, empagliflozin primarily modulates the fat-related metabolic signaling pathway within the heart. Empagliflozin downregulated the protein expression levels of ACOX1, ACADVL and CPT1A in the model group. Overall, our findings demonstrate that empagliflozin provides cardiac protection by targeting metabolic signaling pathways, particularly those related to fat metabolism. Moreover, the identification of cardiac biomarkers in a mouse model of diabetic nephropathy lays the foundation for further exploration of disease biomarkers in cardiac tissue.

Spatial proteomics is a multidimensional technique that studies the spatial distribution and function of proteins within cells or tissues across both spatial and temporal dimensions. This field multidimensionally reveals the complex structure of the human proteome, including the characteristics of protein spatial distribution, dynamic protein translocation, and protein interaction networks. Recently, as a crucial method for studying protein spatial localization, spatial proteomics has been applied in the clinical investigation of various diseases. This review summarizes the fundamental concepts and characteristics of tissue-level spatial proteomics, its research progress in common human diseases such as cancer, neurological disorders, cardiovascular diseases, autoimmune diseases, and anticipates its future development trends. The aim is to highlight the significant impact of spatial proteomics on understanding disease pathogenesis, advancing diagnostic methods, and developing potential therapeutic targets in clinical research.