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Wang J, Pan C, Ma X. Assessment of the Quality Management System for Clinical Nutrition in Jiangsu: Survey Study. JMIR Form Res 2021; 5:e27285. [PMID: 34569942 PMCID: PMC8506260 DOI: 10.2196/27285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND An electronic system that automatically collects medical information can realize timely monitoring of patient health and improve the effectiveness and accuracy of medical treatment. To our knowledge, the application of artificial intelligence (AI) in medical service quality assessment has been minimally evaluated, especially for clinical nutrition departments in China. From the perspective of medical ethics, patient safety comes before any other factors within health science, and this responsibility belongs to the quality management system (QMS) within medical institutions. OBJECTIVE This study aims to evaluate the QMS for clinical nutrition in Jiangsu, monitor its performance in quality assessment and human resource management from a nutrition aspect, and investigate the application and development of AI in medical quality control. METHODS The participants for this study were the staff of 70 clinical nutrition departments of the tertiary hospitals in Jiangsu Province, China. These departments are all members of the Quality Management System of Clinical Nutrition in Jiangsu (QMSNJ). An online survey was conducted on all 341 employees within all clinical nutrition departments based on the staff information from the surveyed medical institutions. The questionnaire contains five sections, and the data analysis and AI evaluation were focused on human resource information. RESULTS A total of 330 questionnaires were collected, with a response rate of 96.77% (330/341). A QMS for clinical nutrition was built for clinical nutrition departments in Jiangsu and achieved its target of human resource improvements, especially among dietitians. The growing number of participating departments (an increase of 42.8% from 2018 to 2020) and the significant growth of dietitians (t93.4=-0.42; P=.02) both show the advancements of the QMSNJ. CONCLUSIONS As the first innovation of an online platform for quality management in Jiangsu, the Jiangsu Province Clinical Nutrition Management Platform was successfully implemented as a QMS for this study. This multidimensional electronic system can help the QMSNJ and clinical nutrition departments achieve quality assessment from various aspects so as to realize the continuous improvement of clinical nutrition. The use of an online platform and AI technology for quality assessment is worth recommending and promoting in the future.
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Affiliation(s)
- Jin Wang
- First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen Pan
- First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xianghua Ma
- First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Kohl M, Stepath M, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M. CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements. Proteomics 2020; 20:e1900143. [PMID: 32086983 DOI: 10.1002/pmic.201900143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 02/07/2020] [Indexed: 01/29/2023]
Abstract
Targeted proteomics techniques allow accurate quantitative measurements of analytes in complex matrices with dynamic linear ranges that span up to 4-5 orders of magnitude. Hence, targeted methods are promising for the development of robust protein assays in several sensitive areas, for example, in health care. However, exploiting the full method potential requires reliable determination of the dynamic range along with related quantification limits for each analyte. Here, a software named CalibraCurve that enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays is presented. The software uses a variety of measures to assess the accuracy of the calibration, namely precision and trueness. Two different kinds of customizable graphs are created (calibration curves and response factor plots). The accuracy measures and the graphs offer an intuitive, detailed, and reliable opportunity to assess the quality of the model fit. Thus, CalibraCurve is deemed a highly useful and flexible tool to facilitate the development and control of reliable SRM/MRM-MS-based proteomics assays.
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Affiliation(s)
- Michael Kohl
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Markus Stepath
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Thilo Bracht
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Dominik A Megger
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany.,Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, D-45 147, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, Gesundheitscampus 4, Bochum, D-44 801, Germany
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Gibbons BC, Fillmore TL, Gao Y, Moore RJ, Liu T, Nakayasu ES, Metz TO, Payne SH. Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards. J Proteome Res 2018; 18:694-699. [PMID: 30525668 DOI: 10.1021/acs.jproteome.8b00688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Targeted proteomics experiments based on selected reaction monitoring (SRM) have gained wide adoption in the use of clinical biomarkers, cellular modeling, and numerous other biological experiments due to their highly accurate and reproducible quantification. The quantitative accuracy in targeted proteomics experiments is reliant on the stable-isotope, heavy-labeled peptide standards that are spiked into a sample and used as a reference when calculating the abundance of endogenous peptides. Therefore, the quality of measurement for these standards is a critical factor in determining whether data acquisition was successful. With improved mass spectrometry (MS) instrumentation that enables the monitoring of hundreds of peptides in hundreds to thousands of samples, quality assessment is increasingly important and cannot be performed manually. We present Q4SRM, a software tool that rapidly checks the signal from all heavy-labeled peptides and flags those that fail quality-control metrics. Using four metrics, the tool detects problems with both individual SRM transitions and the collective group of transitions that monitor a single peptide. The program's speed and simplicity enable its use at the point of data acquisition and can be ideally run immediately upon the completion of a liquid chromatography-SRM-MS analysis.
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Affiliation(s)
- Bryson C Gibbons
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas L Fillmore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Yuqian Gao
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ernesto S Nakayasu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas O Metz
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Samuel H Payne
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
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Lin H, He QY, Shi L, Sleeman M, Baker MS, Nice EC. Proteomics and the microbiome: pitfalls and potential. Expert Rev Proteomics 2018; 16:501-511. [PMID: 30223687 DOI: 10.1080/14789450.2018.1523724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.
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Affiliation(s)
- Huafeng Lin
- a Department of Biotechnology , College of Life Science and Technology, Jinan University , Guangzhou , Guangdong , China.,b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Qing-Yu He
- c Institute of Life and Health Engineering, College of Life Science and Technology , Jinan University , Guangzhou , China
| | - Lei Shi
- b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Mark Sleeman
- d Biomedicine Discovery Institute , Monash University , Melbourne , Australia
| | - Mark S Baker
- e Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia
| | - Edouard C Nice
- f Department of Biochemistry and Molecular Biology , Monash University , Melbourne , Victoria , Australia
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Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer's Disease Brain. Methods Mol Biol 2018; 1523:161-177. [PMID: 27975250 DOI: 10.1007/978-1-4939-6598-4_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent advances in mass spectrometry (MS)-based proteomics have greatly facilitated the robust identification and quantification of posttranslational modifications (PTMs), including those that are present at substoichiometric site occupancies. The abnormal posttranslational modification and accumulation of the microtubule-associated protein tau has been implicated in the pathogenesis of Alzheimer's disease (AD), and it is thought that the primary mode of regulation of tau occurs through PTMs. Several studies have been published regarding tau phosphorylation; however, other tau PTMs such as ubiquitylation, acetylation, methylation, oxidation, sumoylation, nitration, and glycosylation have not been analyzed as extensively. The comprehensive detection and delineation of these PTMs is critical for drug target discovery and validation. Lysine-directed PTMs including ubiquitylation, acetylation, and methylation play key regulatory roles with respect to the rates of tau turnover and aggregation. MS-based analytical approaches have been used to gain insight into the tau lysine-directed PTM signature that is most closely associated with neurofibrillary lesion formation. This chapter provides details pertaining to the liquid chromatography tandem mass spectrometry (LC-MS/MS)-based analysis of the lysine-directed posttranslational modification of tau.
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Bhosale SD, Moulder R, Kouvonen P, Lahesmaa R, Goodlett DR. Mass Spectrometry-Based Serum Proteomics for Biomarker Discovery and Validation. Methods Mol Biol 2017; 1619:451-466. [PMID: 28674903 DOI: 10.1007/978-1-4939-7057-5_31] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Blood protein measurements are used frequently in the clinic in the assessment of patient health. Nevertheless, there remains the need for new biomarkers with better diagnostic specificities. With the advent of improved technology for bioanalysis and the growth of biobanks including collections from specific disease risk cohorts, the plasma proteome has remained a target of proteomics research toward the characterization of disease-related biomarkers. The following protocol presents a workflow for serum/plasma proteomics including details of sample preparation both with and without immunoaffinity depletion of the most abundant plasma proteins and methodology for selected reaction monitoring mass spectrometry validation.
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Affiliation(s)
| | - Robert Moulder
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - David R Goodlett
- Turku Centre for Biotechnology, University of Turku, Turku, Finland. .,Department of Pharmaceutical Science, University of Maryland, 20 North Pine Street, Baltimore, MD, 21201, USA.
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Thomas SN, Zhang H. Targeted proteomic assays for the verification of global proteomics insights. Expert Rev Proteomics 2016; 13:897-899. [PMID: 27565203 DOI: 10.1080/14789450.2016.1229601] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Stefani N Thomas
- a Department of Pathology, Clinical Chemistry Division , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Hui Zhang
- a Department of Pathology, Clinical Chemistry Division , Johns Hopkins University School of Medicine , Baltimore , MD , USA
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Nasir W, Toledo AG, Noborn F, Nilsson J, Wang M, Bandeira N, Larson G. SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis. J Proteome Res 2016; 15:2826-40. [PMID: 27399812 DOI: 10.1021/acs.jproteome.6b00417] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycoproteomics has rapidly become an independent analytical platform bridging the fields of glycomics and proteomics to address site-specific protein glycosylation and its impact in biology. Current glycopeptide characterization relies on time-consuming manual interpretations and demands high levels of personal expertise. Efficient data interpretation constitutes one of the major challenges to be overcome before true high-throughput glycopeptide analysis can be achieved. The development of new glyco-related bioinformatics tools is thus of crucial importance to fulfill this goal. Here we present SweetNET: a data-oriented bioinformatics workflow for efficient analysis of hundreds of thousands of glycopeptide MS/MS-spectra. We have analyzed MS data sets from two separate glycopeptide enrichment protocols targeting sialylated glycopeptides and chondroitin sulfate linkage region glycopeptides, respectively. Molecular networking was performed to organize the glycopeptide MS/MS data based on spectral similarities. The combination of spectral clustering, oxonium ion intensity profiles, and precursor ion m/z shift distributions provided typical signatures for the initial assignment of different N-, O- and CS-glycopeptide classes and their respective glycoforms. These signatures were further used to guide database searches leading to the identification and validation of a large number of glycopeptide variants including novel deoxyhexose (fucose) modifications in the linkage region of chondroitin sulfate proteoglycans.
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Affiliation(s)
- Waqas Nasir
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Alejandro Gomez Toledo
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Fredrik Noborn
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Mingxun Wang
- Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Nuno Bandeira
- Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
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Percy AJ, Byrns S, Pennington SR, Holmes DT, Anderson NL, Agreste TM, Duffy MA. Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential. Expert Rev Proteomics 2016; 13:673-84. [DOI: 10.1080/14789450.2016.1205950] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew J. Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Simon Byrns
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Stephen R. Pennington
- Department of Pathology, School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - N. Leigh Anderson
- Department of Clinical Biomarkers, SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Tasha M. Agreste
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Maureen A. Duffy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
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