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Proteomic Discovery and Validation of Novel Fluid Biomarkers for Improved Patient Selection and Prediction of Clinical Outcomes in Alzheimer’s Disease Patient Cohorts. Proteomes 2022; 10:proteomes10030026. [PMID: 35997438 PMCID: PMC9397030 DOI: 10.3390/proteomes10030026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 01/25/2023] Open
Abstract
Alzheimer’s disease (AD) is an irreversible neurodegenerative disease characterized by progressive cognitive decline. The two cardinal neuropathological hallmarks of AD include the buildup of cerebral β amyloid (Aβ) plaques and neurofibrillary tangles of hyperphosphorylated tau. The current disease-modifying treatments are still not effective enough to lower the rate of cognitive decline. There is an urgent need to identify early detection and disease progression biomarkers that can facilitate AD drug development. The current established readouts based on the expression levels of amyloid beta, tau, and phospho-tau have shown many discrepancies in patient samples when linked to disease progression. There is an urgent need to identify diagnostic and disease progression biomarkers from blood, cerebrospinal fluid (CSF), or other biofluids that can facilitate the early detection of the disease and provide pharmacodynamic readouts for new drugs being tested in clinical trials. Advances in proteomic approaches using state-of-the-art mass spectrometry are now being increasingly applied to study AD disease mechanisms and identify drug targets and novel disease biomarkers. In this report, we describe the application of quantitative proteomic approaches for understanding AD pathophysiology, summarize the current knowledge gained from proteomic investigations of AD, and discuss the development and validation of new predictive and diagnostic disease biomarkers.
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Zhang N, Liu X, Gao S, Wong CC. Parallel Channels-Multidimensional Protein Identification Technology. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1440-1447. [PMID: 32310654 DOI: 10.1021/jasms.0c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Multidimensional protein identification (MudPIT), developed in the Yates Laboratory 20 years ago, is regarded as a powerful tool for proteomics research. Due to its remarkable online separation advantages, MudPIT has been widely used to facilitate discoveries in the field of proteomics research. However, it has one major disadvantage: the process of eluting peptides during strong cation exchange introduces salts, of different concentrations, into the mass spectrometer. Considering the sensitivity of the new generation of high-resolution mass spectrometers, developing a new version of MudPIT that could eliminate the introduction of salts in the elute would be a significant advancement to current technology. Herein, we developed a new, clean version of MudPIT called parallel channels-multidimensional protein identification technology (PC-MudPIT) to overcome this issue. In this design, the original biphasic trapping column was replaced by two parallel analytical column channels. We successfully averted the salt contamination yet retained all the other advantages of MudPIT. A total of 8161 and 7359 protein groups were identified from A549 whole cell lysate using PC-MudPIT and classic MudPIT, respectively. Moreover, we discovered the additional advantage that, in online mode, PC-MudPIT can also be used for an enrichment process of phosphopeptide identification. We identified a total 11453 phosphopeptides using PC-MudPIT and 7729 phosphopeptides using offline TiO2 enrichment followed by classic MudPIT. These advances indicate the possibility of other innovative applications of PC-MudPIT technology in deep proteome exploration.
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Affiliation(s)
- Nan Zhang
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Beijing 100191, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shuaixin Gao
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Beijing 100191, China
| | - Catherine Chiulan Wong
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Beijing 100191, China
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100191, China
- Peking University First Hosptal, Beijing 100034, China
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3
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Cen J, Feng L, Ke H, Bao L, Li LZ, Tanaka Y, Weng J, Su L. Exosomal Thrombospondin-1 Disrupts the Integrity of Endothelial Intercellular Junctions to Facilitate Breast Cancer Cell Metastasis. Cancers (Basel) 2019; 11:cancers11121946. [PMID: 31817450 PMCID: PMC6966578 DOI: 10.3390/cancers11121946] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Transendothelial migration of malignant cells plays an essential role in tumor progression and metastasis. The present study revealed that treating human umbilical vein endothelial cells (HUVECs) with exosomes derived from metastatic breast cancer cells increased the number of cancer cells migrating through the endothelial cell layer and impaired the tube formation of HUVECs. Furthermore, the expression of intercellular junction proteins, including vascular endothelial cadherin (VE-cadherin) and zona occluden-1 (ZO-1), was reduced significantly in HUVECs treated with carcinoma-derived exosomes. Proteomic analyses revealed that thrombospondin-1 (TSP1) was highly expressed in breast cancer cell MDA-MB-231-derived exosomes. Treating HUVECs with TSP1-enriched exosomes similarly promoted the transendothelial migration of malignant cells and decreased the expression of intercellular junction proteins. TSP1-down regulation abolished the effects of exosomes on HUVECs. The migration of breast cancer cells was markedly increased in a zebrafish in vivo model injected with TSP1-overexpressing breast cancer cells. Taken together, these results suggest that carcinoma-derived exosomal TSP1 facilitated the transendothelial migration of breast cancer cells via disrupting the intercellular integrity of endothelial cells.
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Affiliation(s)
- Junyu Cen
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (J.C.); (L.F.); (H.K.); (L.B.)
| | - Lingyun Feng
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (J.C.); (L.F.); (H.K.); (L.B.)
| | - Huichuan Ke
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (J.C.); (L.F.); (H.K.); (L.B.)
| | - Lifeng Bao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (J.C.); (L.F.); (H.K.); (L.B.)
| | - Lin Z. Li
- Department of Radiology and Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, 1-7-1, Sakamoto, Nagasaki 852-8588, Japan;
| | - Jun Weng
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (J.C.); (L.F.); (H.K.); (L.B.)
- Correspondence: (J.W.); (L.S.); Tel.: +86-2787792072 (J.W. & L.S.)
| | - Li Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (J.C.); (L.F.); (H.K.); (L.B.)
- Research Institute of Huazhong University of Science and Technology in Shenzhen, Shenzhen 518063, China
- Correspondence: (J.W.); (L.S.); Tel.: +86-2787792072 (J.W. & L.S.)
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Hinzke T, Kouris A, Hughes RA, Strous M, Kleiner M. More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics. Front Microbiol 2019; 10:238. [PMID: 30837968 PMCID: PMC6383543 DOI: 10.3389/fmicb.2019.00238] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Metaproteomics, the study of protein expression in microbial communities, is a versatile tool for environmental microbiology. Achieving sufficiently high metaproteome coverage to obtain a comprehensive picture of the activities and interactions in microbial communities is one of the current challenges in metaproteomics. An essential step to maximize the number of identified proteins is peptide separation via liquid chromatography (LC) prior to mass spectrometry (MS). Thorough optimization and comparison of LC methods for metaproteomics are, however, currently lacking. Here, we present an extensive development and test of different 1D and 2D-LC approaches for metaproteomic peptide separations. We used fully characterized mock community samples to evaluate metaproteomic approaches with very long analytical columns (50 and 75 cm) and long gradients (up to 12 h). We assessed a total of over 20 different 1D and 2D-LC approaches in terms of number of protein groups and unique peptides identified, peptide spectrum matches (PSMs) generated, the ability to detect proteins of low-abundance species, the effect of technical replicate runs on protein identifications and method reproducibility. We show here that, while 1D-LC approaches are faster and easier to set up and lead to more identifications per minute of runtime, 2D-LC approaches allow for a higher overall number of identifications with up to >10,000 protein groups identified. We also compared the 1D and 2D-LC approaches to a standard GeLC workflow, in which proteins are pre-fractionated via gel electrophoresis. This method yielded results comparable to the 2D-LC approaches, however with the drawback of a much increased sample preparation time. Based on our results, we provide recommendations on how to choose the best LC approach for metaproteomics experiments, depending on the study aims.
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Affiliation(s)
- Tjorven Hinzke
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- Institute of Pharmacy, Department of Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Rebecca-Ayme Hughes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Kim Y, Jeon M, Min H, Son J, Lee J, Kwon OS, Moon MH, Kim KH. Development of a multi-functional concurrent assay using weak cation-exchange solid-phase extraction (WCX-SPE) and reconstitution with a diluted sample aliquot for anti-doping analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:897-905. [PMID: 29572989 DOI: 10.1002/rcm.8119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/09/2018] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE In addition to the development of adequate screening methods for multiple compounds, the World Anti-Doping Agency (WADA) requires anti-doping laboratories to analyze prohibited substances and their metabolites from various classes. This task presents a difficult challenge for all agencies and interests involved in the field of doping control. METHODS A screening method is reported in which hybrid sample preparation was performed using a combination of weak cation-exchange solid-phase extraction (WCX-SPE) and the 'Dilute and Shoot' strategy in order to take advantage of both the methodologies. Target substances were extracted using a WCX cartridge and reconstituted with a diluted sample aliquot that included 20% of an untreated urine sample. The target substances were further analyzed by high-performance liquid chromatography/triple quadrupole mass spectrometry (LC/MS). RESULTS The SPE procedure was optimized using a cartridge-washing step, elution conditions, and elution volume. The cartridge-washing step, which was performed using 10% methanol, improved the overall recovery of target substances. Since the recovery was observed to vary according to the pH of the eluting solution, we applied an elution step using both an acid and a basic organic solvent to achieve complementary recovery. Reconstitution of the diluted aliquot sample was performed to recover the polar substances. CONCLUSIONS The method was validated and applied to real samples in accordance with the external quality assessment scheme of WADA and to the previously reported samples that had provided positive test results. This novel method using hybrid sample preparation and LC/MS could be useful to screen multiple classes of the 264 targeted substances in anti-doping analysis.
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Affiliation(s)
- Yongseok Kim
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Chemistry, Yonsei University, Yonsei-ro 50, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Mijin Jeon
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Hophil Min
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Junghyun Son
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jaeick Lee
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Oh-Seung Kwon
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, Yonsei-ro 50, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Ki Hun Kim
- Doping Control Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
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Yi L, Piehowski PD, Shi T, Smith RD, Qian WJ. Advances in microscale separations towards nanoproteomics applications. J Chromatogr A 2017; 1523:40-48. [PMID: 28765000 PMCID: PMC6042839 DOI: 10.1016/j.chroma.2017.07.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023]
Abstract
Microscale separation (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. In recent decades significant advances have been achieved in MS-based proteomics. However, the current proteomics platforms still face an analytical challenge in overall sensitivity towards nanoproteomics applications for starting materials of less than 1μg total proteins (e.g., cellular heterogeneity in tissue pathologies). Herein, we review recent advances in microscale separation techniques and integrated sample processing strategies that improve the overall sensitivity and proteome coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.
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Affiliation(s)
- Lian Yi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
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7
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Sajic T, Varesio E, Szanto I, Hopfgartner G. Comparison of fractionation strategies for offline two-dimensional liquid chromatography tandem mass spectrometry analysis of proteins from mouse adipose tissue. Anal Biochem 2015; 484:122-32. [DOI: 10.1016/j.ab.2015.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/26/2015] [Accepted: 05/22/2015] [Indexed: 12/22/2022]
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8
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Zhang Y, Liu J, Liu H, He Y, Yi R, Niu Y, Chen T, Yang Q, Zhao Y. Comparative study of the different activities of hepatitis B virus whole-X protein and HBx in hepatocarcinogenesis by proteomics and bioinformatics analysis. Arch Virol 2015; 160:1645-56. [PMID: 25913689 DOI: 10.1007/s00705-015-2421-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/04/2015] [Indexed: 01/30/2023]
Abstract
The hepatitis B virus (HBV) whole-X gene comprises the HBV X gene and the 168-bp region immediately upstream. Although the functions of HBx in hepatocarcinogenesis are well known, the activity of the HBV whole-X protein (HBwx), with 56 additional amino acids, has not yet been explored. In this study, proteomic and bioinformatic analysis was done to determine the protein interaction profiles of HBwx and HBx and to describe their functions in carcinogenesis. A total of 203 proteins were identified that interacted with HBwx, of which 149 were unique, the rest interacting also with HBx, and 73% (148/203) of these proteins are involved in carcinogenesis. Gene ontology (GO) analysis showed that HBwx- and HBx-interacting proteins are involved in different processes, the former mainly in biosynthetic processes (glycolysis, cell-cycle functions, and protein folding), and the latter mainly in localization, viral transcription, biological adhesion and angiogenesis. Pathway networks analysis revealed that proteins interacting with HBx participate mainly in oxidative phosphorylation, localization, the cytoskeleton, and cell adhesion. In contrast, more-specific functional analysis showed that proteins interacting with HBwx are involved in apoptosis and survival, cell-cycle functions, glycolysis, and gluconeogenesis (Pathway Maps); to cellular macromolecular complex assembly, protein folding and mRNA metabolic process (GO Processes); and to regulation of protein folding in the endoplasmic reticulum and cytoplasm, transcription, cell cycle G2-M and cytoskeleton rearrangement (Process Networks). In conclusion, this study shows that HBwx functions in carcinogenesis in a way that is different from that of HBx.
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Affiliation(s)
- Yu Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China
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Hattan SJ, Du J, Parker KC. Bifunctional Glass Membrane Designed to Interface SDS-PAGE Separations of Proteins with the Detection of Peptides by Mass Spectrometry. Anal Chem 2015; 87:3685-93. [DOI: 10.1021/ac503980x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J. Hattan
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
| | - Jie Du
- Toxikon Corporation, 15 Wiggins Avenue, Bedford, Massachusetts 01730, United States
| | - Kenneth C. Parker
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
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10
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Zeng LB, Zhuang XR, Huang LL, Zhang YY, Chen CY, Dong K, Zhang Y, Cui ZL, Ding XL, Chang YF, Guo XK, Zhu YZ. Comparative subproteome analysis of three representative Leptospira interrogans vaccine strains reveals cross-reactive antigens and novel virulence determinants. J Proteomics 2015; 112:27-37. [DOI: 10.1016/j.jprot.2014.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/08/2014] [Accepted: 08/25/2014] [Indexed: 12/26/2022]
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11
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Phospho-proteomic analysis of developmental reprogramming in the moss Physcomitrella patens. J Proteomics 2014; 108:284-94. [DOI: 10.1016/j.jprot.2014.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/12/2014] [Accepted: 05/19/2014] [Indexed: 12/31/2022]
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Yu L, Shen J, Mannoor K, Guarnera M, Jiang F. Identification of ENO1 as a potential sputum biomarker for early-stage lung cancer by shotgun proteomics. Clin Lung Cancer 2014; 15:372-378.e1. [PMID: 24984566 DOI: 10.1016/j.cllc.2014.05.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 01/29/2023]
Abstract
BACKGROUND Lung cancer is the leading cancer killer. Early detection will reduce the related deaths. The objective of this study was to identify potential biomarkers for early-stage lung cancer in sputum supernatant. MATERIALS AND METHODS Using shotgun proteomics, we detected changes in protein profiles that were associated with lung cancer by analyzing sputum supernatants from 6 patients with early-stage lung cancer and 5 cancer-free controls. Using western blotting, we validated the proteomic results in 22 lung cancer cases and 22 controls. Using enzyme-linked immunosorbent assay (ELISA), we evaluated the diagnostic performance of the biomarker candidates in an independent set of 35 cases and 36 controls. RESULTS Proteomics identified 8 biomarker candidates for lung cancer. Western blotting validation of the candidates showed that enolase 1 (ENO1) displayed a higher expression level in patients with cancer than in cancer-free individuals (P = .015). ELISA revealed that the assessment of ENO1 expression in sputum supernatant had 58.33% sensitivity and 80.00% specificity in distinguishing patients with stage I lung cancer from cancer-free individuals. CONCLUSION The analysis of protein biomarkers in sputum may provide a potential approach for the early detection of lung cancer. Future validation of all the candidates defined by shotgun proteomics in a large cohort study may help develop additional biomarkers that can be added to ENO1 to provide more diagnostic efficacy for lung cancer.
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Affiliation(s)
- Lei Yu
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - Jun Shen
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - Kaiissar Mannoor
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - Maria Guarnera
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - Feng Jiang
- Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD
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Wang X, Qi M, Li J, Ji Z, Hu Y, Bao F, Mahalingam R, He Y. The phosphoproteome in regenerating protoplasts from Physcomitrella patens protonemata shows changes paralleling postembryonic development in higher plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2093-106. [PMID: 24700621 PMCID: PMC3991745 DOI: 10.1093/jxb/eru082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The moss Physcomitrella patens is an ideal model plant to study plant developmental processes. To better understand the mechanism of protoplast regeneration, a phosphoproteome analysis was performed. Protoplasts were prepared from protonemata. By 4 d of protoplast regeneration, the first cell divisions had ensued. Through a highly selective titanium dioxide (TiO2)-based phosphopeptide enrichment method and mass spectrometric technology, more than 300 phosphoproteins were identified as protoplast regeneration responsive. Of these, 108 phosphoproteins were present on day 4 but not in fresh protoplasts or those cultured for 2 d. These proteins are catalogued here. They were involved in cell-wall metabolism, transcription, signal transduction, cell growth/division, and cell structure. These protein functions are related to cell morphogenesis, organogenesis, and development adjustment. This study presents a comprehensive analysis of phosphoproteome involved in protoplast regeneration and indicates that the mechanism of plant protoplast regeneration is similar to that of postembryonic development.
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Affiliation(s)
- Xiaoqin Wang
- Key Laboratory of Urban Agriculture (North) Ministry of Agriculture, Beijing University of Agriculture, Beijing 102206, China
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Meiyan Qi
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jingyun Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhongzhong Ji
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yong Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Fang Bao
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ramamurthy Mahalingam
- Department of Biochemistry and Molecular Biology, Oklahoma State University, OK 74078, USA
| | - Yikun He
- College of Life Sciences, Capital Normal University, Beijing 100048, China
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14
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Wang Y, Wang G, Wang Z, Zhang H, Zhang L, Cheng Z. Chicken biliary exosomes enhance CD4(+)T proliferation and inhibit ALV-J replication in liver. Biochem Cell Biol 2014; 92:145-51. [PMID: 24697699 DOI: 10.1139/bcb-2013-0096] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Exosomes, which are small membrane vesicles of endocytic origin, carry lipids, RNA/miRNAs, and proteins and have immune modulatory functions. In this study, we isolated exosomes from the bile of specific pathogen-free chickens, 42-43 days of age, by using an ultracentrifugation and filtration method. The density of the exosomes, isolated by sucrose gradient fractionation, was between 1.13 and 1.19 g/mL. Electron microscopic observation of the liver showed that exosomes were present in the space of Disse and bile canaliculus. Chicken biliary exosomes displayed typical saucer-shaped, rounded morphology. Using liquid chromatography mass spectrum methodology, 196 proteins, including exosomal markers and several unique proteins, were identified and compared with mouse biliary exosomes. Noteworthy, CCCH type zinc finger antiviral protein was found on chicken biliary exosomes never described before. Furthermore, our data show that chicken biliary exosomes promote the proliferation of CD4(+) and CD8(+) T cells and monocytes from liver. In addition, chicken biliary exosomes significantly inhibit avian leukosis virus subgroup J, which is an oncogenic retrovirus, from replicating in the DF-1 cell line. These data indicate that chicken biliary exosomes possess the capacity to influence the immune responses of lymphocytes and inhibit avian leukosis virus subgroup J (ALV-J).
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Affiliation(s)
- Yue Wang
- a College of Veterinary Medicine, Shandong Agricultural University, No. 61, Daizong ST, Tai'an 271018, P.R. China
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15
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Manadas B, Mendes VM, English J, Dunn MJ. Peptide fractionation in proteomics approaches. Expert Rev Proteomics 2014; 7:655-63. [DOI: 10.1586/epr.10.46] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Gao M, Qi D, Zhang P, Deng C, Zhang X. Development of multidimensional liquid chromatography and application in proteomic analysis. Expert Rev Proteomics 2014; 7:665-78. [DOI: 10.1586/epr.10.49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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17
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Lee H, Lee JH, Kim H, Kim SJ, Bae J, Kim HK, Lee SW. A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography system for high-throughput proteomics analysis. J Chromatogr A 2014; 1329:83-9. [PMID: 24412000 DOI: 10.1016/j.chroma.2013.12.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/25/2013] [Accepted: 12/28/2013] [Indexed: 11/19/2022]
Abstract
A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography (DO-MULTI-UPLC) system has been developed for high throughput proteome analyses of complex peptide mixtures. The system employs two online solid phase extraction (SPE) columns (150μm inner diameter×3cm), two capillary reverse phase (RP) columns (75μm×100cm) and a strong cation exchange (SCX) column (150μm×15cm) on a single system utilizing one binary pump and one isocratic pump. With the automated operation of six switching valves, the selection of LC experiments between single-dimensional RPLC and online two-dimensional SCX/RPLC were achieved automatically, without manual intervention, while two RPLC columns were used independently and alternatively. By essentially removing the dead time for column equilibration between experiments, in either 1D mode or 2D experimental mode, the current system was demonstrated to increase the experimental throughput by about two folds, while keeping the inter-column reproducibility of peptide elution time in less than 1% of gradient time. The advantageous features of the proposed system were demonstrated by its application to proteome samples of varying complexities.
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Affiliation(s)
- Hangyeore Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Jung Hwa Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Hokeun Kim
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Su-Jin Kim
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Jingi Bae
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
| | - Hark Kyun Kim
- National Cancer Center, Goyang 410-769, South Korea.
| | - Sang-Won Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea.
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18
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Wang J, Fang DA, Wang Y, Wang YL, Cheng L, He L, Wang Q. Cathepsin A protein from the accessory sex gland of the Chinese mitten crab (Eriocheir sinensis) plays a key role in spermatophore digestion. JOURNAL OF INSECT PHYSIOLOGY 2013; 59:953-960. [PMID: 23871752 DOI: 10.1016/j.jinsphys.2013.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 07/08/2013] [Accepted: 07/10/2013] [Indexed: 06/02/2023]
Abstract
Accessory sex gland (ASG) secretory proteins of the Chinese mitten crab (Eriocheir sinensis) can effectively digest the spermatophore wall. In order to identify which proteins participate in spermatophore wall digestion, a 50-kDa protein secreted from the ASG was purified to homogeneity by a series of isolation steps, including ammonium sulfate fractionation, Sephadex G-25 S gel-filtration, ion exchange chromatography on a DEAE-Sephacel column and Sephacryl S-200 gel-filtration. The purified protein was effective in spermatophore wall rupture, and the subsequent HPLC-ESI-MS/MS shotgun analysis showed the digestive protein to be cathepsin A (cathA). This finding was also confirmed by Western blot analysis and a cathA inhibitor digestion experiment. ELISA analysis showed that cathA enzymatic activity from ASG secretions increased during its purification process. Furthermore, enzymatic activity was significantly higher in the mating period of E. sinensis parallel to the latest developmental stage of the gland. Moreover, analysis from a cathA inhibitor that inhibits spermatophore wall digestion showed that cathA is the main enzyme involved. Hence, we first report the characterization of cathA from the ASG, which might play a key role in digesting the spermatophore wall of E. sinensis.
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Affiliation(s)
- Juan Wang
- School of Life Science, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
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19
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Zheng L, Dong H, Hu L. Zirconium-Cation-Immobilized Core/Shell (Fe3O4@Polymer) Microspheres as an IMAC Material for the Selective Enrichment of Phosphopeptides. Ind Eng Chem Res 2013. [DOI: 10.1021/ie4003377] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leyou Zheng
- NHU Co. Ltd. of Zhejiang, 4 Jiangbei Road,
Xinchang, Zhejiang 312500, P. R. China
| | - Huaping Dong
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing,
Zhejiang 312000, P. R. China
| | - Liujiang Hu
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing,
Zhejiang 312000, P. R. China
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20
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Shotgun proteomic analysis of plasma from dairy cattle suffering from footrot: characterization of potential disease-associated factors. PLoS One 2013; 8:e55973. [PMID: 23418487 PMCID: PMC3572155 DOI: 10.1371/journal.pone.0055973] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/04/2013] [Indexed: 01/17/2023] Open
Abstract
The plasma proteome of healthy dairy cattle and those with footrot was investigated using a shotgun LC-MS/MS approach. In total, 648 proteins were identified in healthy plasma samples, of which 234 were non-redundant proteins and 123 were high-confidence proteins; 712 proteins were identified from footrot plasma samples, of which 272 were non-redundant proteins and 138 were high-confidence proteins. The high-confidence proteins showed significant differences between healthy and footrot plasma samples in molecular weight, isoelectric points and the Gene Ontology categories. 22 proteins were found that may differentiate between the two sets of plasma proteins, of which 16 potential differential expression (PDE) proteins from footrot plasma involved in immunoglobulins, innate immune recognition molecules, acute phase proteins, regulatory proteins, and cell adhesion and cytoskeletal proteins; 6 PDE proteins from healthy plasma involved in regulatory proteins, cytoskeletal proteins and coagulation factors. Of these PDE proteins, haptoglobin, SERPINA10 protein, afamin precursor, haptoglobin precursor, apolipoprotein D, predicted peptidoglycan recognition protein L (PGRP-L) and keratan sulfate proteoglycan (KS-PG) were suggested to be potential footrot-associated factors. The PDE proteins PGRP-L and KS-PG were highlighted as potential biomarkers of footrot in cattle. The resulting protein lists and potential differentially expressed proteins may provide valuable information to increase understanding of plasma protein profiles in cattle and to assist studies of footrot-associated factors.
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21
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Liu Y, Luo X, Hu H, Wang R, Sun Y, Zeng R, Chen H. Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer. PLoS One 2012; 7:e51748. [PMID: 23284758 PMCID: PMC3526638 DOI: 10.1371/journal.pone.0051748] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/05/2012] [Indexed: 01/01/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. Clinically, the treatment of non-small cell lung cancer (NSCLC) can be improved by the early detection and risk screening among population. To meet this need, here we describe the application of extensive peptide level fractionation coupled with label free quantitative proteomics for the discovery of potential serum biomarkers for lung cancer, and the usage of Tissue microarray analysis (TMA) and Multiple reaction monitoring (MRM) assays for the following up validations in the verification phase. Using these state-of-art, currently available clinical proteomic approaches, in the discovery phase we confidently identified 647 serum proteins, and 101 proteins showed a statistically significant association with NSCLC in our 18 discovery samples. This serum proteomic dataset allowed us to discern the differential patterns and abnormal biological processes in the lung cancer blood. Of these proteins, Alpha-1B-glycoprotein (A1BG) and Leucine-rich alpha-2-glycoprotein (LRG1), two plasma glycoproteins with previously unknown function were selected as examples for which TMA and MRM verification were performed in a large sample set consisting about 100 patients. We revealed that A1BG and LRG1 were overexpressed in both the blood level and tumor sections, which can be referred to separate lung cancer patients from healthy cases.
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Affiliation(s)
- Yansheng Liu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyang Luo
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haichuan Hu
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Wang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (RZ); (HC)
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (RZ); (HC)
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22
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Liu Y, Huang W, Zhang R, Wu J, Li L, Tang Y. Proteomic analysis of TNF-α-activated endothelial cells and endothelial microparticles. Mol Med Rep 2012; 7:318-26. [PMID: 23124128 DOI: 10.3892/mmr.2012.1139] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/11/2012] [Indexed: 11/05/2022] Open
Abstract
Endothelial microparticles (EMPs) are small vesicles released from endothelial cells (ECs) and found circulating in the blood. EMPs are formed by a plasma membrane surrounding a small amount of cytosol and contain a subset of cellular proteins. As the number of EMPs in the blood increases with certain diseases, they may be an attractive biomarker for clinical diagnosis. Proteomic analysis of EMPs has been previously performed by mass spectrometry. However, the proteomic information of the ECs that secrete EMPs is lacking. This study introduces an in vitro model of activated ECs we created for proteomic analyses and reports the changes of the protein content in the ECs and EMPs using proteomic methods. Thus, this study provides valuable information for the analysis of the highly dynamic secretion process of EMPs. There is a direct correlation between the proteins that form EMPs and tumor necrosis factor-α (TNF-α)-activated ECs. The endothelial proteins transferred by EMPs may play important roles in the interaction between EMPs and the target cells, which may lead to endothelial dysfunction.
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Affiliation(s)
- Yiyun Liu
- Department of Critical Care Medicine, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
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23
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Tang K, Jiao N, Liu K, Zhang Y, Li S. Distribution and functions of TonB-dependent transporters in marine bacteria and environments: implications for dissolved organic matter utilization. PLoS One 2012; 7:e41204. [PMID: 22829928 PMCID: PMC3400609 DOI: 10.1371/journal.pone.0041204] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
Background Bacteria play critical roles in marine nutrient cycles by incorporating and redistributing dissolved organic matter (DOM) and inorganic nutrients in the ocean. TonB-dependent transporter (TBDT) proteins allow Gram-negative bacteria to take up scarce resources from nutrient-limiting environments as well as siderophores, heme, vitamin B12, and recently identified carbohydrates. Thus, the characterization of TBDT distribution and functions is essential to better understand the contribution TBDT to DOM assimilation and its consequences on nutrient cycling in the environment. Methodology/Principal Findings This study presents the distribution of encoded known and putative TBDT proteins in the genomes of microorganisms and from the Global Ocean Survey data. Using a Lek clustering algorithm and substrate specificities, the TBDT sequences were mainly classified into the following three groups: (1) DOM transporters; (2) Siderophores/Vitamins transporters; and (3) Heme/Hemophores/Iron(heme)-binding protein transporters. Diverse TBDTs were found in the genomes of oligotroph Citromicrobium bathyomarinum JL354 and Citromicrobium sp JLT1363 and were highly expressed in the stationary phase of bacterial growth. The results show that the Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria accounted for the majority of the TBDT gene pool in marine surface waters. Conclusions/Significance The results of this study confirm the ecological importance of TBDTs in DOM assimilation for bacteria in marine environments owing to a wide range of substrate utilization potential in the ubiquitous Gammaproteobacteria and CFB group bacteria.
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Affiliation(s)
- Kai Tang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, China.
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24
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Xie F, Smith RD, Shen Y. Advanced proteomic liquid chromatography. J Chromatogr A 2012; 1261:78-90. [PMID: 22840822 DOI: 10.1016/j.chroma.2012.06.098] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 06/22/2012] [Accepted: 06/27/2012] [Indexed: 12/26/2022]
Abstract
Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput.
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Affiliation(s)
- Fang Xie
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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25
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Lee JH, Hyung SW, Mun DG, Jung HJ, Kim H, Lee H, Kim SJ, Park KS, Moore RJ, Smith RD, Lee SW. Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses. J Proteome Res 2012; 11:4373-81. [PMID: 22709424 DOI: 10.1021/pr3004166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A multifunctional liquid chromatography system that performs 1-dimensional, 2-dimensional (strong cation exchange/reverse phase liquid chromatography or SCX/RPLC) separations and online phosphopeptide enrichment using a single binary nanoflow pump has been developed. With a simple operation of a function selection valve equipped with a SCX column and a TiO2 (titanium dioxide) column, a fully automated selection of three different experiment modes was achieved. Because the current system uses essentially the same solvent flow paths, the same trap column, and the same separation column for reverse-phase separation of 1D, 2D, and online phosphopeptides enrichment experiments, the elution time information obtained from these experiments is in excellent agreement, which facilitates correlating peptide information from different experiments. The final reverse-phase separation of the three experiments is completely decoupled from all of the function selection processes; thereby salts or acids from SCX or TiO2 column do not affect the efficiency of the reverse-phase separation.
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Affiliation(s)
- Jung Hwa Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea
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26
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Pan PW, Zhang Q, Hou J, Liu Z, Bai F, Cao MR, Sun T, Bai G. Cell surface glycoprotein profiling of cancer cells based on bioorthogonal chemistry. Anal Bioanal Chem 2012; 403:1661-70. [DOI: 10.1007/s00216-012-5989-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 03/09/2012] [Accepted: 03/27/2012] [Indexed: 01/06/2023]
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27
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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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28
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Gokce E, Andrews GL, Dean RA, Muddiman DC. Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:610-4. [PMID: 21342794 DOI: 10.1016/j.jchromb.2011.01.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 01/20/2011] [Accepted: 01/26/2011] [Indexed: 11/29/2022]
Abstract
Fractionation prior to mass spectrometry is an indispensable step in proteomics. In this paper we report the success of performing offline reversed phase high pressure liquid chromatography (HPLC) fractionation on a C18 2.0 mm×150 mm column at the peptide level with microliter per minute flow rates prior to online nano-flow reversed phase liquid chromatography mass spectrometry (nanoLC-MS) using the well-studied fungus Saccharomyces cerevisiae. A C18 75 μm×150 mm column was used online and the online elution gradients for each fraction were adjusted in order to obtain well resolved separation. Comparing this method directly to only performing nanoLC-MS we observed a 61.6% increase in the number of identified proteins. At a 1% false discovery rate 1028 proteins were identified using two dimensions of RPLC versus 636 proteins identified in a single nano-flow separation. The majority of proteins identified by one dimension of nano-LC were present in the proteins identified in our two dimensional strategy. Although increasing analysis time, this non-orthogonal and facile pre-fractionation method affords a more comprehensive examination of the proteome.
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Affiliation(s)
- Emine Gokce
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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29
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Jabbour RE, Deshpande SV, Stanford MF, Wick CH, Zulich AW, Snyder AP. A protein processing filter method for bacterial identification by mass spectrometry-based proteomics. J Proteome Res 2010; 10:907-12. [PMID: 21126090 DOI: 10.1021/pr101086a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposable filter unit placed inside a centrifuge vial for processing and digestion of bacterial proteins. Each processing stage allows filtration of excess reactants and unwanted byproduct while retaining the proteins. Upon addition of trypsin, the peptide mixture solution is passed through the filter while retaining the trypsin enzyme. The peptide mixture is then analyzed by LC-MS/MS with an in-house BACid algorithm for a comparison of the experimental unique peptides to a constructed proteome database of bacterial genus, specie, and strain entries. The concentration of bacteria was varied from 10 × 10(7) to 3.3 × 10(3) cfu/mL for analysis of the effect of concentration on the ability of the sample processing, LC-MS/MS, and data analysis methods to identify bacteria. The protein processing method and dilution procedure result in reliable identification of pure suspensions and mixtures at high and low bacterial concentrations.
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30
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Li QR, Xing XB, Chen TT, Li RX, Dai J, Sheng QH, Xin SM, Zhu LL, Jin Y, Pei G, Kang JH, Li YX, Zeng R. Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells. Mol Cell Proteomics 2010; 10:M110.001750. [PMID: 21149613 DOI: 10.1074/mcp.m110.001750] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Embryonic stem cells are pluripotent and capable of unlimited self-renewal. Elucidation of the underlying molecular mechanism may contribute to the advancement of cell-based regenerative medicine. In the present work, we performed a large scale analysis of the phosphoproteome in mouse embryonic stem (mES) cells. Using multiplex strategies, we detected 4581 proteins and 3970 high confidence distinct phosphosites in 1642 phosphoproteins. Notably, 22 prominent phosphorylated stem cell marker proteins with 39 novel phosphosites were identified for the first time by mass spectrometry, including phosphorylation sites in NANOG (Ser-65) and RE1 silencing transcription factor (Ser-950 and Thr-953). Quantitative profiles of NANOG peptides obtained during the differentiation of mES cells revealed that the abundance of phosphopeptides and non-phosphopeptides decreased with different trends. To our knowledge, this study presents the largest global characterization of phosphorylation in mES cells. Compared with a study of ultimately differentiated tissue cells, a bioinformatics analysis of the phosphorylation data set revealed a consistent phosphorylation motif in human and mouse ES cells. Moreover, investigations into phosphorylation conservation suggested that phosphoproteins were more conserved in the undifferentiated ES cell state than in the ultimately differentiated tissue cell state. However, the opposite conclusion was drawn from this conservation comparison with phosphosites. Overall, this work provides an overview of phosphorylation in mES cells and is a valuable resource for the future understanding of basic biology in mES cells.
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Affiliation(s)
- Qing-Run 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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31
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Hao P, Guo T, Li X, Adav SS, Yang J, Wei M, Sze SK. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. J Proteome Res 2010; 9:3520-6. [PMID: 20450224 DOI: 10.1021/pr100037h] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In shotgun proteomics, multidimensional liquid chromatography (MDLC) is commonly used to reduce sample complexity and increase dynamic range of protein identification. Since reversed-phase chromatography is mostly used as the second-dimensional separation before mass spectrometric analysis, the improvement of MDLC primarily depends on the first dimension of separation. Here, we present a novel whole proteome analysis method that separates peptides based on ERLIC. Tryptic peptides were retained on a weak anion exchange column through ERLIC with a high organic mobile phase. They were then distributed into multiple fractions based on both pI and polarity through the simultaneous effect of electrostatic repulsion and hydrophilic interaction when eluted using a salt-free pH gradient of increasing water content. Applying this to rat kidney tissue, we identified 4821 proteins and 30 659 unique peptides with high confidence from two replicates using LTQ-FT. This was 36.2% and 64.3% higher, respectively, than was obtained with the widely used SCX separation mode. Notably, the identification of both highly hydrophobic and basic peptides increased over 120% using the ERLIC method. The results indicate that ERLIC is a promising alternative to SCX as the first dimension of MDLC. In total, 5499 proteins and 35 847 unique peptides of rat kidney tissue are characterized.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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32
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Zhang J, Lanham KA, Peterson RE, Heideman W, Li L. Characterization of the adult zebrafish cardiac proteome using online pH gradient strong cation exchange-RP 2D LC coupled with ESI MS/MS. J Sep Sci 2010; 33:1462-71. [PMID: 20235133 DOI: 10.1002/jssc.200900780] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
2D HPLC separations by coupling strong cation exchange (SCX) and RP fractionation have been widely used in large-scale proteomic studies. Traditionally this method is performed by salt gradient SCX separation followed by RP and MS/MS analysis. The salt gradient SCX method has been known to have low peptide and protein resolution. In this study, we implemented a pH gradient SCX-RP HPLC platform to separate proteome digests from adult zebrafish hearts, followed by ESI quadrupole-TOF MS/MS analysis. This pH gradient SCX method has improved peptide separation, as demonstrated by a greater number of peptides and proteins identified from individual SCX fractions. This pH gradient method also has better MS compatibility owing to lower salt usage. This setup allows fast microflow fractionation in SCX dimension and nanoflow RP separation in the second dimension, and can be easily implemented on conventional capillary LC ESI MS/MS systems. Using this setup, we identified 1375 proteins from adult zebrafish hearts, establishing the first reported experimental data set for the heart proteome of zebrafish. This work laid the foundation for further studies of environmental cardiac toxicology using zebrafish as a model organism.
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Affiliation(s)
- Jiang Zhang
- School of Pharmacy, University of Wisconsin, Madison, WI 53705-2222, USA
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33
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Liu Y, Li C, Xing Z, Yuan X, Wu Y, Xu M, Tu K, Li Q, Wu C, Zhao M, Zeng R. Proteomic mining in the dysplastic liver of WHV/c-myc mice--insights and indicators for early hepatocarcinogenesis. FEBS J 2010; 277:4039-53. [PMID: 20807235 DOI: 10.1111/j.1742-4658.2010.07795.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Because of the asymptomatic process of carcinogenesis, the early detection of cancers such as hepatocellular carcinoma (HCC) is very challenging. Tumor-prone transgenic mouse models of oncogenesis can provide a stable and powerful tool for the analysis of cancer initiation, and are therefore promising for the discovery of early putative biomarkers of HCC. Using a label-free proteomic quantification strategy, we comprehensively investigated the protein expression profile in the livers of three 2-month-old WHV/c-myc mice at the dysplastic stage, with age-matched wt-C57 mice as controls. We identified 2781 proteins, 540 of which were differentially expressed. These proteins successfully characterized certain precancerous biological processes and alterations in transcriptional regulators before tumor onset. Two candidates, FK506-binding protein 4 (FKBP52) and ferritin heavy chain, were taken as examples for a search from the mouse model to clinical human tissues. Their levels in serum samples were determined by western blotting, and showed a noteworthy ability to distinguish between HCC and control cases. Immunohistochemical analysis with tissue microarrays confirmed the differential expression of FKBP52 between HCC and the paired controls (P < 0.001). The regulation of FKBP52 was also discovered to be relevant to HCC staging, with a dramatic decline at stage III (P < 0.05). The potentials of the candidate pool in this study were discussed in terms of delineating c-myc-induced hepatocarcinogenesis and facilitating biomarker discovery for early HCC diagnosis.
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Affiliation(s)
- Yansheng Liu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China
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Tao D, Zhang L, Shan Y, Liang Z, Zhang Y. Recent advances in micro-scale and nano-scale high-performance liquid-phase chromatography for proteome research. Anal Bioanal Chem 2010; 399:229-41. [PMID: 20683586 DOI: 10.1007/s00216-010-3946-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/18/2010] [Accepted: 06/20/2010] [Indexed: 10/25/2022]
Abstract
High-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS-MS) is regarded as one of the most powerful techniques for separation and identification of proteins. Recently, much effort has been made to improve the separation capacity, detection sensitivity, and analysis throughput of micro- and nano-HPLC, by increasing column length, reducing column internal diameter, and using integrated techniques. Development of HPLC columns has also been rapid, as a result of the use of submicrometer packing materials and monolithic columns. All these innovations result in clearly improved performance of micro- and nano-HPLC for proteome research.
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Affiliation(s)
- Dingyin Tao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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35
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Callipo L, Capriotti AL, Cavaliere C, Gubbiotti R, Samperi R, Laganà A. Evaluation of different two-dimensional chromatographic techniques for proteomic analysis of mouse cardiac tissue. Biomed Chromatogr 2010; 25:594-9. [PMID: 20652868 DOI: 10.1002/bmc.1487] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/24/2010] [Accepted: 06/02/2010] [Indexed: 11/09/2022]
Abstract
In proteomics experiments the first critical step after sampling is certainly sample preparation. Multidimensional chromatography techniques have emerged as a powerful tool for the large-scale analysis of such complex samples as biological samples. In order to evaluate these separation techniques, microgram quantities of protein extracted from mouse heart tissue were fractionated by four different chromatographic methods. Regarding peptide-level fractionation, the first dimension of separation was performed with high-pH reversed-phase chromatography (pH-RP) and strong cation exchange chromatography (SCX). Regarding protein-level fractionation, C(8) protein reversed-phase (C(8) -RP Prot) and high-recovery protein reversed-phase (hr-RP Prot) were used instead. The second dimension consisted of a reversed-phase nano-HPLC on-Chip coupled to an electrospray ionization quadrupole time-of-flight mass spectrometer for tandem mass spectrometric analysis. The performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The peptide-level pH-RP and the hr-RP Prot protein-level separations were the best methods, identifying 1338 and 1303 proteins, respectively. The peptide-level SCX, with 509 proteins identified, was the worst method.
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Affiliation(s)
- Luciano Callipo
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
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36
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Zhang X, Liu B, Zhang L, Zou H, Cao J, Gao M, Tang J, Liu Y, Yang P, Zhang Y. Recent advances in proteolysis and peptide/protein separation by chromatographic strategies. Sci China Chem 2010; 53:685-694. [PMID: 32214996 PMCID: PMC7089403 DOI: 10.1007/s11426-010-0135-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 01/28/2010] [Indexed: 11/05/2022]
Abstract
This review gives a broad glance on the progress of recent advances on proteolysis and peptide/protein separation by chromatographic strategies in the past ten years, covering the main research in these areas especially in China. The reviewed research focused on enzymatic micro-reactors and peptide separation in bottom-up approaches, and protein and peptide separation in top-down approaches. The new enzymatic micro-reactor is able to accelerate proteolytic reaction rate from conventionally a couple of hours to a few seconds, and the multiple dimensional chromatographic-separation with various models or arrays could sufficiently separate the proteomic mixture. These advances have significantly promoted the research of protein/peptide separation and identification in proteomics.
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Affiliation(s)
- XiangMin Zhang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - BaoHong Liu
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - LiHua Zhang
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - HanFa Zou
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Jing Cao
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - MingXia Gao
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - Jia Tang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - Yun Liu
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - PengYuan Yang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - YuKui Zhang
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
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Zhang X, Fang A, Riley CP, Wang M, Regnier FE, Buck C. Multi-dimensional liquid chromatography in proteomics--a review. Anal Chim Acta 2010; 664:101-13. [PMID: 20363391 PMCID: PMC2852180 DOI: 10.1016/j.aca.2010.02.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 01/29/2010] [Accepted: 02/01/2010] [Indexed: 12/19/2022]
Abstract
Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. This still-emerging combination of technologies aims to describe and characterize all expressed proteins in a biological system. Because of upper limits on mass detection of mass spectrometers, proteins are usually digested into peptides and the peptides are then separated, identified and quantified from this complex enzymatic digest. The problem in digesting proteins first and then analyzing the peptide cleavage fragments by mass spectrometry is that huge numbers of peptides are generated that overwhelm direct mass spectral analyses. The objective in the liquid chromatography approach to proteomics is to fractionate peptide mixtures to enable and maximize identification and quantification of the component peptides by mass spectrometry. This review will focus on existing multidimensional liquid chromatographic (MDLC) platforms developed for proteomics and their application in combination with other techniques such as stable isotope labeling. We also provide some perspectives on likely future developments.
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Affiliation(s)
- Xiang Zhang
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA.
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38
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Li QR, Fan KX, Li RX, Dai J, Wu CC, Zhao SL, Wu JR, Shieh CH, Zeng R. A comprehensive and non-prefractionation on the protein level approach for the human urinary proteome: touching phosphorylation in urine. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:823-832. [PMID: 20187088 DOI: 10.1002/rcm.4441] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Increasing attention has been paid to the urinary proteome because it holds the promise of discovering various disease biomarkers. However, most of the urine proteomics studies routinely relied on protein pre-fractionation and so far did not present characterization on phosphorylation status. Two robust approaches, integrated multidimensional liquid chromatography (IMDL) and Yin-yang multidimensional liquid chromatography (MDLC) tandem mass spectrometry, were recently developed in our laboratory, with high-coverage identification of peptide mixtures. In this study, we adopted a strategy without pre-fractionation on the protein level for urinary proteome identification, using both the IMDL and the Yin-yang MDLC methods for peptide fractionation followed by identification using a linear ion trap-orbitrap (LTQ-Orbitrap) mass spectrometer with high resolution and mass accuracy. A total of 1310 non-redundant proteins were highly confidently identified from two experiments, significantly including 59 phosphorylation sites. More than half the annotated identifications were membrane-related proteins. In addition, the lysosomal as well as kidney-associated proteins were detected. Compared with the six largest datasets of urinary proteins published previously, we found our data included most of the reported proteins. Our study developed a robust approach for exploring the human urinary proteome, which would provide a catalogue of urine proteins on a global scale. It is the first report, to our best knowledge, to profile the urinary phosphoproteome. This work significantly extends current comprehension of urinary protein modification and its potential biological significance. Moreover, the strategy could further serve as a reference for biomarker discovery.
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Affiliation(s)
- Qing-Run 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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Yuan H, Zhang L, Hou C, Zhu G, Tao D, Liang Z, Zhang Y. Integrated platform for proteome analysis with combination of protein and peptide separation via online digestion. Anal Chem 2010; 81:8708-14. [PMID: 19788244 DOI: 10.1021/ac900310y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An integrated platform with the combination of protein and peptide separation was established via online protein digestion, by which proteins were first separated by a microcolumn packed with mixed weak anion and weak cation exchange (WAX/WCX) particles under a series of salt steps, online digested by a trypsin immobilized microenzymatic reactor (IMER), trapped and desalted by two parallel C8 precolumns, separated by microreversed-phase liquid chromatography (muRPLC) under a linear gradient of organic modifier concentration, and finally identified by electrospray ionization-MS/MS (ESI-MS/MS). To evaluate the performance of such a platform, a mixture of myoglobin, cytochrome c, bovine serum albumin (BSA), and alpha-casein, with mass ranging from 25 ng to 2 microg, was analyzed. Compared to the methods by off-line protein fractionation and shotgun based strategy, the analysis time, including sample preparation, digestion, desalting, separation, and detection, was shortened from ca. 30 to 5 h, and cytochrome c with abundance of 25 ng could be identified with improved sequence coverage. Furthermore, such an integrated platform was successfully applied into the analysis of proteins extracted from human lung cancer cells. Compared with the results obtained by the shotgun approach, the identified protein number was increased by 30%. All these results demonstrated that such an integrated approach would be an attractive alternative to commonly applied approaches for proteome research.
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Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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40
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Cao XJ, Dai J, Xu H, Nie S, Chang X, Hu BY, Sheng QH, Wang LS, Ning ZB, Li YX, Guo XK, Zhao GP, Zeng R. High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans. Cell Res 2009; 20:197-210. [PMID: 19918266 DOI: 10.1038/cr.2009.127] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Leptospirosis is a widespread zoonotic disease caused by pathogenic spirochetes of the genus Leptospira that infects humans and a wide range of animals. By combining computational prediction and high-accuracy tandem mass spectra, we revised the genome annotation of Leptospira interrogans serovar Lai, a free-living pathogenic spirochete responsible for leptospirosis, providing substantial peptide evidence for novel genes and new gene boundaries. Subsequently, we presented a high-coverage proteome analysis of protein expression and multiple posttranslational modifications (PTMs). Approximately 64.3% of the predicted L. interrogans proteins were cataloged by detecting 2 540 proteins. Meanwhile, a profile of multiple PTMs was concurrently established, containing in total 32 phosphorylated, 46 acetylated and 155 methylated proteins. The PTM systems in the serovar Lai show unique features. Unique eukaryotic-like features of L. interrogans protein modifications were demonstrated in both phosphorylation and arginine methylation. This systematic analysis provides not only comprehensive information of high-coverage protein expression and multiple modifications in prokaryotes but also a view suggesting that the evolutionarily primitive L. interrogans shares significant similarities in protein modification systems with eukaryotes.
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Affiliation(s)
- Xing-Jun Cao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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41
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Zhou H, Xiao Y, Li R, Hong S, Li S, Wang L, Zeng R, Liao K. Quantitative analysis of secretome from adipocytes regulated by insulin. Acta Biochim Biophys Sin (Shanghai) 2009; 41:910-21. [PMID: 19902125 DOI: 10.1093/abbs/gmp085] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adipocyte is not only a central player involved in storage and release of energy, but also in regulation of energy metabolism in other organs via secretion of peptides and proteins. During the pathogenesis of insulin resistance and type 2 diabetes, adipocytes are subjected to the increased levels of insulin, which may have a major impact on the secretion of adipokines. We have undertaken cleavable isotope-coded affinity tag (cICAT) and label-free quantitation approaches to identify and quantify secretory factors that are differentially secreted by 3T3-L1 adipocytes with or without insulin treatment. Combination of cICAT and label-free results, there are 317 proteins predicted or annotated as secretory proteins. Among these secretory proteins, 179 proteins and 53 proteins were significantly upregulated and down-regulated, respectively. A total of 77 reported adipokines were quantified in our study, such as adiponectin, cathepsin D, cystatin C, resistin, and transferrin. Western blot analysis of these adipokines confirmed the quantitative results from mass spectrometry, and revealed individualized secreting patterns of these proteins by increasing insulin dose. In addition, 240 proteins were newly identified and quantified as secreted proteins from 3T3-L1 adipocytes in our study, most of which were up-regulated upon insulin treatment. Further comprehensive bioinformatics analysis revealed that the secretory proteins in extracellular matrix-receptor interaction pathway and glycan structure degradation pathway were significantly upregulated by insulin stimulation.
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Affiliation(s)
- Hu Zhou
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuanyuan Xiao
- Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rongxia Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shangyu Hong
- Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sujun Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lianshui Wang
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School, 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, Graduate School, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kan Liao
- Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School, Chinese Academy of Sciences, Shanghai 200031, China
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42
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Isolation and proteomic analysis of the halotolerant alga Dunaliella salina flagella using shotgun strategy. Mol Biol Rep 2009; 37:711-6. [PMID: 19437132 DOI: 10.1007/s11033-009-9563-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 05/01/2009] [Indexed: 10/20/2022]
Abstract
Previous studies have demonstrated that flagella/cilia are critical organelles and play diverse roles of motility, sensory perception and development in many eukaryotic cells. However, there is very little information available about flagella composition in Dunaliella salina, a halotolerant, unicellular biflagellate green alga. In the present study, we used strategy of shotgun proteomics to identify flagella proteins after flagella were released and collected from D. salina. A total of 520 groups of proteins were identified under a stringent filter condition (Xcorr > or =1.9, > or =2.2 and > or =3.75; DeltaCn >/= 0.1). In addition to six kinds of known flagella proteins, the putative flagella proteins of D. salina identified by one or more peptides are abundant in signaling, cell division, metabolism, etc. The findings provide guidance for further studies to elucidate the roles of these proteins in the function and assembly of this organelle in microalgae.
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43
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Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P. Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009; 10:161. [PMID: 19371429 PMCID: PMC2676304 DOI: 10.1186/1471-2164-10-161] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 04/16/2009] [Indexed: 12/11/2022] Open
Abstract
Background Microarrays revolutionized biological research by enabling gene expression comparisons on a transcriptome-wide scale. Microarrays, however, do not estimate absolute expression level accurately. At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown. Results In this study, we evaluate relative accuracy of microarrays and transcriptome sequencing (RNA-Seq) using third methodology: proteomics. We find that RNA-Seq provides a better estimate of absolute expression levels. Conclusion Our result shows that in terms of overall technical performance, RNA-Seq is the technique of choice for studies that require accurate estimation of absolute transcript levels.
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Affiliation(s)
- Xing Fu
- Key lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China.
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44
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Zhou H, Hou W, Denis NJ, Zhou H, Vasilescu J, Zou H, Figeys D. Glycoproteomic reactor for human plasma. J Proteome Res 2009; 8:556-66. [PMID: 19067587 DOI: 10.1021/pr800734r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the development of a glycoproteomic reactor that combines multiple biochemical and chemical protein processing into a single device for the study of N-glycosylated proteins. The glycoproteins are first enriched by concanavalin A affinity chromatography and then transferred onto and efficiently processed in the glycoproteomic reactor. This glycoproteomic reactor combines protein concentration and purification, disulfide bond reduction, peptide-N-glycosidase-mediated (18)O-labeling and deglycosylation, alkylation, tryptic digestion and pH based fractionation in a device that has an interstitial volume (reaction volume) of approximately 1 microL. We demonstrated the potential of the glycoproteomic reactor using human plasma. Under stringent criteria, 82 unique glycopeptides representing 41 unique glycoproteins were identified from as little as 5 microL of human plasma. Our glycoproteomic reactor reduces the sample processing time to less than 1.5 h, reduces the reagent consumption while providing over 1000-fold concentration of the sample, provides efficient removal of high concentration of glycan buffer, and, finally, allows both glycopeptides and nonglycosylated tryptic peptides to be analyzed by the mass spectrometer which provides much greater protein coverage and more reliable identifications.
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Affiliation(s)
- Hu Zhou
- Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
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45
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van de Meent MHM, de Jong GJ. Potential of long capillary monolithic columns for the analysis of protein digests. J Sep Sci 2009; 32:487-93. [DOI: 10.1002/jssc.200800520] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Dai J, Wang LS, Wu YB, Sheng QH, Wu JR, Shieh CH, Zeng R. Fully Automatic Separation and Identification of Phosphopeptides by Continuous pH-Gradient Anion Exchange Online Coupled with Reversed-Phase Liquid Chromatography Mass Spectrometry. J Proteome Res 2008; 8:133-41. [DOI: 10.1021/pr800381w] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- 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
| | - Lian-Shui Wang
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Bo Wu
- 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
| | - 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
| | - Chia-Hui Shieh
- 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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47
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Ning ZB, Li QR, Dai J, Li RX, Shieh CH, Zeng R. Fractionation of Complex Protein Mixture by Virtual Three-Dimensional Liquid Chromatography Based on Combined pH and Salt Steps. J Proteome Res 2008; 7:4525-37. [DOI: 10.1021/pr800318j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Zhi-Bin Ning
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Run Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jie Dai
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong-Xia Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chia-Hui Shieh
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
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48
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Dowell JA, Frost DC, Zhang J, Li L. Comparison of two-dimensional fractionation techniques for shotgun proteomics. Anal Chem 2008; 80:6715-23. [PMID: 18680313 DOI: 10.1021/ac8007994] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional (2D) fractionation is a commonly used tool to increase dynamic range and proteome coverage for bottom-up, shotgun proteomics. However, there are few reports comparing the relative separation efficiencies of 2D methodologies using low-microgram sample quantities. In order to systematically evaluate 2D separation techniques, we fractionated microgram quantities of E. coli protein extract by seven different methods. The first dimension of separation was performed with either reversed-phase high-pressure liquid chromatography (RP-HPLC), gel electrophoresis (SDS-PAGE), or strong cation exchange (SCX-HPLC). The second dimension consisted of a standard reversed-phase capillary HPLC coupled to an electrospray ionization quadrupole time-of-flight mass spectrometer for tandem mass spectrometric analysis. The overall performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The protein-level RP-HPLC and the high-pH RP-HPLC peptide-level separations performed the best, identifying 281 and 266 proteins, respectively. The online pH variance SCX and the SDS-PAGE returned modest performances with 178 and 139 proteins identified, respectively. The offline SCX had the worst performance with 81 proteins identified. We also examined various chromatographic factors that contribute to separation efficiency, including resolving power, orthogonality, and sample loss.
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Affiliation(s)
- James A Dowell
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
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49
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Zhao L, Wu R, Han G, Zhou H, Ren L, Tian R, Zou H. The highly selective capture of phosphopeptides by zirconium phosphonate-modified magnetic nanoparticles for phosphoproteome analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1176-1186. [PMID: 18502663 DOI: 10.1016/j.jasms.2008.04.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 04/09/2008] [Accepted: 04/11/2008] [Indexed: 05/26/2023]
Abstract
The highly selective capture of phosphopeptides from proteolytic digests is a great challenge for the identification of phosphoproteins by mass spectrometry. In this work, the zirconium phosphonate-modified magnetic Fe(3)O(4)/SiO(2) core/shell nanoparticles have been synthesized and successfully applied for the selective capture of phosphopeptides from complex tryptic digests of proteins before the analysis of MALDI-TOF mass spectrometry with the desired convenience of sample handling. The ratio of magnetic nanoparticle to protein and the incubation time for capturing phosphopeptides from complex proteolytic digests were investigated, and the optimized nanoparticle-to-protein ratio and incubation time were between 15:1 to 30:1 and 30 min, respectively. The excellent detection limit of 0.5 fmol beta-casein has been achieved by MALDI-TOF mass spectrometry with the specific capture of zirconium phosphonate-modified magnetic Fe(3)O(4) nanoparticles. The great specificity of zirconium phosphonate-modified magnetic Fe(3)O(4) nanoparticles to phosphopeptides was demonstrated by the selective capture of phosphopeptides from a complex tryptic digest of the mixture of alpha-casein and bovine serum albumin at molar ratio of 1 to 100 in MALDI-TOF-MS analysis. An application of the magnetic nanoparticles to selective capture phosphopeptides from a tryptic digest of mouse liver lysate was further carried out by combining with nano-LC-MS/MS and MS/MS/MS analyses, and a total of 194 unique phosphopeptides were successfully identified.
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Affiliation(s)
- Liang Zhao
- National Chromatographic R and A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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50
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Tang J, Gao M, Deng C, Zhang X. Recent development of multi-dimensional chromatography strategies in proteome research. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:123-32. [PMID: 18289947 PMCID: PMC7185551 DOI: 10.1016/j.jchromb.2008.01.029] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 01/15/2008] [Accepted: 01/18/2008] [Indexed: 11/23/2022]
Abstract
As a complementary approach to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), multi-dimensional chromatography separation methods have been widely applied in all kinds of biological sample investigations. Multi-dimensional liquid chromatography (MDLC) coupled with bio-mass spectrometry (MS) is playing important roles in proteome research due to its high speed, high resolution and high sensitivity. Proteome analysis strategies mainly include bottom-up and top-down approaches which carry out biological sample separation based on peptide and protein levels, respectively. Electrophoretic methods combined with liquid chromatography like IEF-HPLC and HPLC-SDS-PAGE have been successful applied for protein separations. As for MDLC strategy, ion-exchange chromatography (IEX) together with reversed phase liquid chromatography (RPLC) is still a most widely used chromatography in proteome analysis, other chromatographic methods are also frequently used in protein pre-fractionations, while affinity chromatography is usually adopted for specific functional protein analysis. Recent MDLC technologies and applications to variety of proteome analysis have been achieved great development. A digest peptide-based approach as so-called "bottom-up" and intact protein-based approach "top-down" analysis of proteome samples were briefly reviewed in this paper. The diversity of combinations of different chromatography modes to set up MDLC systems was demonstrated and discussed. Novel developments of MDLC techniques such as high-abundance protein depletion and chromatography array were also included in this review.
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Affiliation(s)
- Jia Tang
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Xiangming Zhang
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
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