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Du HL, Chen ZP, Song M, Chen Y, Yu RQ. Novel calibration model maintenance strategy for solving the signal instability in quantitative liquid chromatography–mass spectrometry. J Chromatogr A 2014; 1338:44-50. [DOI: 10.1016/j.chroma.2014.02.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
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Gao X, Wu H, Lee KC, Liu H, Zhao Y, Cai Z, Jiang Y. Stable Isotope N-Phosphorylation Labeling for Peptide de Novo Sequencing and Protein Quantification Based on Organic Phosphorus Chemistry. Anal Chem 2012; 84:10236-44. [DOI: 10.1021/ac301939v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xiang Gao
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Hanzhi Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
| | - Kim-Chung Lee
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
| | - Hongxia Liu
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yufen Zhao
- Department of Chemistry and The
Key Laboratory for Chemical Biology of Fujian Province, College of
Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People’s Republic of China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR, China
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yuyang Jiang
- The Key Laboratory
for Cancer
Metabolomics of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
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Boja ES, Rodriguez H. Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins. Proteomics 2012; 12:1093-110. [PMID: 22577011 DOI: 10.1002/pmic.201100387] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Traditional shotgun proteomics used to detect a mixture of hundreds to thousands of proteins through mass spectrometric analysis, has been the standard approach in research to profile protein content in a biological sample which could lead to the discovery of new (and all) protein candidates with diagnostic, prognostic, and therapeutic values. In practice, this approach requires significant resources and time, and does not necessarily represent the goal of the researcher who would rather study a subset of such discovered proteins (including their variations or posttranslational modifications) under different biological conditions. In this context, targeted proteomics is playing an increasingly important role in the accurate measurement of protein targets in biological samples in the hope of elucidating the molecular mechanism of cellular function via the understanding of intricate protein networks and pathways. One such (targeted) approach, selected reaction monitoring (or multiple reaction monitoring) mass spectrometry (MRM-MS), offers the capability of measuring multiple proteins with higher sensitivity and throughput than shotgun proteomics. Developing and validating MRM-MS-based assays, however, is an extensive and iterative process, requiring a coordinated and collaborative effort by the scientific community through the sharing of publicly accessible data and datasets, bioinformatic tools, standard operating procedures, and well characterized reagents.
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Affiliation(s)
- Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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López E, Madero L, López-Pascual J, Latterich M. Clinical proteomics and OMICS clues useful in translational medicine research. Proteome Sci 2012; 10:35. [PMID: 22642823 PMCID: PMC3536680 DOI: 10.1186/1477-5956-10-35] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 05/04/2012] [Indexed: 12/21/2022] Open
Abstract
Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems, spanning areas of basic biological research, clinical diagnostics, and biomarker discovery directed toward therapeutic applications. Recent advances in protein separation and identification techniques have significantly improved proteomic approaches, leading to enhancement of the depth and breadth of proteome coverage. Proteomic signatures, specific for multiple diseases, including cancer and pre-invasive lesions, are emerging. This article combines, in a simple manner, relevant proteomic and OMICS clues used in the discovery and development of diagnostic and prognostic biomarkers that are applicable to all clinical fields, thus helping to improve applications of clinical proteomic strategies for translational medicine research.
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Affiliation(s)
- Elena López
- Centro de Investigación i + 12, Hospital 12 de Octubre, Av, De Córdoba s/n, 28040, Madrid, Spain.
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López E, Muñoz SR, Pascual JL, Madero L. Relevant phosphoproteomic and mass spectrometry: approaches useful in clinical research. Clin Transl Med 2012; 1:2. [PMID: 23369602 PMCID: PMC3552569 DOI: 10.1186/2001-1326-1-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 03/29/2012] [Indexed: 01/03/2023] Open
Abstract
Background "It's not what we do, it's the way that we do it". Never has this maxim been truer in proteomics than now. Mass Spectrometry-based proteomics/phosphoproteomics tools are critical to understand the structure and dynamics (spatial and temporal) of signalling that engages and migrates through the entire proteome. Approaches such as affinity purification followed by Mass Spectrometry (MS) have been used to elucidate relevant biological questions disease vs. health. Thousands of proteins interact via physical and chemical association. Moreover, certain proteins can covalently modify other proteins post-translationally. These post-translational modifications (PTMs) ultimately give rise to the emergent functions of cells in sequence, space and time. Findings Understanding the functions of phosphorylated proteins thus requires one to study proteomes as linked-systems rather than collections of individual protein molecules. Indeed, the interacting proteome or protein-network knowledge has recently received much attention, as network-systems (signalling pathways) are effective snapshots in time, of the proteome as a whole. MS approaches are clearly essential, in spite of the difficulties of some low abundance proteins for future clinical advances. Conclusion Clinical proteomics-MS has come a long way in the past decade in terms of technology/platform development, protein chemistry, and together with bioinformatics and other OMICS tools to identify molecular signatures of diseases based on protein pathways and signalling cascades. Hence, there is great promise for disease diagnosis, prognosis, and prediction of therapeutic outcome on an individualized basis. However, and as a general rule, without correct study design, strategy and implementation of robust analytical methodologies, the efforts, efficiency and expectations to make biomarkers (especially phosphorylated kinases) a useful reality in the near future, can easily be hampered.
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Affiliation(s)
- Elena López
- Hospital Universitario Infantil Niño Jesús, Av, Menéndez Pelayo 65, 28009 Madrid, Spain.
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Chen CJ, Chen WY, Tseng MC, Chen YR. Tunnel frit: a nonmetallic in-capillary frit for nanoflow ultra high-performance liquid chromatography-mass spectrometryapplications. Anal Chem 2011; 84:297-303. [PMID: 22097963 DOI: 10.1021/ac202549y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this study, an easy method to fabricate a durable in-capillary frit was developed for use in nanoflow liquid chromatography (nanoLC). A small orifice was tunneled into the sol-gel frit during the polymerization process resulting in the simple fabrication of a tunnel frit. A short packing tunnel frit column (2 cm, C(18) particles) was able to sustain over 10,000 psi continuous liquid flow for 10 days without observation of particle loss, and back pressure variation was less than 5%. The tunnel frit was successfully applied to the fabrication of nanoflow ultra high-performance liquid chromatography (nano-UHPLC) trap and analytical columns. In the analysis of tryptic peptides, the tunnel frit trap and analytical columns were demonstrated to have high separation efficiency and sensitivity. In analysis of phosphopeptides, the use of the nonmetallic tunnel frit column showed better sensitivity than the metallic frit column. This design can facilitate the preparation of nano-HPLC and nano-UHPLC columns and the packing material can easily be refilled when the column is severely contaminated or clogged.
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Affiliation(s)
- Chao-Jung Chen
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
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Ning Z, Zhou H, Wang F, Abu-Farha M, Figeys D. Analytical Aspects of Proteomics: 2009–2010. Anal Chem 2011; 83:4407-26. [DOI: 10.1021/ac200857t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China 116023
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Boja ES, Rodriguez H. The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science. Ann Lab Med 2011; 31:61-71. [PMID: 21474978 PMCID: PMC3116002 DOI: 10.3343/kjlm.2011.31.2.61] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 01/21/2011] [Accepted: 02/23/2011] [Indexed: 12/22/2022] Open
Abstract
Better biomarkers are urgently needed to cancer detection, diagnosis, and prognosis. While the genomics community is making significant advances in understanding the molecular basis of disease, proteomics will delineate the functional units of a cell, proteins and their intricate interaction network and signaling pathways for the underlying disease. Great progress has been made to characterize thousands of proteins qualitatively and quantitatively in complex biological systems by utilizing multi-dimensional sample fractionation strategies, mass spectrometry and protein microarrays. Comparative/quantitative analysis of high-quality clinical biospecimen (e.g., tissue and biofluids) of human cancer proteome landscape has the potential to reveal protein/peptide biomarkers responsible for this disease by means of their altered levels of expression, post-translational modifications as well as different forms of protein variants. Despite technological advances in proteomics, major hurdles still exist in every step of the biomarker development pipeline. The National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) has taken a critical step to close the gap between biomarker discovery and qualification by introducing a pre-clinical "verification" stage in the pipeline, partnering with clinical laboratory organizations to develop and implement common standards, and developing regulatory science documents with the US Food and Drug Administration to educate the proteomics community on analytical evaluation requirements for multiplex assays in order to ensure the safety and effectiveness of these tests for their intended use.
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Affiliation(s)
- Emily S. Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Boja E, Rivers R, Kinsinger C, Mesri M, Hiltke T, Rahbar A, Rodriguez H. Restructuring proteomics through verification. Biomark Med 2010; 4:799-803. [PMID: 21133699 PMCID: PMC3041639 DOI: 10.2217/bmm.10.92] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Proteomics technologies have revolutionized cell biology and biochemistry by providing powerful new tools to characterize complex proteomes, multiprotein complexes and post-translational modifications. Although proteomics technologies could address important problems in clinical and translational cancer research, attempts to use proteomics approaches to discover cancer biomarkers in biofluids and tissues have been largely unsuccessful and have given rise to considerable skepticism. The National Cancer Institute has taken a leading role in facilitating the translation of proteomics from research to clinical application, through its Clinical Proteomic Technologies for Cancer. This article highlights the building of a more reliable and efficient protein biomarker development pipeline that incorporates three steps: discovery, verification and qualification. In addition, we discuss the merits of multiple reaction monitoring mass spectrometry, a multiplex targeted proteomics platform, which has emerged as a potentially promising, high-throughput protein biomarker measurements technology for preclinical 'verification'.
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Affiliation(s)
- Emily Boja
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
| | - Robert Rivers
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
| | - Christopher Kinsinger
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
| | - Amir Rahbar
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
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