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Huang L, Shao D, Wang Y, Cui X, Li Y, Chen Q, Cui J. Human body-fluid proteome: quantitative profiling and computational prediction. Brief Bioinform 2021; 22:315-333. [PMID: 32020158 PMCID: PMC7820883 DOI: 10.1093/bib/bbz160] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.
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Affiliation(s)
- Lan Huang
- College of Computer Science and Technology in the Jilin University
| | - Dan Shao
- College of Computer Science and Technology in the Jilin University
- College of Computer Science and Technology in Changchun University
| | - Yan Wang
- College of Computer Science and Technology in the Jilin University
| | - Xueteng Cui
- College of Computer Science and Technology in the Changchun University
| | - Yufei Li
- College of Computer Science and Technology in the Changchun University
| | - Qian Chen
- College of Computer Science and Technology in the Jilin University
| | - Juan Cui
- Department of Computer Science and Engineering in the University of Nebraska-Lincoln
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2
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Abstract
Cell migration plays pivotal roles in many biological processes; however, its underlying mechanism remains unclear. Here, we find that NudC-like protein 2 (NudCL2), a cochaperone of heat shock protein 90 (Hsp90), modulates cell migration by stabilizing both myosin-9 and lissencephaly protein 1 (LIS1). Either knockdown or knockout of NudCL2 significantly increases single-cell migration, but has no significant effect on collective cell migration. Immunoprecipitation–mass spectrometry and western blotting analyses reveal that NudCL2 binds to myosin-9 in mammalian cells. Depletion of NudCL2 not only decreases myosin-9 protein levels, but also results in actin disorganization. Ectopic expression of myosin-9 efficiently reverses defects in actin disorganization and single-cell migration in cells depleted of NudCL2. Interestingly, knockdown of myosin-9 increases both single and collective cell migration. Depletion of LIS1, a NudCL2 client protein, suppresses both single and collective cell migration, which exhibits the opposite effect compared with myosin-9 depletion. Co-depletion of myosin-9 and LIS1 promotes single-cell migration, resembling the phenotype caused by NudCL2 depletion. Furthermore, inhibition of Hsp90 ATPase activity also reduces the Hsp90-interacting protein myosin-9 stability and increases single-cell migration. Forced expression of Hsp90 efficiently reverses myosin-9 protein instability and the defects induced by NudCL2 depletion, but not vice versa. Taken together, these data suggest that NudCL2 plays an important role in the precise regulation of cell migration by stabilizing both myosin-9 and LIS1 via Hsp90 pathway.
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Boschetti E, Hernández-Castellano LE, Righetti PG. Progress in farm animal proteomics: The contribution of combinatorial peptide ligand libraries. J Proteomics 2019; 197:1-13. [DOI: 10.1016/j.jprot.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/17/2019] [Accepted: 02/07/2019] [Indexed: 02/08/2023]
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4
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Silva MLS. Lectin-based biosensors as analytical tools for clinical oncology. Cancer Lett 2018; 436:63-74. [PMID: 30125611 DOI: 10.1016/j.canlet.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/17/2022]
Abstract
The review focus on the use of lectin-based biosensors in the oncology field, and ponders the potentialities of using these devices as analytical tools to monitor the levels of cancer glycobiomarkers in biological fluids, helping in the diagnosis, prognosis and treatment assessment. Several examples of lectin-based biosensors directed for cancer biomarkers are described and discussed, and their potential application in the clinic is considered, taking into account their analytical features, advantages and performance in sample analysis. Technical and practical aspects in the construction process, which are specific for lectin biosensors, are debated, as well as the requirements in sample collection and processing, and biosensor validation. Today's challenges for real implementation of these devices in the clinic are presented, along with the future trends in the field.
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Affiliation(s)
- M Luísa S Silva
- Centre of Chemical Research, Autonomous University of Hidalgo State, Carr. Pachuca-Tulancingo Km 4.5, 42076, Pachuca, Hidalgo, Mexico; LAQV/REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy of the University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal.
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5
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Tu C, Fiandalo MV, Pop E, Stocking JJ, Azabdaftari G, Li J, Wei H, Ma D, Qu J, Mohler JL, Tang L, Wu Y. Proteomic Analysis of Charcoal-Stripped Fetal Bovine Serum Reveals Changes in the Insulin-like Growth Factor Signaling Pathway. J Proteome Res 2018; 17:2963-2977. [PMID: 30014700 DOI: 10.1021/acs.jproteome.8b00135] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Charcoal-stripped fetal bovine serum (CS-FBS) is commonly used to study androgen responsiveness and androgen metabolism in cultured prostate cancer (CaP) cells. Switching CaP cells from FBS to CS-FBS may reduce the activity of androgen receptor (AR), inhibit cell proliferation, or modulate intracellular androgen metabolism. The removal of proteins by charcoal stripping may cause changes in biological functions and has not yet been investigated. Here we profiled proteins in FBS and CS-FBS using an ion-current-based quantitative platform consisting of reproducible surfactant-aided precipitation/on-pellet digestion, long-column nanoliquid chromatography separation, and ion-current-based analysis. A total of 143 proteins were identified in FBS, among which 14 proteins including insulin-like growth factor 2 (IGF-2) and IGF binding protein (IGFBP)-2 and -6 were reduced in CS-FBS. IGF-1 receptor (IGF1R) and insulin receptor were sensitized to IGFs in CS-FBS. IGF-1 and IGF-2 stimulation fully compensated for the loss of AR activity to maintain cell growth in CS-FBS. Endogenous production of IGF and IGFBPs was verified in CaP cells and clinical CaP specimens. This study provided the most comprehensive protein profiles of FBS and CS-FBS and offered an opportunity to identify new protein regulators and signaling pathways that regulate AR activity, androgen metabolism, and proliferation of CaP cells.
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Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences , State University of New York at Buffalo , 285 Kapoor Hall , Buffalo , New York 14260 , United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street , Buffalo , New York 14203 , United States
| | - Michael V Fiandalo
- Department of Urology, Roswell Park Comprehensive Cancer Center , Elm and Carlton Streets , Buffalo , New York 14263 , United States
| | - Elena Pop
- Department of Urology, Roswell Park Comprehensive Cancer Center , Elm and Carlton Streets , Buffalo , New York 14263 , United States
| | - John J Stocking
- Department of Urology, Roswell Park Comprehensive Cancer Center , Elm and Carlton Streets , Buffalo , New York 14263 , United States
| | - Gissou Azabdaftari
- Department of Pathology, Roswell Park Comprehensive Cancer Center , Elm and Carlton Streets , Buffalo , New York 14263 , United States
| | - Jun Li
- Department of Pharmaceutical Sciences , State University of New York at Buffalo , 285 Kapoor Hall , Buffalo , New York 14260 , United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street , Buffalo , New York 14203 , United States
| | - Hua Wei
- Department of Pharmacy, Changzheng Hospital , Second Military Medical University , 415 Fengyang Road , Shanghai 200003 , China
| | - Danjun Ma
- College of Mechanical Engineering , Dongguan University of Technology , 1 Daxue Road , Dongguan , Guangdong 523808 , China
| | - Jun Qu
- Department of Pharmaceutical Sciences , State University of New York at Buffalo , 285 Kapoor Hall , Buffalo , New York 14260 , United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street , Buffalo , New York 14203 , United States
| | - James L Mohler
- Department of Urology, Roswell Park Comprehensive Cancer Center , Elm and Carlton Streets , Buffalo , New York 14263 , United States
| | - Li Tang
- Department of Cancer Prevention and Control , Roswell Park Comprehensive Cancer Center , Elm and Carlton Streets , Buffalo , New York 14263 , United States
| | - Yue Wu
- Department of Urology, Roswell Park Comprehensive Cancer Center , Elm and Carlton Streets , Buffalo , New York 14263 , United States
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6
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Zhong X, Li L, Wang M, Luo W, Tan Q, Xu F, Zhu W, Wang Q, Wang T, Hou M, Nadimity N, Xue X, Chen J, Ma W, Gao AC, Zhou Q. A proteomic approach to elucidate the multiple targets of selenium-induced cell-growth inhibition in human lung cancer. Thorac Cancer 2018; 2:164-178. [PMID: 27755845 DOI: 10.1111/j.1759-7714.2011.00066.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Methylseleninic acid (MSA) has been implicated as a promising anticancer agent for lung cancer. However, the underlying molecular mechanism(s) responsible for MSA's action is not well understood. Our study aimed to examine the cellular effects of MSA on L9981 human high-metastatic large cell lung cancer cells and gain insights into its possible molecular mechanism(s) through a proteomic approach. METHODS L9981 cells were exposed to MSA at different concentrations and time points. The effects of MSA on cell proliferation and apoptosis were detected by cell viability analyzer Vi-CELL and flow cytometric analysis, respectively. We analyzed the alterations in the proteome profile of L9981 cells induced by MSA using the 2-D difference in gel electrophoresis (2-D DIGE) and identified the differentially expressed proteins using a liquid chromatography system followed by tandem mass spectrometry (LC-MS/MS). RESULTS We found that MSA inhibited cell proliferation in a dose-dependent manner and significantly induced early apoptosis in L9981 cells. 2-D DIGE showed that MSA induced significant changes (>1.29 fold) in the expression levels of 42 protein spots compared to the untreated control (P < 0.05). As identified by LC-MS/MS, proteins that underwent changes in response to MSA were related to various biological functions, including: (i) endoplasmic reticulum stress (upregulation of molecular chaperones like heat shock protein A5, protein disulfide-isomerase precursor, and calreticulin precursor); (ii) oxidative stress response/ thioredoxin system (decreased thioredoxin-like protein 1 and increased thioredoxin reductase 1); (iii) translation regulation (downregulation of translation factors like elongation factor 1-beta and eukaryotic translation initiation factor 6); (iv) mitochondrial bioenergetic function (upregulation of adenosine triphosphate synthase subunit beta and mitochondria); and (v) cell signal transduction regulation (decreased peptidyl-prolyl cis-trans isomerase A and 14-3-3 protein gamma). The protein and gene expression levels of those proteins of interest were further confirmed by Western blot and/or real-time reverse transcription polymerase chain reaction. CONCLUSION Our results suggest that MSA may inhibit cell proliferation and induce apoptosis in lung cancer by modulating multiple targets involved in various crucial cellular processes.
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Affiliation(s)
- Xiaorong Zhong
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Lu Li
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Min Wang
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Wei Luo
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Qingwei Tan
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Feng Xu
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Wen Zhu
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Qi Wang
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Ting Wang
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Mei Hou
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Nagalakshmi Nadimity
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Xingyang Xue
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Jun Chen
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Wei Ma
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Allen C Gao
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
| | - Qinghua Zhou
- The Key Laboratory of Lung Cancer Molecular Biology in Sichuan Province, West China Hospital, Sichuan University, Sichuan, ChinaTianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, ChinaGraduate Program of Pharmacology and Toxicology and Cancer Center, University of California at Davis, Sacramento, California, USADepartment of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian, ChinaDepartment of Respiratory Medicine, the Second Hospital affiliated to Dalian Medical University, Dalian, China
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7
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Zhang M, An B, Qu Y, Shen S, Fu W, Chen YJ, Wang X, Young R, Canty JM, Balthasar JP, Murphy K, Bhattacharyya D, Josephs J, Ferrari L, Zhou S, Bansal S, Vazvaei F, Qu J. Sensitive, High-Throughput, and Robust Trapping-Micro-LC-MS Strategy for the Quantification of Biomarkers and Antibody Biotherapeutics. Anal Chem 2018; 90:1870-1880. [PMID: 29276835 PMCID: PMC5960441 DOI: 10.1021/acs.analchem.7b03949] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
For LC-MS-based targeted quantification of biotherapeutics and biomarkers in clinical and pharmaceutical environments, high sensitivity, high throughput, and excellent robustness are all essential but remain challenging. For example, though nano-LC-MS has been employed to enhance analytical sensitivity, it falls short because of its low loading capacity, poor throughput, and low operational robustness. Furthermore, high chemical noise in protein bioanalysis typically limits the sensitivity. Here we describe a novel trapping-micro-LC-MS (T-μLC-MS) strategy for targeted protein bioanalysis, which achieves high sensitivity with exceptional robustness and high throughput. A rapid, high-capacity trapping of biological samples is followed by μLC-MS analysis; dynamic sample trapping and cleanup are performed using pH, column chemistry, and fluid mechanics separate from the μLC-MS analysis, enabling orthogonality, which contributes to the reduction of chemical noise and thus results in improved sensitivity. Typically, the selective-trapping and -delivery approach strategically removes >85% of the matrix peptides and detrimental components, markedly enhancing sensitivity, throughput, and operational robustness, and narrow-window-isolation selected-reaction monitoring further improves the signal-to-noise ratio. In addition, unique LC-hardware setups and flow approaches eliminate gradient shock and achieve effective peak compression, enabling highly sensitive analyses of plasma or tissue samples without band broadening. In this study, the quantification of 10 biotherapeutics and biomarkers in plasma and tissues was employed for method development. As observed, a significant sensitivity gain (up to 25-fold) compared with that of conventional LC-MS was achieved, although the average run time was only 8 min/sample. No appreciable peak deterioration or loss of sensitivity was observed after >1500 injections of tissue and plasma samples. The developed method enabled, for the first time, ultrasensitive LC-MS quantification of low levels of a monoclonal antibody and antigen in a tumor and cardiac troponin I in plasma after brief cardiac ischemia. This strategy is valuable when highly sensitive protein quantification in large sample sets is required, as is often the case in typical biomarker validation and pharmaceutical investigations of antibody therapeutics.
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Affiliation(s)
- Ming Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Bo An
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Yang Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Wei Fu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
- Department of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuan-Ju Chen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xue Wang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Rebeccah Young
- Division of Cardiovascular Medicine, Western New York Department of Veterans of Affairs Medical Center, Buffalo, New York 14203, United States
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, United States
| | - John M Canty
- Division of Cardiovascular Medicine, Western New York Department of Veterans of Affairs Medical Center, Buffalo, New York 14203, United States
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, United States
| | - Joseph P Balthasar
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Keeley Murphy
- Thermo Scientific, San Jose, California 95134, United States
| | | | | | - Luca Ferrari
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Shaolian Zhou
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Surendra Bansal
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Faye Vazvaei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
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8
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Jia D, Wang B, Li X, Peng W, Zhou J, Tan H, Tang J, Huang Z, Tan W, Gan B, Yang Z, Zhao J. Proteomic Analysis Revealed the Fruiting-Body Protein Profile of Auricularia polytricha. Curr Microbiol 2017; 74:943-951. [DOI: 10.1007/s00284-017-1268-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/19/2017] [Indexed: 02/07/2023]
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9
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Naryzhny S. Towards the Full Realization of 2DE Power. Proteomes 2016; 4:proteomes4040033. [PMID: 28248243 PMCID: PMC5260966 DOI: 10.3390/proteomes4040033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/29/2023] Open
Abstract
Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology.
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Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya 10, Moscow 119121, Russia.
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad region, Gatchina 188300, Russia.
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10
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Richens JL, Spencer HL, Butler M, Cantlay F, Vere KA, Bajaj N, Morgan K, O'Shea P. Rationalising the role of Keratin 9 as a biomarker for Alzheimer's disease. Sci Rep 2016; 6:22962. [PMID: 26973255 PMCID: PMC4789650 DOI: 10.1038/srep22962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
Keratin 9 was recently identified as an important component of a biomarker panel which demonstrated a high diagnostic accuracy (87%) for Alzheimer's disease (AD). Understanding how a protein which is predominantly expressed in palmoplantar epidermis is implicated in AD may shed new light on the mechanisms underlying the disease. Here we use immunoassays to examine blood plasma expression patterns of Keratin 9 and its relationship to other AD-associated proteins. We correlate this with the use of an in silico analysis tool VisANT to elucidate possible pathways through which the involvement of Keratin 9 may take place. We identify possible links with Dickkopf-1, a negative regulator of the wnt pathway, and propose that the abnormal expression of Keratin 9 in AD blood and cerebrospinal fluid may be a result of blood brain barrier dysregulation and disruption of the ubiquitin proteasome system. Our findings suggest that dysregulated Keratin 9 expression is a consequence of AD pathology but, as it interacts with a broad range of proteins, it may have other, as yet uncharacterized, downstream effects which could contribute to AD onset and progression.
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Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hannah L Spencer
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Molly Butler
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fiona Cantlay
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kelly-Ann Vere
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Nin Bajaj
- Department of Neurology, Nottingham University Hospitals NHS Trust, Queen's Medical Centre, Nottingham, United Kingdom
| | - Kevin Morgan
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
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11
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Tu C, Mammen MJ, Li J, Shen X, Jiang X, Hu Q, Wang J, Sethi S, Qu J. Large-scale, ion-current-based proteomics investigation of bronchoalveolar lavage fluid in chronic obstructive pulmonary disease patients. J Proteome Res 2013; 13:627-639. [PMID: 24188068 DOI: 10.1021/pr4007602] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteomic analysis of bronchoalveolar lavage fluid (BALF) in chronic obstructive pulmonary disease (COPD) patients may provide new biomarkers and deeper understanding of the disease mechanisms but remains challenging. Here we describe an ion-current-based strategy for comparative analysis of BALF proteomes from patients with moderate and stable COPD versus healthy controls. The strategy includes an efficient preparation procedure providing quantitative recovery and a nano-LC/MS analysis with a long, heated column. Under optimized conditions, high efficiency and reproducibility were achieved for each step, enabling a "20-plex" comparison of clinical subjects (n = 10/group). Without depletion/fractionation, a total of 423 unique protein groups were quantified under stringent criteria with at least two quantifiable peptides. Seventy-six proteins were determined as significantly altered in COPD, which represent a diversity of biological processes such as alcohol metabolic process, gluconeogenesis/glycolysis, inflammatory response, proteolysis, and oxidation reduction. Interestingly, altered alcohol metabolism responding to oxidant stress is a novel observation in COPD. The prominently elevated key enzymes involved in alcohol metabolism (e.g., ADH1B, ALDH2, and ALDH3A1) may provide a reasonable explanation for a bewildering observation in COPD patients known for decades: the underestimation of the blood alcohol concentrations through breath tests. These discoveries could provide new insights for identifying novel biomarkers and pathological mediators in clinical studies.
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Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | | | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Xiaomeng Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Xiaosheng Jiang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY14203
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY14203
| | - Sanjay Sethi
- University at Buffalo, SUNY.,WNY VA Healthcare System, NY 14203 USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260 USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA
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12
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Bai HX, Liu XH, Yang F, Yang XR, Wang EK. A Prefractionation Method Can Separate Proteomic Proteins into Multigroups by One-step Extraction. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Millioni R, Franchin C, Tessari P, Polati R, Cecconi D, Arrigoni G. Pros and cons of peptide isolectric focusing in shotgun proteomics. J Chromatogr A 2013; 1293:1-9. [PMID: 23639126 DOI: 10.1016/j.chroma.2013.03.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 02/03/2023]
Abstract
In shotgun proteomics, protein mixtures are proteolytically digested before tandem mass spectrometry (MS/MS) analysis. Biological samples are generally characterized by a very high complexity, therefore a step of peptides fractionation before the MS analysis is essential. This passage reduces the sample complexity and increases its compatibility with the sampling performance of the instrument. Among all the existing approaches for peptide fractionation, isoelectric focusing has several peculiarities that are theoretically known but practically rarely exploited by the proteomics community. The main aim of this review is to draw the readers' attention to these unique qualities, which are not accessible with other common approaches, and that represent important tools to increase confidence in the identification of proteins and some post-translational modifications. The general characteristics of different methods to perform peptide isoelectric focusing with natural and artificial pH gradients, the existing instrumentation, and the informatics tools available for isoelectric point calculation are also critically described. Finally, we give some general conclusions on this strategy, underlying its principal limitations.
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Affiliation(s)
- Renato Millioni
- Department of Medicine, University of Padova, Via Giustiniani 2, 35121 Padova, Italy; Proteomics Center of Padova University, VIMM and Padova University Hospital, Via G. Orus 2/B, 35129 Padova, Italy.
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14
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Jin T, Zeng L, Lin YY, Lu YY, Liang GW. Characteristics of protein variants in trichlorphon-resistant Bactrocera dorsalis (Diptera; Tephritidae) larvae. GENETICS AND MOLECULAR RESEARCH 2012; 11:2608-19. [DOI: 10.4238/2012.july.10.12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Li C, Ruan HQ, Liu YS, Xu MJ, Dai J, Sheng QH, Tan YX, Yao ZZ, Wang HY, Wu JR, Zeng R. Quantitative Proteomics Reveal up-regulated Protein Expression of the SET Complex Associated with Hepatocellular Carcinoma. J Proteome Res 2011; 11:871-85. [DOI: 10.1021/pr2006999] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chen Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong-Qiang Ruan
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan-Sheng Liu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Meng-Jie Xu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Dai
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Quan-Hu Sheng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ye-Xiong Tan
- Eastern Hepatobiliary Surgery Hospital, No. 225, Changhai Road, Shanghai 200438, China
| | - Zhen-Zhen Yao
- Department of Biochemistry & Molecular Biology, Second Military Medical University, Shanghai 200438, China
| | - Hong-Yang Wang
- Eastern Hepatobiliary Surgery Hospital, No. 225, Changhai Road, Shanghai 200438, China
| | - Jia-Rui Wu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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16
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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17
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Tu C, Li J, Young R, Page BJ, Engler F, Halfon MS, Canty JM, Qu J. Combinatorial peptide ligand library treatment followed by a dual-enzyme, dual-activation approach on a nanoflow liquid chromatography/orbitrap/electron transfer dissociation system for comprehensive analysis of swine plasma proteome. Anal Chem 2011; 83:4802-13. [PMID: 21491903 DOI: 10.1021/ac200376m] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The plasma proteome holds enormous clinical potential, yet an in-depth analysis of the plasma proteome remains a daunting challenge due to its high complexity and the extremely wide dynamic range in protein concentrations. Furthermore, existing antibody-based approaches for depleting high-abundance proteins are not adaptable to the analysis of the animal plasma proteome, which is often essential for experimental pathology/pharmacology. Here we describe a highly comprehensive method for the investigation of the animal plasma proteome which employs an optimized combinatorial peptide ligand library (CPLL) treatment to reduce the protein concentration dynamic range and a dual-enzyme, dual-activation strategy to achieve high proteomic coverage. The CPLL treatment enriched the lower abundance proteins by >100-fold when the samples were loaded in moderately denaturing conditions with multiple loading-washing cycles. The native and the CPLL-treated plasma were digested in parallel by two enzymes (trypsin and GluC) carrying orthogonal specificities. By performing this differential proteolysis, the proteome coverage is improved where peptides produced by only one enzyme are poorly detectable. Digests were fractionated with high-resolution strong cation exchange chromatography and then resolved on a long, heated nano liquid chromatography column. MS analysis was performed on a linear triple quadrupole/orbitrap with two complementary activation methods (collisionally induced dissociation (CID) and electron transfer dissociation). We applied this optimized strategy to investigate the plasma proteome from swine, a prominent animal model for cardiovascular diseases (CVDs). This large-scale analysis results in identification of a total of 3421 unique proteins, spanning a concentration range of 9-10 orders of magnitude. The proteins were identified under a set of commonly accepted criteria, including a precursor mass error of <15 ppm, Xcorr cutoffs, and ≥2 unique peptides at a peptide probability of ≥95% and a protein probability of ≥99%, and the peptide false-positive rate of the data set was 1.8% as estimated by searching the reversed database. CPLL treatment resulted in 55% more identified proteins over those from native plasma; moreover, compared with using only trypsin and CID, the dual-enzyme/activation approach enabled the identification of 2.6-fold more proteins and substantially higher sequence coverage for most individual proteins. Further analysis revealed 657 proteins as significantly associated with CVDs (p < 0.05), which constitute five CVD-related pathways. This study represents the first in-depth investigation of a nonhuman plasma proteome, and the strategy developed here is adaptable to the comprehensive analysis of other highly complex proteomes.
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Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York 14260, USA
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18
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Millioni R, Tolin S, Puricelli L, Sbrignadello S, Fadini GP, Tessari P, Arrigoni G. High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PLoS One 2011; 6:e19603. [PMID: 21573190 PMCID: PMC3087803 DOI: 10.1371/journal.pone.0019603] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/06/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND To date, the complexity of the plasma proteome exceeds the analytical capacity of conventional approaches to isolate lower abundance proteins that may prove to be informative biomarkers. Only complex multistep separation strategies have been able to detect a substantial number of low abundance proteins (<100 ng/ml). The first step of these protocols is generally the depletion of high abundance proteins by the use of immunoaffinity columns or, alternatively, the enrichment of by the use of solid phase hexapeptides ligand libraries. METHODOLOGY/PRINCIPAL FINDINGS Here we present a direct comparison of these two approaches. Following either approach, the plasma sample was further fractionated by SCX chromatography and analyzed by RP-LC-MS/MS with a Q-TOF mass spectrometer. The depletion of the 20 most abundant plasma proteins allowed the identification of about 25% more proteins than those detectable following low abundance proteins enrichment. The two datasets are partially overlapping and the identified proteins belong to the same order of magnitude in terms of plasma concentration. CONCLUSIONS/SIGNIFICANCE Our results show that the two approaches give complementary results. However, the enrichment of low abundance proteins has the great advantage of obtaining much larger amount of material that can be used for further fractionations and analyses and emerges also as a cheaper and technically simpler approach. Collectively, these data indicate that the enrichment approach seems more suitable as the first stage of a complex multi-step fractionation protocol.
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Affiliation(s)
- Renato Millioni
- Department of Clinical and Experimental Medicine, Division of Metabolism, University of Padua, Padua, Italy.
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19
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Li MY, Peng F, Zuo JH, Yi H, Tang CE, Li C, Zhang PF, Chen ZC, Xiao ZQ. Enhancing the stability of 18O-labeled peptides through removal of immobilized trypsin by ZipTips. Anal Biochem 2011; 408:37-45. [DOI: 10.1016/j.ab.2010.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 07/30/2010] [Accepted: 08/26/2010] [Indexed: 10/19/2022]
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20
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Zhu XJ, Liu X, Jin Q, Cai Y, Yang Y, Zhou T. The L279P mutation of nuclear distribution gene C (NudC) influences its chaperone activity and lissencephaly protein 1 (LIS1) stability. J Biol Chem 2010; 285:29903-10. [PMID: 20675372 DOI: 10.1074/jbc.m110.105494] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
LIS1, a gene mutated in classical lissencephaly, plays essential roles in cytoplasmic dynein regulation, mitosis and cell migration. However, the regulation of LIS1 (lissencephaly protein 1) protein remains largely unknown. Genetic studies in Aspergillus nidulans have uncovered that the Nud (nuclear distribution) pathway is involved in the regulation of cytoplasmic dynein complex and a temperature-sensitive mutation in the nudC gene (L146P) greatly reduces the protein levels of NudF, an Aspergillus ortholog of LIS1. Here, we showed that L146 in Aspergillus NudC and its flanking region were highly conservative during evolution. The similar mutation in human NudC (L279P) obviously led to reduced LIS1 and cellular phenotypes similar to those of LIS1 down-regulation. To explore the underlying mechanism, we found that the p23 domain-containing protein NudC bound to the molecular chaperone Hsp90, which is also associated with LIS1. Inhibition of Hsp90 chaperone function by either geldanamycin or radicicol resulted in a decrease in LIS1 levels. Ectopic expression of Hsp90 partially reversed the degradation of LIS1 caused by overexpression of NudC-L279P. Furthermore, NudC was found to regulate the ATPase activity of Hsp90, which was repressed by the mutation of L279P. Interestingly, NudC itself was shown to possess a chaperone function, which also was suppressed by the L279P mutation. Together, these data suggest that NudC may be involved in the regulation of LIS1 stability by its chaperone function.
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Affiliation(s)
- Xiao-Jing Zhu
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
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21
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Yang G, Li Q, Ren S, Lu X, Fang L, Zhou W, Zhang F, Xu F, Zhang Z, Zeng R, Lottspeich F, Chen Z. Proteomic, functional and motif-based analysis of C-terminal Src kinase-interacting proteins. Proteomics 2009; 9:4944-61. [PMID: 19743411 DOI: 10.1002/pmic.200800762] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
C-terminal Src kinase (Csk) that functions as an essential negative regulator of Src family tyrosine kinases (SFKs) interacts with tyrosine-phosphorylated molecules through its Src homology 2 (SH2) domain, allowing it targeting to the sites of SFKs and concomitantly enhancing its kinase activity. Identification of additional Csk-interacting proteins is expected to reveal potential signaling targets and previously undescribed functions of Csk. In this study, using a direct proteomic approach, we identified 151 novel potential Csk-binding partners, which are associated with a wide range of biological functions. Bioinformatics analysis showed that the majority of identified proteins contain one or several Csk-SH2 domain-binding motifs, indicating a potentially direct interaction with Csk. The interactions of Csk with four proteins (partitioning defective 3 (Par3), DDR1, SYK and protein kinase C iota) were confirmed using biochemical approaches and phosphotyrosine 1127 of Par3 C-terminus was proved to directly bind to Csk-SH2 domain, which was consistent with predictions from in silico analysis. Finally, immunofluorescence experiments revealed co-localization of Csk with Par3 in tight junction (TJ) in a tyrosine phosphorylation-dependent manner and overexpression of Csk, but not its SH2-domain mutant lacking binding to phosphotyrosine, promoted the TJ assembly in Madin-Darby canine kidney cells, implying the involvement of Csk-SH2 domain in regulating cellular TJs. In conclusion, the newly identified potential interacting partners of Csk provided new insights into its functional diversity in regulation of numerous cellular events, in addition to controlling the SFK activity.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
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Nissum M, Foucher AL. Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis. Expert Rev Proteomics 2008; 5:571-87. [PMID: 18761468 DOI: 10.1586/14789450.5.4.571] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Due to ease of accessibility, plasma has become the sample of choice for proteomics studies directed towards biomarker discovery intended for use in diagnostics, prognostics and even in theranostics. The result of these extensive efforts is a long list of potential biomarkers, very few of which have led to clinical utility. Why have so many potential biomarkers failed validation? Herein, we address certain issues encountered, which complicate biomarker discovery efforts originating from plasma. The advantages of stabilizing the sample at collection by the addition of protease inhibitors are discussed. The principles of free-flow electrophoresis (FFE) separation are provided together with examples applying to various studies. Finally, particular attention is given to plasma or serum analysis using multidimensional separation strategies into which the FFE is incorporated. The advantages of using FFE separation in these workflows are discussed.
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Affiliation(s)
- Mikkel Nissum
- BD Diagnostics, Am Klopferspitz 19a, D-82152 Martinsried, Germany.
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Li SJ, Peng M, Li H, Liu BS, Wang C, Wu JR, Li YX, Zeng R. Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res 2008; 37:D907-12. [PMID: 18978022 PMCID: PMC2686600 DOI: 10.1093/nar/gkn849] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.
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Affiliation(s)
- Su-Jun Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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24
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Li RX, Chen HB, Tu K, Zhao SL, Zhou H, Li SJ, Dai J, Li QR, Nie S, Li YX, Jia WP, Zeng R, Wu JR. Localized-statistical quantification of human serum proteome associated with type 2 diabetes. PLoS One 2008; 3:e3224. [PMID: 18795103 PMCID: PMC2529402 DOI: 10.1371/journal.pone.0003224] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 08/11/2008] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Recent advances in proteomics have shed light to discover serum proteins or peptides as biomarkers for tracking the progression of diabetes as well as understanding molecular mechanisms of the disease. RESULTS In this work, human serum of non-diabetic and diabetic cohorts was analyzed by proteomic approach. To analyze total 1377 high-confident serum-proteins, we developed a computing strategy called localized statistics of protein abundance distribution (LSPAD) to calculate a significant bias of a particular protein-abundance between these two cohorts. As a result, 68 proteins were found significantly over-represented in the diabetic serum (p<0.01). In addition, a pathway-associated analysis was developed to obtain the overall pathway bias associated with type 2 diabetes, from which the significant over-representation of complement system associated with type 2 diabetes was uncovered. Moreover, an up-stream activator of complement pathway, ficolin-3, was observed over-represented in the serum of type 2 diabetic patients, which was further validated with statistic significance (p = 0.012) with more clinical samples. CONCLUSIONS The developed LSPAD approach is well fit for analyzing proteomic data derived from biological complex systems such as plasma proteome. With LSPAD, we disclosed the comprehensive distribution of the proteins associated with diabetes in different abundance levels and the involvement of ficolin-related complement activation in diabetes.
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Affiliation(s)
- Rong-Xia Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hai-Bing Chen
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai No. 6 People's Hospital Affiliated to Jiaotong University, Shanghai, China
| | - Kang Tu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shi-Lin Zhao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hu Zhou
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Su-Jun Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jie Dai
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qing-Run Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Song Nie
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Xue Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei-Ping Jia
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai No. 6 People's Hospital Affiliated to Jiaotong University, Shanghai, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia-Rui Wu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science & Technology of China, Hefei, Anhui, China
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25
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Pernemalm M, Orre LM, Lengqvist J, Wikström P, Lewensohn R, Lehtiö J. Evaluation of three principally different intact protein prefractionation methods for plasma biomarker discovery. J Proteome Res 2008; 7:2712-22. [PMID: 18549256 DOI: 10.1021/pr700821k] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aim of this study was to evaluate three principally different top-down protein prefractionation methods for plasma: high-abundance protein depletion, size fractionation and peptide ligand affinity beads, focusing in particular on compatibility with downstream analysis, reproducibility and analytical depth. Our data clearly demonstrates the benefit of high-abundance protein depletion. However, MS/MS analysis of the proteins eluted from the high-abundance protein depletion column show that more proteins than aimed for are removed and, in addition, that the depletion efficacy varies between the different high-abundance proteins. Although a smaller number of proteins were identified per fraction using the peptide ligand affinity beads, this technique showed to be both robust and versatile. Size fractionation, as performed in this study, focusing on the low molecular weight proteome using a combination of gel filtration chromatography and molecular weight cutoff filters, showed limitations in the molecular weight cutoff precision leading detection of high molecular weight proteins and, in the case of the cutoff filters, high variability. GeLC-MS/MS analysis of the fractionation methods in combination with pathway analysis demonstrates that increased fractionation primarily leads to high proteome coverage of pathways related to biological functions of plasma, such as acute phase reaction, complement cascade and coagulation. Further, the prefractionation methods in this study induces limited effect on the proportion of tissue proteins detected, thereby highlighting the importance of extensive or targeted downstream fractionation.
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Affiliation(s)
- Maria Pernemalm
- Karolinska Biomics Center, Karolinska University Hospital, Karolinska Institutet, Z5:02, 171 76 Stockholm, Sweden
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26
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Affiliation(s)
- Haleem J Issaq
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, P.O. Box B, Frederick, Maryland 21702, USA
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Qian WJ, Jacobs JM, Liu T, Camp DG, Smith RD. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics 2006; 5:1727-44. [PMID: 16887931 PMCID: PMC1781927 DOI: 10.1074/mcp.m600162-mcp200] [Citation(s) in RCA: 274] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Recent advances in proteomics technologies provide tremendous opportunities for biomarker-related clinical applications; however, the distinctive characteristics of human biofluids such as the high dynamic range in protein abundances and extreme complexity of the proteomes present tremendous challenges. In this review we summarize recent advances in LC-MS-based proteomics profiling and its applications in clinical proteomics as well as discuss the major challenges associated with implementing these technologies for more effective candidate biomarker discovery. Developments in immunoaffinity depletion and various fractionation approaches in combination with substantial improvements in LC-MS platforms have enabled the plasma proteome to be profiled with considerably greater dynamic range of coverage, allowing many proteins at low ng/ml levels to be confidently identified. Despite these significant advances and efforts, major challenges associated with the dynamic range of measurements and extent of proteome coverage, confidence of peptide/protein identifications, quantitation accuracy, analysis throughput, and the robustness of present instrumentation must be addressed before a proteomics profiling platform suitable for efficient clinical applications can be routinely implemented.
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Affiliation(s)
- Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Liu T, Qian WJ, Gritsenko MA, Xiao W, Moldawer LL, Kaushal A, Monroe ME, Varnum SM, Moore RJ, Purvine SO, Maier RV, Davis RW, Tompkins RG, Camp DG, Smith RD. High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics 2006; 5:1899-913. [PMID: 16684767 PMCID: PMC1783978 DOI: 10.1074/mcp.m600068-mcp200] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although human plasma represents an attractive sample for disease biomarker discovery, the extreme complexity and large dynamic range in protein concentrations present significant challenges for characterization, candidate biomarker discovery, and validation. Herein we describe a strategy that combines immunoaffinity subtraction and subsequent chemical fractionation based on cysteinyl peptide and N-glycopeptide captures with two-dimensional LC-MS/MS to increase the dynamic range of analysis for plasma. Application of this "divide-and-conquer" strategy to trauma patient plasma significantly improved the overall dynamic range of detection and resulted in confident identification of 22,267 unique peptides from four different peptide populations (cysteinyl peptides, non-cysteinyl peptides, N-glycopeptides, and non-glycopeptides) that covered 3,654 different proteins with 1,494 proteins identified by multiple peptides. Numerous low abundance proteins were identified, exemplified by 78 "classic" cytokines and cytokine receptors and by 136 human cell differentiation molecules. Additionally a total of 2,910 different N-glycopeptides that correspond to 662 N-glycoproteins and 1,553 N-glycosylation sites were identified. A panel of the proteins identified in this study is known to be involved in inflammation and immune responses. This study established an extensive reference protein database for trauma patients that provides a foundation for future high throughput quantitative plasma proteomic studies designed to elucidate the mechanisms that underlie systemic inflammatory responses.
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Affiliation(s)
- Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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