Journal of proteomics最新文献

{"title":"Proteomic analysis of peripheral blood mononuclear cells in first episode psychosis – Protein and peptide-centered approaches to elucidate potential diagnostic biomarkers","authors":"Catia Santa ,&nbsp;João E. Rodrigues ,&nbsp;Ana Martinho ,&nbsp;Vera M. Mendes ,&nbsp;Nuno Madeira ,&nbsp;Manuel Coroa ,&nbsp;Vítor Santos ,&nbsp;Sofia Morais ,&nbsp;Miguel Bajouco ,&nbsp;Hélder Costa ,&nbsp;Sandra I. Anjo ,&nbsp;Inês Baldeiras ,&nbsp;Antonio Macedo ,&nbsp;Bruno Manadas","doi":"10.1016/j.jprot.2024.105296","DOIUrl":"10.1016/j.jprot.2024.105296","url":null,"abstract":"<div><p>Diagnosing patients suffering from psychotic disorders is far from being achieved with molecular support, despite all the efforts to study these disorders from different perspectives. Characterizing the proteome of easily obtainable blood specimens, such as the peripheral blood mononuclear cells (PBMCs), has particular interest in biomarker discovery and generating pathophysiological knowledge. This approach has been explored in psychiatry, and while generating valuable information, it has not translated into meaningful biomarker discovery. In this project, we report the proof-of-concept of a methodology that aims to explore further information obtained with classical proteomics approaches that is easily overlooked. PBMC samples from first-episode psychosis and control subjects were subjected to a SWATH-MS approach, and the classical protein relative quantification was performed, where 389 proteins were found to be important to distinguish the two groups. Individual analysis of the quantified peptides was also performed, highlighting peptides of unchanged proteins that were significantly altered. With the combination of protein- and peptide-centered proteomics approaches, it is possible to highlight that information about proteoforms, namely regulation at the peptide level possibly due to post-translational modifications, is routinely overlooked and that its diagnostic potential should be further explored.</p></div><div><h3>Significance</h3><p>Our exploratory findings highlight the potential of MS-based proteomics strategies, combining protein- and peptide-centered approaches, to aid clinical decision-making in first-episode psychosis, helping to establish early biomarkers for schizophrenia and other psychotic disorders. Particularly, the less popular peptide-centered approach allows the identification/measurement of overlooked modulated peptides that may have potential biomarker characteristics. The application in parallel of protein- and peptide-centered strategies is transversal to research of other diseases, potentially allowing a more comprehensive characterization of the metabolic/pathophysiological alterations related to a specific disease.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"309 ","pages":"Article 105296"},"PeriodicalIF":2.8,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142097584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA-seq reveals the important role of transcriptional regulator DeoR1 in regulating Brucella abortus various pathways","authors":"Zhiqiang Li ,&nbsp;Shuli Wang ,&nbsp;Qifeng Li ,&nbsp;Qiuhui Lin ,&nbsp;Chunmei Zhang ,&nbsp;Li Xi ,&nbsp;Yanyan Cui ,&nbsp;Yawen Dai ,&nbsp;Shuanghong Yin ,&nbsp;Yu Zhang ,&nbsp;Hui Zhang","doi":"10.1016/j.jprot.2024.105297","DOIUrl":"10.1016/j.jprot.2024.105297","url":null,"abstract":"<div><p><em>Brucella</em> spp. is an intracellular bacterium that uses its transcriptional regulator DeoR1 to promote intracellular transport and survival, but the molecular mechanism remains unknown. To analyze the role of DeoR1 in the virulence of <em>B. abortus</em> and the genes regulated by DeoR1, we created a A19Δ<em>deoR1</em> mutant of <em>B. abortus</em> A19 (A19). Virulence assay was performed using a murine macrophage cell line (RAW264.7) and mice. We observed that A19Δ<em>deoR1</em> mutant is attenuated in RAW264.7 cells and mice. We performed RNA-seq whole transcriptome analysis of A19Δ<em>deoR1</em> and A19 from infected RAW264.7 cells. A total of 135 differentially expressed genes were identified, including 100 up-regulated and 35 down-regulated genes. These differentially expressed genes were involved in amino acid synthesis and metabolism, energy production and conversion, stress proteins, chaperonin, hypothetical proteins and protein of unknown function, cell wall/membrane/envelope, intracellular transporting and secretion, and transcriptional regulator. Interestingly, genes involved in the intracellular trafficking and secretion were significantly down-regulated in A19Δ<em>deoR1</em>. Furthermore, selected RNA-seq results were experimentally confirmed by qRT-PCR. Overall, these results deciphered differential phenomena associated with virulence in A19Δ<em>deoR1</em> and A19 from infected RAW264.7 cells, which provided important information for understanding the detailed role of DeoR1 in <em>Brucella</em> pathogenesis.</p></div><div><h3>Significance</h3><p>Transcriptional regulators are predominant bacterial signal transduction factors. The pathogenicity of <em>Brucella</em> is due to its ability to regulate the expression of virulence related genes. Transcriptional regulators are designed to regulate gene expression and enact an appropriate adaptive physiological response. Here, a total of 135 differentially expressed genes were identified in transcriptional regulator <em>deoR1</em> mutant.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"309 ","pages":"Article 105297"},"PeriodicalIF":2.8,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142096984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Journal of Proteomics – « Renaissance »!","authors":"Jean Armengaud","doi":"10.1016/j.jprot.2024.105295","DOIUrl":"10.1016/j.jprot.2024.105295","url":null,"abstract":"","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"307 ","pages":"Article 105295"},"PeriodicalIF":2.8,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142083356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combination of transcriptomics and proteomics for analyzing potential biomarker and molecular mechanism underlying skeletal muscle atrophy","authors":"Lin Yin ,&nbsp;Shasha Wu ,&nbsp;Peirong Bai ,&nbsp;Xuena Wang","doi":"10.1016/j.jprot.2024.105283","DOIUrl":"10.1016/j.jprot.2024.105283","url":null,"abstract":"<div><h3>Background</h3><p>The skeletal muscle atrophy is prevalently occurred in numerous chronic disease complications. Despite its important clinical significance, there are currently no therapeutic drugs, so new biomarkers and molecular mechanisms need to be discovered urgently.</p></div><div><h3>Methods</h3><p>Transcriptome and proteome sequencing data were collected from normal and skeletal muscle atrophic mice. The differentially expressed genes (DEGs) and proteins (DEPs) were analyzed. Applying PPI analysis to obtain overlapping genes and proteins, which were next subjected to GO and KEGG enrichment analysis. Combined analysis of transcriptomics and proteomics was performed to get key genes that were simultaneously found in GO and KEGG enrichment results. Subsequently, RT-qPCR and immunofluorescence were constructed to verify the expression of screened key genes.</p></div><div><h3>Results</h3><p>By combination of transcriptomics, proteomics and RT-qPCR results, we identified 14 key genes (<em>Cav1</em>, <em>Col3a1</em>, <em>Dnaja1</em>, <em>Postn</em>, <em>Ptges3</em>, <em>Cd44</em>, <em>Clec3b</em>, <em>Igfbp6</em>, <em>Lamc1</em>, <em>Alb</em>, <em>Itga6</em>, <em>Mmp2</em>, <em>Timp2</em> and <em>Cd9</em>) that were markedly different in atrophic mice. Single-gene GSEA and immunofluorescence suggested <em>Cd9</em> was probably the biomarker for skeletal muscle atrophy.</p></div><div><h3>Conclusions</h3><p>Our study hinted that <em>Cd9</em> was potential biomarker and may interfere with skeletal muscle atrophy through process of aerobic respiration, oxidative phosphorylation, and metabolism of amino acids and fatty acids.</p></div><div><h3>Significance</h3><p>The present study holds the subsequent significance:</p><p>Frist, we investigated biomarkers for skeletal muscle atrophy using multi-omics approach. A total of 14 genes were markedly different in skeletal muscle atrophic mice. We finally found <em>Cd9</em> is a potential biomarker for skeletal muscle atrophy. Our work presents novel biomarkers and potential regulatory mechanisms for the early detection and intervention of muscle atrophy.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"309 ","pages":"Article 105283"},"PeriodicalIF":2.8,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187439192400215X/pdfft?md5=9cfdcab1399585f8c87bdb693fc46387&pid=1-s2.0-S187439192400215X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The RNA N6-methyladenosine demethylase FTO regulates ATG5 to inhibit malignant progression of uveal melanoma","authors":"Yating Yang ,&nbsp;Yusheng Zhong ,&nbsp;Cheng Chi ,&nbsp;Xiacheng Lin ,&nbsp;Xuemei Zhu ,&nbsp;Xun Deng ,&nbsp;Jianhong Liang ,&nbsp;Yong Cheng","doi":"10.1016/j.jprot.2024.105282","DOIUrl":"10.1016/j.jprot.2024.105282","url":null,"abstract":"<div><h3>Purpose</h3><p>This research aimed to identify the function of fat mass- and obesity-associated protein (FTO), an eraser of N6-methyladenosine (m6A), and explore its possible mechanisms in uveal melanoma (UVM).</p></div><div><h3>Methods</h3><p>We performed quantitative real-time PCR (qPCR), Western blotting and gene correlation analysis with GEPIA2 to assess FTO expression and identify its potential targets in UVM. CCK-8, colony formation, cell cycle, cell apoptosis, wound healing and Transwell invasion assays were utilized to assess cell viability, cell cycle distribution, apoptosis, migration and invasion. Western blotting, qPCR and methylated RNA immunoprecipitation–qPCR (MeRIP–qPCR) were carried out to explore the underlying mechanism of FTO in 2 UVM cell lines.</p></div><div><h3>Results</h3><p>FTO, a key m6A demethylase, was found to be upregulated in human UVM tissues compared with normal choroid tissues. Knockdown of FTO in Mel270 and OMM2.3 cells significantly promoted proliferation and migration and suppressed apoptosis. Mechanistically, knockdown of FTO decreased the expression of ATG5, an autophagy-related gene, leading to attenuation of autophagosome formation, thereby inhibiting autophagy. Upon FTO knockdown, increased levels of methylated ATG5 and decreased ATG5 stability were detected. Furthermore, ATG5 dramatically alleviated FTO downregulation-induced tumor growth and metastasis.</p></div><div><h3>Conclusions</h3><p>Our research highlights the importance of the m6A demethylase FTO in UVM by demonstrating that it direct regulates ATG5-induced autophagy in an m6A-dependent manner. These findings suggest that FTO may serve as a potential therapeutic target for UVM.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"309 ","pages":"Article 105282"},"PeriodicalIF":2.8,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924002148/pdfft?md5=c89c66871793b38320b1321f2c2c8248&pid=1-s2.0-S1874391924002148-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the mysteries of chicken proteomics: Insights into follicle development and reproduction","authors":"Armughan Ahmed Wadood ,&nbsp;Zhang Xiquan","doi":"10.1016/j.jprot.2024.105281","DOIUrl":"10.1016/j.jprot.2024.105281","url":null,"abstract":"<div><p>Chicken proteomics is a valuable method for comprehending the many mechanisms involved in follicle growth and reproduction in birds. This study offers a thorough summary of the latest progress in chicken proteomics research, specifically highlighting the knowledge obtained regarding follicle development and reproductive physiology. Proteomic studies have revealed essential proteins and pathways that play a role in follicle development, including those that control oocyte size, maturation, and ovulation. Proteomic investigations have provided insight into the molecular pathways that govern reproductive processes. By utilizing advanced proteomic technologies, including mass spectrometry and protein microarray analysis, we have been able to identify and measure many proteins in chicken follicles at their different developmental stages. The utilization of proteomic methods has enabled the identification of previously unknown biomarkers for reproductive efficiency that expedited the creation of innovative diagnostic instruments for monitoring reproductive health in chicken. Chicken proteomics not only offers insights into follicle growth and reproduction but also uncovers the effects of environmental influences on reproductive function. This provides new opportunities for exploring the molecular pathways that cause these effects. The integration of current data with upcoming proteomic technologies offers the potential for innovative strategies to enhance chicken reproduction.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"308 ","pages":"Article 105281"},"PeriodicalIF":2.8,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic insights into adventitious root formation in Larix kaempferi","authors":"Haifei Hao ,&nbsp;Baohui Xie ,&nbsp;Dadi Zhao ,&nbsp;Jiaqi Kang ,&nbsp;Xiangning Jiang ,&nbsp;Ying Gai","doi":"10.1016/j.jprot.2024.105288","DOIUrl":"10.1016/j.jprot.2024.105288","url":null,"abstract":"<div><p>The adventitious root formaton (ARF) in excised plant parts is essential for the survival of isolated plant fragments. In this study, we explored the complex mechanisms of ARF in <em>Larix kaempferi</em> by conducting a comprehensive proteomic analysis across three distinct stages: the induction of adventitious root primordia (C1, 0–25 d), the formation of adventitious root primordia (C2, 25–35 d), and the elongation of adventitious roots (C3, 35–45 d). We identified 1976 proteins, with 263 and 156 proteins exhibiting increased abundance in the C2/C1 and C3/C2 transitions, respectively. In contrast, a decrease in the abundance of 106 and 132 proteins suggests a significant demand for metabolic processes during the C2/C1 phase. The abundance of IAA-amino acid hydrolase and S-adenosylmethionine synthase were increased in the C2/C1 phase, underscoring the role of auxin in adventitious root induction. The decrease in abundance of photosynthesis-related proteins during the C2/C1 phase highlights the significance of initial light conditions in adventitious root induction. Moreover, variation in cell wall synthesis and metabolic proteins in the C2/C1 and C3/C2 stages suggests that cell wall metabolism is integral to adventitious root regeneration. Gene Ontology enrichment analysis revealed pathways related to protein modification enzymes, including deubiquitinases and kinases, which are crucial for modulating protein modifications to promote ARF. Furthermore, the increased abundance of antioxidant enzymes, such as peroxidases and glutathione peroxidases, indicates a potential approach for enhancing ARF by supplementing the culture medium with antioxidants. Our study provides insights into metabolic changes during ARF in <em>L. kaempferi</em>, offering strategies to enhance adventitious root regeneration. These findings have the potential to refine plant propagation techniques and expedite breeding processes.</p></div><div><h3>Signficance</h3><p>The main challenge in the asexual reproduction technology of <em>Larix kaempferi</em> lies in adventitious root formation (ARF). While numerous studies have concentrated on the efficiency of ARF, proteomic data are currently scarce. In this study, we collected samples from three stages of ARF in <em>L. kaempferi</em> and subsequently performed proteomic analysis. The data generated not only reveal changes in protein abundance but also elucidate key metabolic processes involved in ARF. These insights offer a novel perspective on addressing the challenge of adventurous root regeneration.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"307 ","pages":"Article 105288"},"PeriodicalIF":2.8,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining proteomics and Phosphoproteomics to investigate radiation-induced rectal fibrosis in rats and the effects of pSTAT3 inhibitor S3I-201 on human intestinal fibroblasts","authors":"Hongfeng Pan ,&nbsp;Zeyi Zhao ,&nbsp;Yuanchang Zhu ,&nbsp;Yihuang Gao ,&nbsp;Haoyang Ruan ,&nbsp;Ying Huang ,&nbsp;Pan Chi ,&nbsp;Shenghui Huang","doi":"10.1016/j.jprot.2024.105287","DOIUrl":"10.1016/j.jprot.2024.105287","url":null,"abstract":"<div><h3>Objective</h3><p>To investigate the regulatory mechanisms of radiation-induced rectal fibrosis (RIRF) and assess the therapeutic potential of S3I-201.</p></div><div><h3>Methods</h3><p>Sprague-Dawley rats were divided into control and radiation groups, with the latter exposed to 20 Gray pelvic X-rays. After 10 weeks, rectal tissues were analyzed using tandem mass tag (TMT) proteomics and phosphoproteomics. Pathway enrichment was performed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, with secondary annotation using Cluego. Representative proteins and their phosphorylated counterparts were validated through immunoblotting in another cohort. STAT3 levels in rectal tissues from irradiated and non-irradiated colorectal cancer patients were examined, and the effects of S3I-201 on human rectal fibroblasts were evaluated.</p></div><div><h3>Results</h3><p>The radiation group showed significant inflammatory responses and collagen deposition in the rat rectal walls. Enrichment analysis revealed that radiation-induced proteins and phosphoproteins were primarily involved in extracellular matrix-receptor interaction and the MAPK signaling pathway. Immunoblotting indicated increased expression of p-CAMKII, p-MRACKS, p-Cfl1, p-Myl9, and p-STAT3 in the radiation group compared to the control, while p-AKT1 expression decreased. Elevated phosphorylation of STAT3 was observed in submucosal fibroblasts of the post-radiation human rectum. S3I-201 specifically inhibited STAT3 phosphorylation and suppressed activation of human rectal fibroblasts, also inhibiting the pro-fibrotic effects of the classical TGF-β/Smad/CTGF pathway.</p></div><div><h3>Conclusion</h3><p>By integrating phosphoproteomics and proteomics, this study elucidated the protein regulatory network of RIRF and identified the potential therapeutic targets, including phosphoproteins such as STAT3 in managing RIRF.</p></div><div><h3>Significance</h3><p>In our research, we employed TMT labeling alongside LC-MS/MS techniques to comprehensively explore the proteomic and phosphoproteomic landscapes in rat models of radiation-induced intestinal fibrosis (RIRF). Our analysis revealed the function and pathways of proteins and phosphorylated proteins triggered by radiation, as well as those with protective roles. We mapped a network of interactions among these proteins and validated key protein expression levels using quantitative methods. Furthermore, we investigated STAT3 as a potential therapeutic target, assessing the efficacy of the inhibitor S3I-201 in laboratory settings, and highlighting its potential for RIRF treatment. Overall, our findings provide groundbreaking insights into the mechanisms underlying RIRF, paving the way for the development of future antifibrotic therapies.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"308 ","pages":"Article 105287"},"PeriodicalIF":2.8,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma proteomics implicate glutamic oxaloacetic transaminases as potential markers for acute myocardial infarction","authors":"Qinjiang Wei ,&nbsp;Kela Li ,&nbsp;Liye Su ,&nbsp;Tuan Cen ,&nbsp;Suren R. Sooranna ,&nbsp;Xinshou Pan ,&nbsp;Zhaohe Huang ,&nbsp;Yan Liu","doi":"10.1016/j.jprot.2024.105286","DOIUrl":"10.1016/j.jprot.2024.105286","url":null,"abstract":"<div><h3>Aim</h3><p>To provide a novel perspective on the pathogenesis of acute myocardial infarction (AMI) patients with respect to glutamic oxaloacetic transaminase (GOT).</p></div><div><h3>Methods</h3><p>The plasma proteome of 20 patients with AMI were matched for age and sex and compared with 10 healthy individuals. We analyzed the mass spectrum data and compared the signal intensity of the corresponding peptides which related to their corresponding proteins. A sample-specific protein database was constructed and a quality control analysis was conducted to screen out the key regulatory proteins under specific experimental conditions. The data from 37 new AMI patients and 13 healthy adults were subjected to parallel reaction monitoring (PRM) to verify the target proteins found. Finally, the survival status of the key genes (&gt; 1.5-fold) in the PPI were analyzed.</p></div><div><h3>Results</h3><p>2589 and 2162 proteins were identified and quantified, respectively, and 143 differentially expressed proteins (DEPs) (≥1.5-fold) were found between the AMI and control groups. Of these 90 and 53 were significantly up-regulated and down-regulated, respectively. Gene ontology, KEGG enrichment, protein domain and cluster analysis as well as PPI networks of the DEPs revealed a central role of acute inflammatory response processes in patients with AMI. A cluster of proteins were found to be related to cysteine, methionine, arginine, proline, phenylalanine and propanoate metabolism as well as the cAMP signaling pathway. PPI network analysis showed CHI3L1, COPB2, GOT2, MB, CYCS, GOT1, CKM, SAA1 and PRKCD and RPS3 were in key positions, but only MB, CKM, GOT1, PRKCD, CYCS and GOT2 were found in a cluster. PRM verified the high levels of MB, CKM, GOT1 and GOT2 in 37 AMI patients but there was no statistical difference in the survival status for patients with either high or low expression levels of these proteins.</p></div><div><h3>Conclusions</h3><p>Our findings showed that acute inflammatory response processes play a central role in patients with AMI. Cysteine and methionine metabolism was also activated, in which GOT1 and GOT2 were key proteins. These pathways might be potential targets for diagnosis and novel therapies to improve the poor outcomes observed in patients with heart failure.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"308 ","pages":"Article 105286"},"PeriodicalIF":2.8,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924002185/pdfft?md5=e1c3cf6107381ccc30e14b6f69c777ba&pid=1-s2.0-S1874391924002185-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using long columns to quantify over 9200 unique protein groups from brain tissue in a single injection on an Orbitrap Exploris 480 mass spectrometer","authors":"Xianyin Lai,&nbsp;Guihong Qi","doi":"10.1016/j.jprot.2024.105285","DOIUrl":"10.1016/j.jprot.2024.105285","url":null,"abstract":"<div><p>The most exciting advancement in LC-MS/MS-based bottom-up proteomics has centered around enhancing mass spectrometers. Among these, the latest and most advanced mass spectrometer for bottom-up proteomics is the Orbitrap Astral that has the highest scan rate to accelerate throughput and the highest sensitivity to handle a very small amount of peptide samples and to achieve deeper proteomics. However, its affordability remains a challenge for most laboratories. While significant strides have been made in improving mass spectrometry, advancing liquid chromatography (LC) to achieve deeper proteomics has not achieved significant successes since the innovation of Multidimensional Protein Identification Technology (MudPIT) in 2001. To achieve deeper proteomics in a less labor-intensive and more reproducible approach while using a more cost-effective mass spectrometer, such as the Orbitrap Exploris 480, we evaluated trap columns as long as 40 cm and analytical column as long as 600 cm besides sample loading amount, gradient time, and analytical column particle size to enable a fractionation-free method for a single injection to obtain deeper proteomics. The length of trap and analytic columns is the key factor. Using a 30 cm trap column and 250 cm analytical column with other optimized LC conditions, we quantified over 9200 unique protein groups from brain tissue in a single injection using a 24-h gradient on an Orbitrap Exploris 480 mass spectrometer.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"308 ","pages":"Article 105285"},"PeriodicalIF":2.8,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}