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Characterization of Extracellular Vesicle Cargo in Sjögren's Syndrome through a SWATH-MS Proteomics Approach

Francesco Finamore, Antonella Cecchettini, Elisa Ceccherini, Giovanni Signore, Francesco Ferro, Silvia Rocchiccioli, Chiara Baldini
2021 International Journal of Molecular Sciences  
In this pilot study, a SWATH-MS approach was used to monitor extracellular vesicles-enriched saliva (EVs) sub-proteome in pSS patients, to compare it with whole saliva (WS) proteome, and assess differential  ...  Among those, 121 proteins were found to be differentially expressed in pSS, 82% were found to be upregulated, and 18% downregulated in pSS samples.  ...  Therefore, in this pilot study, we used a sequential window acquisition of all the theoretical fragment ion spectra (SWATH-MS) approach to monitor the dynamics of EVs sub-proteome in pSS salivary samples  ... 
doi:10.3390/ijms22094864 pmid:34064456 pmcid:PMC8124455 fatcat:4kak26psejc2pagor2tbvm4fjm

Corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a label-free SWATH-MS quantification approach

Byung Soo Kang, Thomas Chuen Lam, Jimmy Ka-wai Cheung, King Kit Li, Chea-su Kee
2021 Scientific Reports  
This study first aimed to establish the entire chicken corneal proteome.  ...  In addition to consistent findings on posterior segment anomalies in high myopia (e.g., scleral remodeling), more recent biometric and biomechanical data in myopic humans and animal models also indicate  ...  Authors thank the University Research Facility in Life Science  ... 
doi:10.1038/s41598-021-84904-4 pmid:33750851 pmcid:PMC7943770 fatcat:3bl2qvpbgndkfdvld7ufh2lej4

Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects

Tanushree Halder, Mukesh Choudhary, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
2022 Proteomes  
However, the use of proteomics to improve RSA traits in wheat is in its infancy.  ...  directions for harnessing proteomics in wheat improvement.  ...  Dissanayake for providing guidance on proteomic methodologies, and Samalka Wijeweera for providing relevant literature on drought stress.  ... 
doi:10.3390/proteomes10020017 pmid:35645375 pmcid:PMC9150004 fatcat:3cowbd7xdjebtgxbj56mwovupi

Human Proteome Project and Current Bioinformatics Status in Disease Diagnosis and Treatment

Pervez Anwar, Ayesha Javed, Izba Amjad, Iqra Arif, Attiqa Sadiqa, Huria Akram, Laraib Azhar, Bobbie-Jo M, Webb-Robertson
2018 Journal of Proteomics and Genomics research  
The goal related proteomic study is to draft the entire human proteome in disease diagnosis by using bioinformatics tools.  ...  Extensive study of human proteome project has been proved helpful in disease treatment at translational and post- translational levels.  ...  HPP strongly agree proteome exchange of all data set and Guideline and conformation of novel findings provided by SRM and SWATH-MS methods [40] [38] 2015 Matrices for Human Proteome Project (HPP): Tissue  ... 
doi:10.14302/issn.2326-0793.jpgr-18-2004 fatcat:hfk3cr7mfzfejmjmzxn2pu3sty

Current Status of Two-Dimensional Gel Electrophoresis and Multi-Dimensional Liquid Chromatography as Proteomic Separation Techniques

Xianquan Zhan
2015 Annals of Chromatography and Separation Techniques  
technique in the field of proteomics since the terms "proteome" and "proteomics" were proposed in 1994 [8] .  ...  Moreover, proteome is dynamic, and alters with different conditions such as different physiological processes, different pathological processes, and different disease status, etc [1-3].  ...  Those MDLC-MS/MS techniques have extensively used in the field of proteomics because of their high-throughput, high-accuracy, and high-sensitivity in analysis of a proteome, and that they easily overcome  ... 
doi:10.36876/acst.1009 fatcat:2bjsgczlnnfrlbodp5ijduw5zy

Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives

Arash Assadsangabi, Caroline A. Evans, Bernard M. Corfe, Alan Lobo
2019 Gastroenterology Research and Practice  
Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved.  ...  Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression.  ...  Dependent acquisition and data-independent acquisition (MS E [207, 208] , SWATH) [209, 210] Gastroenterology Research and Practice Proteomic Techniques The implementation of proteomic techniques  ... 
doi:10.1155/2019/1426954 pmid:30774653 pmcid:PMC6350533 fatcat:ioce5as4qff7xm5roah3cnvk5q

Mass Spectrometric-Based Proteomics for Biomarker Discovery in Osteosarcoma: Current Status and Future Direction

Nutnicha Sirikaew, Dumnoensun Pruksakorn, Parunya Chaiyawat, Somchai Chutipongtanate
2022 International Journal of Molecular Sciences  
mass spectrometric-based proteomics in future osteosarcoma research.  ...  In this review, we provide an overview of proteomics studies of osteosarcoma, indicate potential biomarkers that might be promising therapeutic targets, and discuss the challenges and opportunities of  ...  (SWATH).  ... 
doi:10.3390/ijms23179741 pmid:36077137 pmcid:PMC9456544 fatcat:itmrxepizfdd5gxwej2wtys5na

Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS

Tatjana Sajic, Yansheng Liu, Eirini Arvaniti, Silvia Surinova, Evan G. Williams, Ralph Schiess, Ruth Hüttenhain, Atul Sethi, Sheng Pan, Teresa A. Brentnall, Ru Chen, Peter Blattmann (+7 others)
2018 Cell Reports  
Graphical Abstract Highlights d SWATH-MS glycoproteomics enables large-scale plasma analysis across multiple cancers d Localized-stage carcinomas display common blood changes related to platelet proteins  ...  followed by SWATH-MS.  ...  To increase the analytical depth of the blood proteome, we subjected the samples to glycoprotein enrichment and acquired proteomics data using reproducible, highly multiplexed SWATH-MS.  ... 
doi:10.1016/j.celrep.2018.04.114 pmid:29847809 fatcat:lywsfkqon5ht5eauetxiefqzui

On the Road to Accurate Protein Biomarkers in Prostate Cancer Diagnosis and Prognosis: Current Status and Future Advances

Yiwu Yan, Su Yeon Yeon, Chen Qian, Sungyong You, Wei Yang
2021 International Journal of Molecular Sciences  
The past decade has witnessed the commercialization of multiple PC protein biomarkers with improved performance, remarkable progress in proteomic technologies for global discovery and targeted validation  ...  In this review, we summarize these advances and discuss the challenges and potential solutions for identifying and validating clinically useful protein biomarkers in PC diagnosis and prognosis.  ...  MS-Based Multiplexed Targeted Proteomics Currently, the most widely used MS-based multiplexed targeted proteomics approaches are selected reaction monitoring (SRM) [104] , also called multiple reaction  ... 
doi:10.3390/ijms222413537 pmid:34948334 pmcid:PMC8703658 fatcat:2oey2uhnyjds7a2zgq73ee3jiu

Mass spectrometry-based proteomic quest for diabetes biomarkers

Shiying Shao, Tiannan Guo, Ruedi Aebersold
2015 Biochimica et Biophysica Acta - Proteins and Proteomics  
Here, we review the current status of biomarker discovery in DM, and describe the pressure cycling technology (PCT)-Sequential Window Acquisition of all Theoretical fragment-ion (SWATH) workflow for sample-processing  ...  Identification of new diabetic biomarkers assisted by mass spectrometry (MS)-based proteomics may offer solution for the clinical challenges.  ...  Currently, enormous efforts have been invested to protein-based biomarker research, triggering rapid progress on MS-based proteomics in recent years.  ... 
doi:10.1016/j.bbapap.2014.12.012 pmid:25556002 fatcat:2iyq7ifaqze5nirqrvlsdlw4qq

Proteomics, Personalized Medicine and Cancer

Miao Su, Zhe Zhang, Li Zhou, Chao Han, Canhua Huang, Edouard C Nice
2021 Cancers  
As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses.  ...  In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection  ...  However, the current method of choice is becoming data independent analysis (DIA) [30] , in particular SWATH-MS [31] .  ... 
doi:10.3390/cancers13112512 pmid:34063807 fatcat:h3pu42iddnh43ovn6okwrmvq7y

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project

Gilbert S. Omenn, Lydie Lane, Emma K. Lundberg, Christopher M. Overall, Eric W. Deutsch
2017 Journal of Proteome Research  
Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.  ...  identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 (https://hupo.org/Guidelines), up from 13,664 in 2012-12 and 16,518 in 2016-04.  ...  ., from the Knut and Alice Wallenberg Foundation and EU 7th Framework; and C.M.O. by a Canadian Institutes of Health Research 7-year Foundation Grant and a Canada Research Chair in Protease Proteomics  ... 
doi:10.1021/acs.jproteome.7b00375 pmid:28853897 pmcid:PMC5872831 fatcat:kccrhpwwpzhqzjsssoxtqg42ji

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Jesse G. Meyer, Birgit Schilling
2017 Espert Review of Proteomics  
., SWATH).  ...  Areas covered-This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e.g  ...  Insights into proteomic changes of CVF and possible physiological mechanisms may prove useful in the future for biomarkers of fertility status.  ... 
doi:10.1080/14789450.2017.1322904 pmid:28436239 pmcid:PMC5671767 fatcat:xyxt3geop5hchap6rxlhvf36su

Emerging Proteomic Technologies Provide Enormous and Underutilized Potential for Brain Cancer Research

Qiang Tian, Vineet Sangar, Nathan D. Price
2015 Molecular & Cellular Proteomics  
in the future.  ...  Mass spectrometry based proteomics with increased specificity, coverage and throughput will be pervasive in proteomics investigations of brain.  ...  Promise of Global Proteomics via SWATH-SWATH-MS (Sequential Window Acquisition of all THeoretical Mass Spectra) (21) promises to be the long-awaited first truly global approach in proteomics with the  ... 
doi:10.1074/mcp.r115.053884 pmid:26407994 pmcid:PMC4739660 fatcat:335eayrit5apjfvcuarrxfwipe

Targeted Proteomics in Translational and Clinical Studies [chapter]

Eslam Nouri-Nigjeh, Ru Chen, Sheng Pan
2015 Recent Advances in Proteomics Research  
The unbiased nature of DIA methods would enable a wider analytical scope and a greater robustness in targeted analysis, representing a paradigm shift in targeted proteomics.  ...  While significant amount of discovery works have been carried out in both genomics and proteomics for an assortment of diseases, it has been challenging in further characterizing individual protein targets  ...  Current status and further research Currently, SRM is the gold standard for mass spectrometry-based targeted analysis and has been widely applied in a broad range of translational and clinical studies.  ... 
doi:10.5772/61710 fatcat:gv7w26x3pna5hgtgxu544iw6ne
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