IF 4

Proteomes Pub Date : 2024-10-14 DOI: 10.3390/proteomes12040030

Hicham Benabdelkamel, Refat M Nimer, Afshan Masood, Maha Al Mogren, Anas M Abdel Rahman, Assim A Alfadda

{"title":"Multiple Reaction Monitoring-Mass Spectrometric Immunoassay Analysis of Parathyroid Hormone Fragments with Vitamin D Deficiency in Patients with Diabetes Mellitus.","authors":"Hicham Benabdelkamel, Refat M Nimer, Afshan Masood, Maha Al Mogren, Anas M Abdel Rahman, Assim A Alfadda","doi":"10.3390/proteomes12040030","DOIUrl":"https://doi.org/10.3390/proteomes12040030","url":null,"abstract":"Current immunoassay techniques for analyzing clinically relevant parathyroid hormone (PTH) circulating fragments cannot distinguish microheterogeneity among structurally similar molecular species. This hinders the identification of molecular species and the capture of target analyte information. Since structural modifications are important in disease pathways, mass spectrometry can detect, identify, and quantify heterogeneous ligands captured by antibodies. We aimed to create a sensitive and selective multiple reaction monitoring-mass spectrometric immunoassay analysis (MRM-MSIA)-based method for detecting and quantifying PTH fragments or proteoforms for clinical research. Our study established MRM transitions using triple-quadrupole tandem mass spectrometry for the signature peptides of five PTH fragments. This method was validated according to FDA guidelines, employing the mass spectrometric immunoassay (MSIA) protocol to bolster detection selectivity and sensitivity. This validated approach was applied by analyzing samples from type 2 diabetes mellitus (T2DM) patients with and without vitamin D deficiency. We found serum PTH fragments associated with vitamin D deficiency in patients with and without T2DM. We developed and validated the MRM-MSIA technique specifically designed for the detection and quantification (amino acid (aa38-44), (aa45-51), and (aa65-75)) of these fragments associated with vitamin D deficiency and T2DM. This study is the first to accurately quantify plasma PTH fragments using MRM-MSIA, demonstrating its potential for clinical diagnostics.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Circulating Factors as Potential Biomarkers of Cardiovascular Damage Progression Associated with Type 2 Diabetes. 作为与 2 型糖尿病相关的心血管损伤进展潜在生物标志物的循环因子。

IF 4

Proteomes Pub Date : 2024-10-11 DOI: 10.3390/proteomes12040029

Giovanni Sartore, Francesco Piarulli, Eugenio Ragazzi, Alice Mallia, Stefania Ghilardi, Massimo Carollo, Annunziata Lapolla, Cristina Banfi

{"title":"Circulating Factors as Potential Biomarkers of Cardiovascular Damage Progression Associated with Type 2 Diabetes.","authors":"Giovanni Sartore, Francesco Piarulli, Eugenio Ragazzi, Alice Mallia, Stefania Ghilardi, Massimo Carollo, Annunziata Lapolla, Cristina Banfi","doi":"10.3390/proteomes12040029","DOIUrl":"https://doi.org/10.3390/proteomes12040029","url":null,"abstract":"Background: Diabetes, particularly type 2 diabetes (T2D), is linked with an increased risk of developing coronary heart disease (CHD). The present study aimed to evaluate potential circulating biomarkers of CHD by adopting a targeted proteomic approach based on proximity extension assays (PEA). Methods: The study was based on 30 patients with both T2D and CHD (group DC), 30 patients with T2D without CHD (group DN) and 29 patients without diabetes but with a diagnosis of CHD (group NC). Plasma samples were analyzed using PEA, with an Olink Target 96 cardiometabolic panel expressed as normalized protein expression (NPX) units. Results: Lysosomal Pro-X carboxypeptidase (PRCP), Liver carboxylesterase 1 (CES1), Complement C2 (C2), and Intercellular adhesion molecule 3 (ICAM3) were lower in the DC and NC groups compared with the DN groups. Lithostathine-1-alpha (REG1A) and Immunoglobulin lambda constant 2 (IGLC2) were found higher in the DC group compared to DN and NC groups. ROC analysis suggested a significant ability of the six proteins to distinguish among the three groups (whole model test p < 0.0001, AUC 0.83-0.88), with a satisfactory discriminating performance in terms of sensitivity (77-90%) and specificity (70-90%). A possible role of IGLC2, PRCP, and REG1A in indicating kidney impairment was found, with a sensitivity of 92% and specificity of 83%. Conclusions: The identified panel of six plasma proteins, using a targeted proteomic approach, provided evidence that these parameters could be considered in the chronic evolution of T2D and its complications.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Towards Characterization of Hass Avocado Peel and Pulp Proteome during Postharvest Shelf Life. 哈斯鳄梨果皮和果肉蛋白质组在采后保质期内的特征描述。

IF 4

Proteomes Pub Date : 2024-09-28 DOI: 10.3390/proteomes12040028

Carolina Camacho-Vázquez, José Miguel Elizalde-Contreras, Francisco Antonio Reyes-Soria, Juan Luis Monribot-Villanueva, José Antonio Guerrero-Analco, Janet Juarez-Escobar, Olinda Velázquez-López, Thuluz Meza-Menchaca, Esaú Bojórquez-Velázquez, Jesús Alejandro Zamora-Briseño, Monica Ramirez-Vazquez, Guadalupe Alheli González Barrenechea, Enrique Ibarra-Laclette, Eliel Ruiz-May

{"title":"Towards Characterization of Hass Avocado Peel and Pulp Proteome during Postharvest Shelf Life.","authors":"Carolina Camacho-Vázquez, José Miguel Elizalde-Contreras, Francisco Antonio Reyes-Soria, Juan Luis Monribot-Villanueva, José Antonio Guerrero-Analco, Janet Juarez-Escobar, Olinda Velázquez-López, Thuluz Meza-Menchaca, Esaú Bojórquez-Velázquez, Jesús Alejandro Zamora-Briseño, Monica Ramirez-Vazquez, Guadalupe Alheli González Barrenechea, Enrique Ibarra-Laclette, Eliel Ruiz-May","doi":"10.3390/proteomes12040028","DOIUrl":"https://doi.org/10.3390/proteomes12040028","url":null,"abstract":"In recent years, avocados have gained worldwide popularity as a nutritive food. This trend is causing a rise in the production of this fruit, which is accompanied by several problems associated with monocultural practices. Despite massive economic gains, limited molecular and structural information has been generated about avocado ripening. In fact, limited studies have attempted to unravel the proteome complexity dynamics of avocado fruit. We therefore conducted a comparative proteomics study on avocado peel and pulp during the postharvest shelf life using tandem mass tag synchronous precursor selection triple-stage mass spectrometry. We identified 3161 and 1128 proteins in the peel and pulp, respectively. Peels exhibited major over-accumulation of proteins associated with water deprivation and oxidative stress, along with abscisic acid biosynthesis. Ethylene, jasmonic acid, phenylpropanoid, and flavonoid biosynthesis pathways were activated. Structurally, we observed the accumulation of lignin and a reduction in cuticular thickness, which coincides with the reduction in the levels of long-chain acyl-coenzyme A synthetase and a marginal increase in 10,16-dihydroxyhexadecanoic acid. Our study sheds light on the association of proteome modulation with the structural features of Hass avocado. Its detailed characterization will provide an alternative for better preservation during the postharvest period.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protein Extraction Methods Suitable for Muscle Tissue Proteomic Analysis. 适用于肌肉组织蛋白质组分析的蛋白质提取方法。

IF 4

Proteomes Pub Date : 2024-09-25 DOI: 10.3390/proteomes12040027

Lorenza Vantaggiato, Claudia Landi, Enxhi Shaba, Daniela Rossi, Vincenzo Sorrentino, Luca Bini

{"title":"Protein Extraction Methods Suitable for Muscle Tissue Proteomic Analysis.","authors":"Lorenza Vantaggiato, Claudia Landi, Enxhi Shaba, Daniela Rossi, Vincenzo Sorrentino, Luca Bini","doi":"10.3390/proteomes12040027","DOIUrl":"https://doi.org/10.3390/proteomes12040027","url":null,"abstract":"Muscle tissue is one of the most dynamic and plastic tissues of the mammalian body and covers different roles, such as force generation and metabolic control. Muscular proteomics provides an important opportunity to reveal the molecular mechanisms behind muscle pathophysiology. To ensure successful proteomic analysis, it is necessary to have an efficient and reproducible protein extraction method. This study aimed to evaluate the efficacy of two different extraction protocols of muscle samples for two-dimensional gel electrophoresis. In particular, mouse muscle proteins were extracted by an SDS-based buffer (Method A) and by a UREA/CHAPS/DTE/TRIS solution (Method B). The efficacies of the methods were assessed by performing an image analysis of the 2DE gels and by statistical and multivariate analyses. The 2DE gels in both preparations showed good resolution and good spot overlapping. Methods A and B produced 2DE gels with different means of total spots, higher for B. Image analysis showed different patterns of protein abundance between the protocols. The results showed that the two methods extract and solubilize proteins with different chemical-physical characteristics and different cellular localizations. These results attest the efficacy and reproducibility of both protein extraction methods, which can be parallelly applied for comprehensive proteomic profiling of muscle tissue.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 4","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142516594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-Omic Approaches in Cancer-Related Micropeptide Identification. 癌症相关微肽鉴定中的多肽方法

IF 4

Proteomes Pub Date : 2024-09-13 DOI: 10.3390/proteomes12030026

Katarina Vrbnjak, Raj Nayan Sewduth

{"title":"Multi-Omic Approaches in Cancer-Related Micropeptide Identification.","authors":"Katarina Vrbnjak, Raj Nayan Sewduth","doi":"10.3390/proteomes12030026","DOIUrl":"10.3390/proteomes12030026","url":null,"abstract":"Despite the advances in modern cancer therapy, malignant diseases are still a leading cause of morbidity and mortality worldwide. Conventional treatment methods frequently lead to side effects and drug resistance in patients, highlighting the need for novel therapeutic approaches. Recent findings have identified the existence of non-canonical micropeptides, an additional layer of the proteome complexity, also called the microproteome. These small peptides are a promising class of therapeutic agents with the potential to address the limitations of current cancer treatments. The microproteome is encoded by regions of the genome historically annotated as non-coding, and its existence has been revealed thanks to recent advances in proteomic and bioinformatic technology, which dramatically improved the understanding of proteome complexity. Micropeptides have been shown to be biologically active in several cancer types, indicating their therapeutic role. Furthermore, they are characterized by low toxicity and high target specificity, demonstrating their potential for the development of better tolerated drugs. In this review, we survey the current landscape of known micropeptides with a role in cancer progression or treatment, discuss their potential as anticancer agents, and describe the methodological challenges facing the proteome field of research.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142294052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transforming Clinical Research: The Power of High-Throughput Omics Integration. 变革临床研究：高通量 Omics 整合的力量。

IF 4

Proteomes Pub Date : 2024-09-06 DOI: 10.3390/proteomes12030025

Rui Vitorino

{"title":"Transforming Clinical Research: The Power of High-Throughput Omics Integration.","authors":"Rui Vitorino","doi":"10.3390/proteomes12030025","DOIUrl":"10.3390/proteomes12030025","url":null,"abstract":"High-throughput omics technologies have dramatically changed biological research, providing unprecedented insights into the complexity of living systems. This review presents a comprehensive examination of the current landscape of high-throughput omics pipelines, covering key technologies, data integration techniques and their diverse applications. It looks at advances in next-generation sequencing, mass spectrometry and microarray platforms and highlights their contribution to data volume and precision. In addition, this review looks at the critical role of bioinformatics tools and statistical methods in managing the large datasets generated by these technologies. By integrating multi-omics data, researchers can gain a holistic understanding of biological systems, leading to the identification of new biomarkers and therapeutic targets, particularly in complex diseases such as cancer. The review also looks at the integration of omics data into electronic health records (EHRs) and the potential for cloud computing and big data analytics to improve data storage, analysis and sharing. Despite significant advances, there are still challenges such as data complexity, technical limitations and ethical issues. Future directions include the development of more sophisticated computational tools and the application of advanced machine learning techniques, which are critical for addressing the complexity and heterogeneity of omics datasets. This review aims to serve as a valuable resource for researchers and practitioners, highlighting the transformative potential of high-throughput omics technologies in advancing personalized medicine and improving clinical outcomes.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142294053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigating the Prognostic Potential of Plasma ST2 in Patients with Peripheral Artery Disease: Identification and Evaluation. 研究外周动脉疾病患者血浆 ST2 的预后潜力：鉴定与评估。

IF 4

Proteomes Pub Date : 2024-08-29 DOI: 10.3390/proteomes12030024

Ben Li, Farah Shaikh, Abdelrahman Zamzam, Rawand Abdin, Mohammad Qadura

{"title":"Investigating the Prognostic Potential of Plasma ST2 in Patients with Peripheral Artery Disease: Identification and Evaluation.","authors":"Ben Li, Farah Shaikh, Abdelrahman Zamzam, Rawand Abdin, Mohammad Qadura","doi":"10.3390/proteomes12030024","DOIUrl":"10.3390/proteomes12030024","url":null,"abstract":"Soluble interleukin 1 receptor-like 1 (ST2) is a circulating protein demonstrated to be associated with cardiovascular diseases; however, it has not been studied as a biomarker for peripheral artery disease (PAD). Using a prospectively recruited cohort of 476 patients (312 with PAD and 164 without PAD), we conducted a prognostic study of PAD using clinical/biomarker data. Plasma concentrations of three circulating proteins [ST2, cytokine-responsive gene-2 (CRG-2), vascular endothelial growth factor (VEGF)] were measured at baseline and the cohort was followed for 2 years. The outcome of interest was a 2-year major adverse limb event (MALE; composite of major amputation, vascular intervention, or acute limb ischemia). Using 10-fold cross-validation, a random forest model was trained using clinical characteristics and plasma ST2 levels. The primary model evaluation metric was the F1 score. Out of the three circulating proteins analyzed, ST2 was the only one that was statistically significantly higher in individuals with PAD compared to patients without PAD (mean concentration in plasma of 9.57 [SD 5.86] vs. 11.39 [SD 6.43] pg/mL, p < 0.001). Over a 2-year period, 28 (9%) patients with PAD experienced MALE. Our predictive model, incorporating clinical features and plasma ST2 levels, achieved an F1 score of 0.713 for forecasting 2-year MALE outcomes. Patients identified as high-risk by this model showed a significantly increased likelihood of developing MALE (HR 1.06, 95% CI 1.02-1.13, p = 0.003). By combining clinical characteristics and plasma ST2 levels, our proposed predictive model offers accurate risk assessment for 2-year MALE in PAD patients. This algorithm supports risk stratification in PAD, guiding clinical decisions regarding further vascular evaluation, specialist referrals, and appropriate medical or surgical interventions, thereby potentially enhancing patient outcomes.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11417877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142294051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Current Molecular and Cellular Landscape of Chronic Obstructive Pulmonary Disease (COPD): A Review of Therapies and Efforts towards Personalized Treatment. 慢性阻塞性肺病 (COPD) 目前的分子和细胞状况：慢性阻塞性肺病（COPD）当前的分子和细胞状况：疗法回顾与个性化治疗努力。

IF 4

Proteomes Pub Date : 2024-08-16 DOI: 10.3390/proteomes12030023

Luke A Farrell, Matthew B O'Rourke, Matthew P Padula, Fernando Souza-Fonseca-Guimaraes, Gaetano Caramori, Peter A B Wark, Shymali C Dharmage, Phillip M Hansbro

{"title":"The Current Molecular and Cellular Landscape of Chronic Obstructive Pulmonary Disease (COPD): A Review of Therapies and Efforts towards Personalized Treatment.","authors":"Luke A Farrell, Matthew B O'Rourke, Matthew P Padula, Fernando Souza-Fonseca-Guimaraes, Gaetano Caramori, Peter A B Wark, Shymali C Dharmage, Phillip M Hansbro","doi":"10.3390/proteomes12030023","DOIUrl":"10.3390/proteomes12030023","url":null,"abstract":"Chronic obstructive pulmonary disease (COPD) ranks as the third leading cause of global illness and mortality. It is commonly triggered by exposure to respiratory irritants like cigarette smoke or biofuel pollutants. This multifaceted condition manifests through an array of symptoms and lung irregularities, characterized by chronic inflammation and reduced lung function. Present therapies primarily rely on maintenance medications to alleviate symptoms, but fall short in impeding disease advancement. COPD's diverse nature, influenced by various phenotypes, complicates diagnosis, necessitating precise molecular characterization. Omics-driven methodologies, including biomarker identification and therapeutic target exploration, offer a promising avenue for addressing COPD's complexity. This analysis underscores the critical necessity of improving molecular profiling to deepen our comprehension of COPD and identify potential therapeutic targets. Moreover, it advocates for tailoring treatment strategies to individual phenotypes. Through comprehensive exploration-based molecular characterization and the adoption of personalized methodologies, innovative treatments may emerge that are capable of altering the trajectory of COPD, instilling optimism for efficacious disease-modifying interventions.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Low-Abundance Plasma Proteome Reveals Differentially Abundant Proteins Associated with Breast Implant Capsular Contracture: A Pilot Study. 低丰度血浆蛋白质组揭示了与乳房假体囊性挛缩相关的不同丰度蛋白质：一项试点研究。

IF 4

Proteomes Pub Date : 2024-08-06 DOI: 10.3390/proteomes12030022

Md Arifur Rahman, Ardeshir Amirkhani, Maria Mempin, Seong Beom Ahn, Anand K Deva, Mark S Baker, Karen Vickery, Honghua Hu

{"title":"The Low-Abundance Plasma Proteome Reveals Differentially Abundant Proteins Associated with Breast Implant Capsular Contracture: A Pilot Study.","authors":"Md Arifur Rahman, Ardeshir Amirkhani, Maria Mempin, Seong Beom Ahn, Anand K Deva, Mark S Baker, Karen Vickery, Honghua Hu","doi":"10.3390/proteomes12030022","DOIUrl":"10.3390/proteomes12030022","url":null,"abstract":"Capsular contracture (CC) is one of the most common postoperative complications associated with breast implant-associated infections. The mechanisms that lead to CC remain poorly understood. Plasma is an ideal biospecimen for early proteomics biomarker discovery. However, as high-abundance proteins mask signals from low-abundance proteins, identifying novel or specific proteins as biomarkers for a particular disease has been hampered. Here, we employed depletion of high-abundance plasma proteins followed by Tandem Mass Tag (TMT)-based quantitative proteomics to compare 10 healthy control patients against 10 breast implant CC patients. A total of 450 proteins were identified from these samples. Among them, 16 proteins were significantly differentially expressed in which 5 proteins were upregulated and 11 downregulated in breast implant CC patients compared to healthy controls. Gene Ontology enrichment analysis revealed that proteins related to cell, cellular processes and catalytic activity were highest in the cellular component, biological process, and molecular function categories, respectively. Further, pathway analysis revealed that inflammatory responses, focal adhesion, platelet activation, and complement and coagulation cascades were enriched pathways. The differentially abundant proteins from TMT-based quantitative proteomics have the potential to provide important information for future mechanistic studies and in the development of breast implant CC biomarkers.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigating and Annotating the Human Peptidome Profile from Urine under Normal Physiological Conditions. 调查和注释正常生理条件下尿液中的人类肽组图谱

IF 4

Proteomes Pub Date : 2024-06-25 DOI: 10.3390/proteomes12030018

Amr Elguoshy, Keiko Yamamoto, Yoshitoshi Hirao, Tomohiro Uchimoto, Kengo Yanagita, Tadashi Yamamoto

{"title":"Investigating and Annotating the Human Peptidome Profile from Urine under Normal Physiological Conditions.","authors":"Amr Elguoshy, Keiko Yamamoto, Yoshitoshi Hirao, Tomohiro Uchimoto, Kengo Yanagita, Tadashi Yamamoto","doi":"10.3390/proteomes12030018","DOIUrl":"10.3390/proteomes12030018","url":null,"abstract":"Examining the composition of the typical urinary peptidome and identifying the enzymes responsible for its formation holds significant importance, as it mirrors the normal physiological state of the human body. Any deviation from this normal profile could serve as an indicator of pathological processes occurring in vivo. Consequently, this study focuses on characterizing the normal urinary peptidome and investigating the various catalytic enzymes that are involved in generating these native peptides in urine. Our findings reveal that 1503 endogenous peptides, corresponding to 436 precursor proteins, were consistently identified robustly in at least 10 samples out of a total of 19 samples. Notably, the liver and kidneys exhibited the highest number of tissue-enriched or enhanced genes in the analyzed urinary peptidome. Furthermore, among the catalytic types, CTSD (cathepsin D) and MMP2 (matrix metalloproteinase-2) emerged as the most prominent peptidases in the aspartic and metallopeptidases categories, respectively. A comparison of our dataset with two of the most comprehensive urine peptidome datasets to date indicates a consistent relative abundance of core endogenous peptides for different proteins across all three datasets. These findings can serve as a foundational reference for the discovery of biomarkers in various human diseases.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"12 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11270373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141760618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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