PROTEOMICS – Clinical Applications最新文献_第5页

A novel micropeptide, Slitharin, exerts cardioprotective effects in myocardial infarction. 一种新型微肽--Slitharin对心肌梗塞患者有保护心脏的作用。

IF 2.1 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-03-05 DOI: 10.1002/prca.202300128

Ahmed G E Ibrahim, Alessandra Ciullo, Shukuro Yamaguchi, Chang Li, Travis Antes, Xaviar Jones, Liang Li, Ramachandran Murali, Innokentiy Maslennikov, Niveda Sundararaman, Daniel Soetkamp, Eugenio Cingolani, Jennifer Van Eyk, Eduardo Marbán

{"title":"A novel micropeptide, Slitharin, exerts cardioprotective effects in myocardial infarction.","authors":"Ahmed G E Ibrahim, Alessandra Ciullo, Shukuro Yamaguchi, Chang Li, Travis Antes, Xaviar Jones, Liang Li, Ramachandran Murali, Innokentiy Maslennikov, Niveda Sundararaman, Daniel Soetkamp, Eugenio Cingolani, Jennifer Van Eyk, Eduardo Marbán","doi":"10.1002/prca.202300128","DOIUrl":"10.1002/prca.202300128","url":null,"abstract":"Purpose: Micropeptides are an emerging class of proteins that play critical roles in cell signaling. Here, we describe the discovery of a novel micropeptide, dubbed slitharin (Slt), in conditioned media from Cardiosphere-derived cells (CDCs), a therapeutic cardiac stromal cell type.Experimental design: We performed mass spectrometry of peptide-enriched fractions from the conditioned media of CDCs and a therapeutically inert cell type (human dermal fibrobasts). We then evaluated the therapeutic capacity of the candidate peptide using an in vitro model of cardiomyocyte injury and a rat model of myocardial infarction.Results: We identified a novel 24-amino acid micropeptide (dubbed Slitharin [Slt]) with a non-canonical leucine start codon, arising from long intergenic non-coding (LINC) RNA 2099. Neonatal rat ventricular myocytes (NRVMs) exposed to Slt were protected from hypoxic injury in vitro compared to a vehicle or scrambled control. Transcriptomic analysis of cardiomyocytes exposed to Slt reveals cytoprotective capacity, putatively through regulation of stress-induced MAPK-ERK. Slt also exerted cardioprotective effects in rats with myocardial infarction as shown by reduced infarct size 48 h post-injury. Conclusions and clinical relavance: Thus, Slt is a non-coding RNA-derived micropeptide, identified in the extracellular space, with a potential cardioprotective function.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11374934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140040180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

"Hide and seek": Misleading transferrin variants in PMM2-CDG complicate diagnostics. “捉迷藏”:PMM2-CDG中误导性转铁蛋白变异使诊断复杂化。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-03-01 Epub Date: 2023-10-24 DOI: 10.1002/prca.202300040

Alexandre Raynor, Arnaud Bruneel, Pieter Vermeersch, Sophie Cholet, Sebastian Friedrich, Matthias Eckenweiler, Anke Schumann, Simone Hengst, Ali Tunç Tuncel, François Fenaille, Christian Thiel, Daisy Rymen

{"title":"\"Hide and seek\": Misleading transferrin variants in PMM2-CDG complicate diagnostics.","authors":"Alexandre Raynor, Arnaud Bruneel, Pieter Vermeersch, Sophie Cholet, Sebastian Friedrich, Matthias Eckenweiler, Anke Schumann, Simone Hengst, Ali Tunç Tuncel, François Fenaille, Christian Thiel, Daisy Rymen","doi":"10.1002/prca.202300040","DOIUrl":"10.1002/prca.202300040","url":null,"abstract":"Purpose: Congenital disorders of glycosylation (CDG) are one of the fastest growing groups of inborn errors of metabolism. Despite the availability of next-generation sequencing techniques and advanced methods for evaluation of glycosylation, CDG screening mainly relies on the analysis of serum transferrin (Tf) by isoelectric focusing, HPLC or capillary electrophoresis. The main pitfall of this screening method is the presence of Tf protein variants within the general population. Although reports describe the role of Tf variants leading to falsely abnormal results, their significance in confounding diagnosis in patients with CDG has not been documented so far. Here, we describe two PMM2-CDG cases, in which Tf variants complicated the diagnostic.Experimental design: Glycosylation investigations included classical screening techniques (capillary electrophoresis, isoelectric focusing and HPLC of Tf) and various confirmation techniques (two-dimensional electrophoresis, western blot, N-glycome, UPLC-FLR/QTOF MS with Rapifluor). Tf variants were highlighted following neuraminidase treatment. Sequencing of PMM2 was performed.Results: In both patients, Tf screening pointed to CDG-II, while second-line analyses pointed to CDG-I. Tf variants were found in both patients, explaining these discrepancies. PMM2 causative variants were identified in both patients.Conclusion and clinical relevance: We suggest that a neuraminidase treatment should be performed when a typical CDG Tf pattern is found upon initial screening analysis.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50158637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A comparative proteomic analysis for non-invasive early prediction of hypoxic-ischemic injury in asphyxiated neonates. 无创早期预测窒息新生儿缺氧缺血性损伤的比较蛋白质组学分析。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-03-01 Epub Date: 2023-10-03 DOI: 10.1002/prca.202200054

Sumrati Gurtoo, Gayathree Karthikkeyan, Santosh Kumar Behera, Chinmaya Narayana Kotimoole, Mohd Altaf Najar, Prashant Kumar Modi, Sahana Ks, Sneha M Pinto, Arun Ab

{"title":"A comparative proteomic analysis for non-invasive early prediction of hypoxic-ischemic injury in asphyxiated neonates.","authors":"Sumrati Gurtoo, Gayathree Karthikkeyan, Santosh Kumar Behera, Chinmaya Narayana Kotimoole, Mohd Altaf Najar, Prashant Kumar Modi, Sahana Ks, Sneha M Pinto, Arun Ab","doi":"10.1002/prca.202200054","DOIUrl":"10.1002/prca.202200054","url":null,"abstract":"Aim: Hypoxic Ischemic Encephalopathy (HIE) is one of the principal causes of neonatal mortality and long-term morbidity worldwide. The neonatal signs of mild cerebral injury are subtle, making an early precise diagnosis difficult. Delayed detection, poor prognosis, and lack of specific biomarkers for the disease are increasing mortality rates. In this study, we intended to identify specific biomarkers using comparative proteomic analysis to predict the severity of perinatal asphyxia so that its outcome can also be prevented.Experimental design: A case-control study was conducted on 38 neonates, and urine samples were collected within 24 and 72 h of life. A tandem mass spectrometry-based quantitative proteomics approach, followed by validation via sandwich ELISA, was performed.Results: The LC-MS/MS-based proteomics analysis resulted in the identification of 1201 proteins in urine, with 229, 244, and 426 being differentially expressed in HIE-1, HIE-2, and HIE-3, respectively. Axon guidance, Diseases of programmed cell death, and Detoxification of reactive oxygen species pathways were significantly enriched in mild HIE versus severe HIE. Among the differentially expressed proteins in various stages of HIE, we chose to validate four proteins - APP, AGT, FABP1, and FN1 - via sandwich ELISA. Individual and cumulative ROC curves were plotted. AGT and FABP1 together showed high sensitivity, specificity, and accuracy as potential biomarkers for early diagnosis of HIE.Conclusion: Establishing putative urinary biomarkers will facilitate clinicians to more accurately screen neonates for brain injury and monitor the disease progression. Prompt treatment of neonates may reduce mortality and neurodevelopmental impairment.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41125935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Human peripheral blood mononuclear cells as a valuable source of disease-related biomarkers: Evidence from comparative proteomics studies. 人类外周血单核细胞作为疾病相关生物标志物的宝贵来源：来自比较蛋白质组学研究的证据。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-03-01 Epub Date: 2023-11-07 DOI: 10.1002/prca.202300072

Michal Alexovič, Csilla Uličná, Ján Sabo, Katarina Davalieva

{"title":"Human peripheral blood mononuclear cells as a valuable source of disease-related biomarkers: Evidence from comparative proteomics studies.","authors":"Michal Alexovič, Csilla Uličná, Ján Sabo, Katarina Davalieva","doi":"10.1002/prca.202300072","DOIUrl":"10.1002/prca.202300072","url":null,"abstract":"Purpose: The discovery of specific and sensitive disease-associated biomarkers for early diagnostic purposes of many diseases is still highly challenging due to various complex molecular mechanisms triggered, high variability of disease-related interactions, and an overlap of manifestations among diseases. Human peripheral blood mononuclear cells (PBMCs) contain protein signatures corresponding to essential immunological interplay. Certain diseases stimulate PBMCs and contribute towards modulation of their proteome which can be effectively identified and evaluated via the comparative proteomics approach.Experimental design: In this review, we made a detailed survey of the PBMCS-derived protein biomarker candidates for a variety of diseases, published in the last 15 years. Articles were preselected to include only comparative proteomics studies.Results: PBMC-derived biomarkers were investigated for cancer, glomerular, neurodegenerative/neurodevelopmental, psychiatric, chronic inflammatory, autoimmune, endocrinal, infectious, and other diseases. A detailed review of these studies encompassed the proteomics platforms, proposed candidate biomarkers, their immune cell type specificity, and potential clinical application.Conclusions: Overall, PBMCs have shown a solid potential in giving early diagnostic and prognostic biomarkers for many diseases. The future of PBMC biomarker research should reveal its full potential through well-designed comparative studies and extensive testing of the most promising protein biomarkers identified so far.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71485207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative comparison of the renal pelvic urine and bladder urine to examine modifications of the urine proteome by the lower urinary tract. 定量比较肾盂尿和膀胱尿，研究下尿路对尿液蛋白质组的改变。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-03-01 Epub Date: 2023-08-13 DOI: 10.1002/prca.202300004

Yilin Pan, Christine Yim-Ping Wong, Haiying Ma, Ryan Tsz-Hei Tse, Carol Ka-Lo Cheng, Miaomiao Tan, Peter Ka-Fung Chiu, Jeremy Yuen-Chun Teoh, Xin Wang, Chi-Fai Ng, Liang Zhang

{"title":"Quantitative comparison of the renal pelvic urine and bladder urine to examine modifications of the urine proteome by the lower urinary tract.","authors":"Yilin Pan, Christine Yim-Ping Wong, Haiying Ma, Ryan Tsz-Hei Tse, Carol Ka-Lo Cheng, Miaomiao Tan, Peter Ka-Fung Chiu, Jeremy Yuen-Chun Teoh, Xin Wang, Chi-Fai Ng, Liang Zhang","doi":"10.1002/prca.202300004","DOIUrl":"10.1002/prca.202300004","url":null,"abstract":"Purpose: Urine proteome is a valuable reservoir of biomarkers for disease diagnosis and monitoring. Following formation as the plasma filtrate in the kidney, urine is progressively modified by the active reabsorption and secretion of the urinary tract. However, little is known about how the urine proteome changes as it passes along the urinary tract.Experimental design: To investigate this, we compared the proteome composition of the renal pelvis urine (RPU) and individually self-voided bladder urine (BU) collected from seven unilateral urinary tract obstruction male patients by LC-MS/MS screening. To our knowledge, this is the first proteomic comparison of RPU and BU samples from the same individual.Results: Overall, RPU and BU proteomes did not exhibit proteins that were exclusively present in all samples of one urine type while in none of the other type. Nonetheless, BU had more overrepresented proteins that were observed at a higher frequency than RPU. Label-free quantitative analyses revealed BU-RPU differential proteins that are enriched in exosomes and extracellular proteins. However, the differences were not significant after corrections for multiple testing. Interestingly, we observed a significant increase of collagen peptides with hydroxyproline modifications in the BU samples, suggesting differences in protein modifications.Conclusions and clinical relevance: Our study revealed no substantial differences at the protein level between the BU and RPU samples. Future investigations with expanded cohorts would provide more insights about the urothelial-urinary interactions.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9990697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Parallel accumulation-serial fragmentation method for in-depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer. 采用平行累积-序列片段分析法对非小细胞肺癌患者支气管肺泡灌洗液进行深入的蛋白质组学分析。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-03-01 Epub Date: 2024-01-31 DOI: 10.1002/prca.202300053

Hung M Vu, Sunghyun Huh, Jun Hyung Lee, Seung Hyeun Lee, Min-Sik Kim

{"title":"Parallel accumulation-serial fragmentation method for in-depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer.","authors":"Hung M Vu, Sunghyun Huh, Jun Hyung Lee, Seung Hyeun Lee, Min-Sik Kim","doi":"10.1002/prca.202300053","DOIUrl":"10.1002/prca.202300053","url":null,"abstract":"Purpose: Advances in mass spectrometry-based quantitative proteomic analysis have successfully demonstrated the in-depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectrometers escalating the sensitivity and throughput. Utilizing these advantages, herein, we employed the parallel accumulation-serial fragmentation (PASEF) implanted in a timsTOF Pro mass spectrometer to examine the alteration of BALF proteomes in patients with nonsmall cell lung cancers (NSCLCs).Experimental design: BALF proteins were processed from patients with NSCLC and analyzed in a timsTOF Pro mass spectrometer with the PASEF method using a peptide input of 100 ng. Label-free mass spectrometry data were analyzed in the FragPipe platform.Results: We quantitated over 1400 proteins from a single injection of 100 ng of peptides per sample with a median of ∼2000 proteins. We were able to find a few potential biomarker proteins upregulated in NSCLC.Conclusions and clinical relevance: The alterations of the BALF proteome landscape vary among patients with NSCLC as previously observed in patients with small-cell lung cancers. The PASEF method has significantly enhanced the sensitivity and throughput, demonstrating its effectiveness in clinical research and application.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomic landscape of primary and metastatic brain tumors for heterogeneity discovery. 用于异质性发现的原发性和转移性脑肿瘤的蛋白质组学景观。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-03-01 Epub Date: 2023-09-19 DOI: 10.1002/prca.202300010

Shuang Yang, Chengbin Zhou, Lei Zhang, Yueting Xiong, Yongtao Zheng, Liuguan Bian, Xiaohui Liu

{"title":"Proteomic landscape of primary and metastatic brain tumors for heterogeneity discovery.","authors":"Shuang Yang, Chengbin Zhou, Lei Zhang, Yueting Xiong, Yongtao Zheng, Liuguan Bian, Xiaohui Liu","doi":"10.1002/prca.202300010","DOIUrl":"10.1002/prca.202300010","url":null,"abstract":"Purpose: Despite recent advancements in our understanding of driver gene mutations and heterogeneity within brain tumors, whether primary or metastatic (also known as secondary), our comprehension of proteomic changes remains inadequate. The aim of this study is to provide an informative source for brain tumor researches, and distinguish primary brain tumors and secondary brain tumors from extracranial origins based on proteomic analysis.Experimental design: We assembled the most frequent brain tumors as follows: gliomas from WHO grade 2 to 4, with IDH1 mutations and wildtypes; brain metastases (BrMs) originating from lung cancer (LC), breast cancer (BC), ovarian cancer (OC), and colorectal cancer (CC). A total of 29 tissue samples were analyzed by label free quantitative mass spectrometry-based proteomics.Results: In total, 8165 protein groups were quantified, of which 4383 proteins were filtered at 50% valid intensity values for downstream analysis. Proteomic analysis of BrMs reveals conserved features shared among multiple origins. While proteomic heterogeneities were found for discriminating different grades of gliomas, as well as IDH1 mutant and wildtype gliomas. In addition, notable distinctions were observed at the pathway level between BrMs and gliomas. Specifically, BrMs exhibited characteristic pathways focused on proliferation and immunomodulation after colonizing the brain, whereas gliomas primarily engaged in invasion processes.Conclusions and clinical relevance: We characterized an extensive proteomic landscape of BrMs and gliomas. These findings have promising implications for the development of targeted therapies for BrMs and gliomas.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41150294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rare HER2 L796P missense mutation promotes the growth and oncogenic signaling in breast cancer cells. 罕见的 HER2 L796P 错义突变促进了乳腺癌细胞的生长和致癌信号传导。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-01-01 Epub Date: 2023-09-06 DOI: 10.1002/prca.202300061

Dongxue Zhang, Xiaoyu Shi, Weimin Zheng, Xian Zhang, Yun Chen

{"title":"Rare HER2 L796P missense mutation promotes the growth and oncogenic signaling in breast cancer cells.","authors":"Dongxue Zhang, Xiaoyu Shi, Weimin Zheng, Xian Zhang, Yun Chen","doi":"10.1002/prca.202300061","DOIUrl":"10.1002/prca.202300061","url":null,"abstract":"Purpose: This research aimed to find potential HER2 mutations that would have an impact on breast cancer and investigate the underlying mechanism.Experimental design: This study first investigated 238 pairs of breast cancer and para-cancerous tissue samples from patients on the targeted next-generation sequencing (tNGS) platform. CCK-8 and clone formation assay were used to investigate whether the mutation exerts proliferative effects on breast cancer cells. In addition, mass spectrometry-based comparative proteomic and phosphoproteomic analyses of the mutation types and wild types of MCF-7 cell lines were carried out.Results: Among the identified mutations, a new mutation HER2 L796P promoted the proliferation of breast cancer cells and had resistance to lapatinib using CCK-8 cell proliferation assay and clone formation assay. The bioinformatic analysis showed that RAS family proteins and ERK phosphorylated proteins significantly increased in the L796P mutant cells. The Gene Ontology (GO) analysis revealed that L796P mutation affected the function of breast cancer at the level of upstream genes in the MAPK and PI3K-AKT-TOR pathways.Conclusions and clinical relevance: This study demonstrated that a rare mutation HER2 L796P could be a potential therapeutic target for the clinical management of breast cancer.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10170719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Design of experiments approach for systematic optimization of a single-shot diaPASEF plasma proteomics workflow applicable for high-throughput. 用于系统优化适用于高通量的单次 diaPASEF 血浆蛋白质组学工作流程的实验设计方法。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-01-01 Epub Date: 2023-08-31 DOI: 10.1002/prca.202300006

Shawn J Rice, Chandra P Belani

{"title":"Design of experiments approach for systematic optimization of a single-shot diaPASEF plasma proteomics workflow applicable for high-throughput.","authors":"Shawn J Rice, Chandra P Belani","doi":"10.1002/prca.202300006","DOIUrl":"10.1002/prca.202300006","url":null,"abstract":"Purpose: Plasma is an abundant source of protein biomarkers. Mass spectrometry (MS) is an effective means to measure a large number of proteins in a single run. The recent development of data-independent acquisition with parallel accumulation and serial fragmentation (diaPASEF) on a trapped ion mobility spectrometer (TIMS) affords deep proteomic coverage with short liquid chromatography gradients. In this work, we utilized a process optimization approach, design of experiments (DoE), to maximize precursor identification for a plasma proteomic diaPASEF workflow.Experimental design: A partial factorial design was used to screen 11 sample preparation factors and six diaPASEF MS acquisition factors. Selected factors were optimized using the response surface method.Results: Three important sample preparation factors and the two important MS acquisition factors were identified in the screening experiments and were selected for separate optimization experiments. The optimal parameters were compared to our standard plasma proteomics workflows using either a 1-h or overnight trypsin digestion. The optimized method outperformed the 1-h digestion, and it was similar in performance to the overnight digestion, however, the optimized method could be completed in a day.Conclusion and clinical relevance: We have used DoE to report an optimized plasma proteomics workflow for diaPASEF, however, established methods are already highly optimized, and resources may be better spent on running samples than comprehensive optimization.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10119351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Associations of inflammation-related proteome with demographic and clinical characteristics of people with HIV in South Africa. 炎症相关蛋白质组与南非艾滋病病毒感染者的人口和临床特征之间的关系。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-01-01 Epub Date: 2023-09-06 DOI: 10.1002/prca.202300015

Junyu Chen, Qin Hui, Chang Liu, Jaysingh Brijkumar, Johnathan A Edwards, Claudia E Ordóñez, Mathew R Dudgeon, Henry Sunpath, Selvan Pillay, Pravi Moodley, Daniel R Kuritzkes, Mohamed Y S Moosa, Tooru Nemoto, Vincent C Marconi, Yan V Sun

{"title":"Associations of inflammation-related proteome with demographic and clinical characteristics of people with HIV in South Africa.","authors":"Junyu Chen, Qin Hui, Chang Liu, Jaysingh Brijkumar, Johnathan A Edwards, Claudia E Ordóñez, Mathew R Dudgeon, Henry Sunpath, Selvan Pillay, Pravi Moodley, Daniel R Kuritzkes, Mohamed Y S Moosa, Tooru Nemoto, Vincent C Marconi, Yan V Sun","doi":"10.1002/prca.202300015","DOIUrl":"10.1002/prca.202300015","url":null,"abstract":"Purpose: Elevated levels of inflammation associated with human immunodeficiency virus (HIV) infection are one of the primary causes for the burden of age-related diseases among people with HIV (PWH). Circulating proteins can be used to investigate pathways to inflammation among PWH.Experimental design: We profiled 73 inflammation-related protein markers and assessed their associations with chronological age, sex, and CD4+ cell count among 87 black South African PWH before antiretroviral therapy (ART).Results: We identified 1, 1, and 14 inflammatory proteins significantly associated with sex, CD4+ cell count, and age respectively. Twelve out of 14 age-associated proteins have been reported to be associated with age in the general population, and 4 have previously shown significant associations with age for PWH. Furthermore, many of the age-associated proteins such as CST5, CCL23, SLAMF1, MMP-1, MCP-1, and CDCP1 have been linked to chronic diseases such as cardiovascular disease and neurocognitive decline in the general population. We also found a synergistic interaction between male and older age accounting for excessive expression of CST5.Conclusions and clinical relevance: We found that advanced age may lead to the elevation of multiple inflammatory proteins among PWH. We also demonstrated the potential utility of proteomics for evaluating and characterizing the inflammatory status of PWH.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10177819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0