1
|
Zhao Y, Zhao X, Duan L, Hou R, Gu Y, Liu Z, Chen J, Wu F, Yang L, Le XC, Wang Q, Yan X. Reinvent Aliphatic Arsenicals as Reversible Covalent Warheads toward Targeted Kinase Inhibition and Non-acute Promyelocytic Leukemia Cancer Treatment. J Med Chem 2024; 67:5458-5472. [PMID: 38556750 DOI: 10.1021/acs.jmedchem.3c02076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The success of arsenic in acute promyelocytic leukemia (APL) treatment is hardly transferred to non-APL cancers, mainly due to the low selectivity and weak binding affinity of traditional arsenicals to oncoproteins critical for cancer survival. We present herein the reinvention of aliphatic trivalent arsenicals (As) as reversible covalent warheads of As-based targeting inhibitors toward Bruton's tyrosine kinase (BTK). The effects of As warheads' valency, thiol protection, methylation, spacer length, and size on inhibitors' activity were studied. We found that, in contrast to the bulky and rigid aromatic As warhead, the flexible aliphatic As warheads were well compatible with the well-optimized guiding group to achieve nanomolar inhibition against BTK. The optimized As inhibitors effectively blocked the BTK-mediated oncogenic signaling pathway, leading to elevated antiproliferative activities toward lymphoma cells and xenograft tumor. Our study provides a promising strategy enabling rational design of new aliphatic arsenic-based reversible covalent inhibitors toward non-APL cancer treatment.
Collapse
Affiliation(s)
- Yang Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xinyue Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lewei Duan
- Laboratory of Epigenetics at Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
| | - Ruxue Hou
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuxin Gu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Liu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianbin Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Feizhen Wu
- Laboratory of Epigenetics at Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Limin Yang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Qiuquan Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaowen Yan
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| |
Collapse
|
2
|
Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
Collapse
Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| |
Collapse
|
3
|
Li X, Sun B, Zhu J, Qian M, Chen Y. Construction of a Mass-Tagged Oligo Probe Set for Revealing Protein Ratiometric Relationship Associated with EGFR-HER2 Heterodimerization in Living Cells. Anal Chem 2022; 94:8838-8846. [PMID: 35709389 DOI: 10.1021/acs.analchem.1c04989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein dimerization, as the most common form of protein-protein interaction, can manifest more significant roles in cellular signaling than individual monomers. For example, excessive formation of EGFR-HER2 dimer has been implicated in cancer development and therapeutic resistance in addition to the overexpression of EGFR and HER2 proteins. Thus, quantitative evaluation of these heterodimers in living cells and revelation of their ratiometric relationship with protein monomers in dimerization may provide insights into clinical cancer management. To achieve this goal, the prerequisite is protein heterodimer quantification. Given the current lack of quantitative methods, we constructed a mass-tagged oligo nanoprobe set for quantification of EGFR-HER2 dimer in living cells. The mass-tagged oligo nanoprobe set contained two targeting probes (nucleic acid aptamers), a connector probe, a hairpin probe, and a photocleavable mass-tagged probe. Two distinct aptamers can recognize target protein monomers and initiate the subsequent hybridization cascade involving binding to the connector probe, formation of an initiator strand, opening of a hairpin probe, and ensuing hybridization with a photocleavable mass-tagged probe. Ultimately, the mass tag was released under ultraviolet light and then subjected to mass spectrometric analysis. In this way, the information regarding the interaction between two protein monomers was successfully converted to the quantitative signal of the mass tag. Using the assay, the expression level of EGFR-HER2 dimer and its relationship with individual protein monomers were determined in four breast cancer cell lines. We are among the first to obtain the absolute level of protein heterodimer, and this quantitative information may be vital in understanding the molecular basis of cancer.
Collapse
Affiliation(s)
- Xiaoxu Li
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Bo Sun
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.,Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang 222002, China
| | - Jianhua Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Moting Qian
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.,State Key Laboratory of Reproductive Medicine, Nanjing 210029, China.,Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Nanjing 211166, China
| |
Collapse
|
4
|
Hu Y, Wang Z, Liu L, Zhu J, Zhang D, Xu M, Zhang Y, Xu F, Chen Y. Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine. Chem Sci 2021; 12:7993-8009. [PMID: 34257858 PMCID: PMC8230026 DOI: 10.1039/d1sc00271f] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering "what", "where", "how many" and "whose" chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.
Collapse
Affiliation(s)
- Yechen Hu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Zhongcheng Wang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University Wuhan 430071 China
| | - Jianhua Zhu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Dongxue Zhang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Mengying Xu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Yuanyuan Zhang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- State Key Laboratory of Reproductive Medicine, Key Laboratory of Cardiovascular & Cerebrovascular Medicine Nanjing 210029 China
| |
Collapse
|
5
|
Pero-Gascon R, Giménez E, Sanz-Nebot V, Benavente F. Enrichment of histidine containing peptides by on-line immobilised metal affinity solid-phase extraction capillary electrophoresis-mass spectrometry. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
6
|
Neubert H, Shuford CM, Olah TV, Garofolo F, Schultz GA, Jones BR, Amaravadi L, Laterza OF, Xu K, Ackermann BL. Protein Biomarker Quantification by Immunoaffinity Liquid Chromatography–Tandem Mass Spectrometry: Current State and Future Vision. Clin Chem 2020; 66:282-301. [DOI: 10.1093/clinchem/hvz022] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 12/19/2022]
Abstract
Abstract
Immunoaffinity–mass spectrometry (IA-MS) is an emerging analytical genre with several advantages for profiling and determination of protein biomarkers. Because IA-MS combines affinity capture, analogous to ligand binding assays (LBAs), with mass spectrometry (MS) detection, this platform is often described using the term hybrid methods. The purpose of this report is to provide an overview of the principles of IA-MS and to demonstrate, through application, the unique power and potential of this technology. By combining target immunoaffinity enrichment with the use of stable isotope-labeled internal standards and MS detection, IA-MS achieves high sensitivity while providing unparalleled specificity for the quantification of protein biomarkers in fluids and tissues. In recent years, significant uptake of IA-MS has occurred in the pharmaceutical industry, particularly in the early stages of clinical development, enabling biomarker measurement previously considered unattainable. By comparison, IA-MS adoption by CLIA laboratories has occurred more slowly. Current barriers to IA-MS use and opportunities for expanded adoption are discussed. The path forward involves identifying applications for which IA-MS is the best option compared with LBA or MS technologies alone. IA-MS will continue to benefit from advances in reagent generation, more sensitive and higher throughput MS technologies, and continued growth in use by the broader analytical community. Collectively, the pursuit of these opportunities will secure expanded long-term use of IA-MS for clinical applications.
Collapse
|
7
|
Quantitation of Glycopeptides by ESI/MS - size of the peptide part strongly affects the relative proportions and allows discovery of new glycan compositions of Ceruloplasmin. Glycoconj J 2019; 36:13-26. [PMID: 30612270 DOI: 10.1007/s10719-018-9852-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
Abstract
Significant changes of glycan structures are observed in humans if diseases like cancer, arthritis or inflammation are present. Thus, interest in biomarkers based on glycan structures has rapidly emerged in recent years and monitoring disease specific changes of glycosylation and their quantification is of great interest. Mass spectrometry is most commonly used to characterize and quantify glycopeptides and glycans liberated from the glycoprotein of interest. However, ionization properties of glycopeptides can strongly depend on their composition and can therefore lead to intensities that do not reflect the actual proportions present in the intact glycoprotein. Here we show that an increase in the length of the peptide can lead to a more accurate determination and quantification of the glycans. The four glycosylation sites of human serum ceruloplasmin from 17 different individuals were analyzed using glycopeptides of varying peptide lengths, obtained by action of different proteases and by limited digestion. In most cases, highly sialylated compositions showed an increased relative abundance with increasing peptide length. We observed a relative increase of triantennary glycans of up to a factor of three and, even more, MS peaks corresponding to tetraantennary compositions on ceruloplasmin at glycosite 137N in all 17 samples, which we did not detect using a bottom up approach. The data presented here leads to the conclusion that a middle down - or when possible a top down - approach is favorable for qualitative and quantitative analysis of the glycosylation of glycoproteins.
Collapse
|
8
|
Cao T, Lv J, Zhang L, Yan G, Lu H. Selective Enrichment and Quantification of N-Terminal Glycine Peptides via Sortase A Mediated Ligation. Anal Chem 2018; 90:14303-14308. [DOI: 10.1021/acs.analchem.8b03562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
9
|
Calderón-Celis F, Encinar JR. A reflection on the role of ICP-MS in proteomics: Update and future perspective. J Proteomics 2018; 198:11-17. [PMID: 30445180 DOI: 10.1016/j.jprot.2018.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/08/2018] [Accepted: 11/11/2018] [Indexed: 01/02/2023]
Abstract
Mass spectrometry is the technique of reference for the identification and quantification of proteins. Whereas ESI and MALDI ionization sources are inherently not quantitative being highly influenced by the chemical nature of the analyte and the matrix, ICP-MS uses a hard ionization source that destroys proteins into its atoms and measures the elemental signal, which is independent of its chemical environment. As a consequence, ICP-MS turns up as an excellent technique for the screening, mapping and quantification of peptides and proteins in a sample through elemental detection (any element but C, H, N, or O) once they have been previously separated by chromatography. In this time, great efforts have been put in developing instrumentation and new methodologies that enable a better, more efficient, and more useful analysis of proteins with ICP-MS. Moreover, quantitative capabilities but lack of molecular information of ICP has led to a synergic relationship both with identifying capabilities of ESI-MS, or the use of protein-specific antibodies carrying an elemental label. JOURNAL SIGNIFICANCE: We are delighted to participate in this special issue and have the chance to congratulate Journal of Proteomics for its 10th Anniversary, and wish for many further successful anniversaries. During this last decade, Journal of Proteomics has been a clear promotor of works integrating ICP-MS for proteomics analysis. In fact, already in 2009, a review was published by invitation of the editor in chief focused on the established and potential role of ICP-MS in different areas of the proteomics analysis at the time: "The emerging role of ICP-MS in proteomics" [1]. Even though ICP-MS is not fully known or acknowledged in the proteomics world yet, its impact was significant as demonstrated by the really high interest in such publication (over 150 citations). Since then, several excellent papers relating to ICP-MS applications in proteomics have been published in this journal. Following the trend, we expect through this personal view of the current standing of ICP-MS in proteomics to enlighten the readers of Journal of Proteomics with a vision of the full present and future potential of ICP-MS in proteomics.
Collapse
Affiliation(s)
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Spain.
| |
Collapse
|
10
|
Dahabiyeh LA. The discovery of protein biomarkers in pre-eclampsia: the promising role of mass spectrometry. Biomarkers 2018; 23:609-621. [DOI: 10.1080/1354750x.2018.1474257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lina A. Dahabiyeh
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
| |
Collapse
|
11
|
Calvete JJ, Petras D, Calderón-Celis F, Lomonte B, Encinar JR, Sanz-Medel A. Protein-species quantitative venomics: looking through a crystal ball. J Venom Anim Toxins Incl Trop Dis 2017; 23:27. [PMID: 28465678 PMCID: PMC5408492 DOI: 10.1186/s40409-017-0116-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/19/2017] [Indexed: 12/16/2022] Open
Abstract
In this paper we discuss recent significant developments in the field of venom research, specifically the emergence of top-down proteomic applications that allow achieving compositional resolution at the level of the protein species present in the venom, and the absolute quantification of the venom proteins (the term “protein species” is used here to refer to all the different molecular forms in which a protein can be found. Please consult the special issue of Jornal of Proteomics “Towards deciphering proteomes via the proteoform, protein speciation, moonlighting and protein code concepts” published in 2016, vol. 134, pages 1-202). Challenges remain to be solved in order to achieve a compact and automated platform with which to routinely carry out comprehensive quantitative analysis of all toxins present in a venom. This short essay reflects the authors’ view of the immediate future in this direction for the proteomic analysis of venoms, particularly of snakes.
Collapse
Affiliation(s)
- Juan J Calvete
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, C.S.I.C, Jaime Roig 11, 46010 Valencia, Spain
| | - Daniel Petras
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA USA
| | | | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| |
Collapse
|
12
|
Ciccimaro E, Zhu Y, Ostanin D, Suchard S, MacGuire J, Xiao Q, Dongre A, Chimalakonda A, Olah T, Shipkova P. Antibody Drug-Target Engagement Measurement in Tissue Using Quantitative Affinity Extraction Liquid Chromatography–Mass Spectrometry: Method Development and Qualification. Anal Chem 2017; 89:5115-5123. [DOI: 10.1021/acs.analchem.7b00688] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Eugene Ciccimaro
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Yongxin Zhu
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Dmitry Ostanin
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Suzanne Suchard
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Jamus MacGuire
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Qing Xiao
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Ashok Dongre
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | | | - Timothy Olah
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Petia Shipkova
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| |
Collapse
|
13
|
Calderón-Celis F, Diez-Fernández S, Costa-Fernández JM, Encinar JR, Calvete JJ, Sanz-Medel A. Elemental Mass Spectrometry for Absolute Intact Protein Quantification without Protein-Specific Standards: Application to Snake Venomics. Anal Chem 2016; 88:9699-9706. [PMID: 27593495 DOI: 10.1021/acs.analchem.6b02585] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Absolute protein quantification methods based on molecular mass spectrometry usually require stable isotope-labeled analogous standards for each target protein or peptide under study, which in turn must be certified using natural standards. In this work, we report a direct and accurate methodology based on capLC-ICP-QQQ and online isotope dilution analysis for the absolute and sensitive quantification of intact proteins. The combination of the postcolumn addition of 34S and a generic S-containing internal standard spiked to the sample provides full compound independent detector response and thus protein quantification without the need for specific standards. Quantitative recoveries, using a chromatographic core-shell C4 column for the various protein species assayed were obtained (96-100%). Thus, the proposed strategy enables the accurate quantification of proteins even if no specific standards are available for them. In addition, to the best of our knowledge, we obtained the lowest detection limits reported in the quantitative analysis of intact proteins by direct measurement of sulfur with ICPMS (358 fmol) and protein (ranging from 7 to 15 fmol depending on the assayed protein). The quantitative results for individual and simple mixtures of model proteins were statistically indistinguishable from the manufacturer's values. Finally, the suitability of the strategy for real sample analysis (including quantitative protein recovery from the column) was illustrated for the individual absolute quantification of the proteins and whole protein content in a venom sample. Parallel capLC-ESI-QTOF analysis was employed to identify the proteins, a prerequisite to translate the mass of quantified S for each chromatographic peak into individual protein mass.
Collapse
Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Silvia Diez-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| |
Collapse
|
14
|
Mesmin C, van Oostrum J, Domon B. Complexity reduction of clinical samples for routine mass spectrometric analysis. Proteomics Clin Appl 2016; 10:315-22. [PMID: 26680238 DOI: 10.1002/prca.201500135] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/26/2015] [Accepted: 12/09/2015] [Indexed: 01/05/2023]
Abstract
The precise measurement of protein abundance levels in highly complex biological samples such as plasma remains challenging. The wide range of protein concentrations impairs the detection of low-abundant species and the high number of peptide components to analyze results in interferences leading to erroneous quantitative results. The advances in MS instrumentation, with improved selectivity and sensitivity, partially address these issues, but sample preparation techniques remain the pivotal element to obtain robust routine mass spectrometric assays with a low LOD. A number of methodologies have been proposed and refined over the past two decades to reduce the range of protein concentrations and the number of peptide components. Whereas most of the methods have proven their utility for discovery studies, only a few are actually applicable to routine quantitative studies. In this account, common protein- and peptide-based fractionation methods are discussed, and illustrated with practical examples, with a focus on methods suited for clinical samples scheduled for biomarker validation assays and subsequent routine clinical mass spectrometric analyses.
Collapse
Affiliation(s)
- Cédric Mesmin
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Jan van Oostrum
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| |
Collapse
|
15
|
Dong M, Bian Y, Dong J, Wang K, Liu Z, Qin H, Ye M, Zou H. Selective Enrichment of Cysteine-Containing Phosphopeptides for Subphosphoproteome Analysis. J Proteome Res 2015; 14:5341-7. [PMID: 26552605 DOI: 10.1021/acs.jproteome.5b00830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the natural amino acids, cysteine is unique since it can form a disulfide bond through oxidation and reduction of sulfhydryl and thus plays a pervasive role in modulation of proteins activities and structures. Crosstalk between phosphorylation and other post-translational modifications has become a recurrent theme in cell signaling regulation. However, the crosstalk between the phosphorylation and the formation and reductive cleavage of disulfide bond has not been investigated so far. To facilitate the study of this crosstalk, it is important to explore the subset of phosphoproteome where phosphorylations are occurred near to cysteine in the protein sequences. In this study, we developed a straightforward sequential enrichment method by combining the thiol affinity chromatography with the immobilized titanium ion affinity chromatography to selectively enrich cysteine-containing phosphopeptides. The high specificity and high sensitivity of this method were demonstrated by analyzing the samples of Jurkat cells. This "divide and conquer" strategy by specific analysis of a subphosphoproteome enables identification of more low abundant phosphosites than the conventional global phosphoproteome approach. Interestingly, amino acid residues surrounding the identified phosphosites were enriched with buried residues (L, V, A, C) while depleted with exposed residues (D, E, R, K). Also, the phosphosites identified by this approach showed a dramatic decrease in locating in disorder regions compared to that identified by conventional global phosphoproteome. Further analysis showed that more proline directed kinases and fewer acidophilic kinases were responsible for the phosphorylation sites of this subphosphoproteome.
Collapse
Affiliation(s)
- Mingming Dong
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Dong
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Keyun Wang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheyi Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| |
Collapse
|
16
|
Yao Y, Huang J, Cheng K, Pan Y, Qin H, Ye M, Zou H. Specific Enrichment of Peptides with N-Terminal Serine/Threonine by a Solid-Phase Capture-Release Approach for Efficient Proteomics Analysis. Anal Chem 2015; 87:11353-60. [DOI: 10.1021/acs.analchem.5b02711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yating Yao
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junfeng Huang
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Cheng
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanbo Pan
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongqiang Qin
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Mingliang Ye
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Hanfa Zou
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| |
Collapse
|
17
|
Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LCJ, Wollscheid B, Zhang H, Aebersold R. Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics 2014; 13:1753-68. [PMID: 24741114 PMCID: PMC4083113 DOI: 10.1074/mcp.m114.038273] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/04/2014] [Indexed: 12/31/2022] Open
Abstract
The identification of biomarkers indicating the level of aggressiveness of prostate cancer (PCa) will address the urgent clinical need to minimize the general overtreatment of patients with non-aggressive PCa, who account for the majority of PCa cases. Here, we isolated formerly N-linked glycopeptides from normal prostate (n = 10) and from non-aggressive (n = 24), aggressive (n = 16), and metastatic (n = 25) PCa tumor tissues and analyzed the samples using SWATH mass spectrometry, an emerging data-independent acquisition method that generates a single file containing fragment ion spectra of all ionized species of a sample. The resulting datasets were searched using a targeted data analysis strategy in which an a priori spectral reference library representing known N-glycosites of the human proteome was used to identify groups of signals in the SWATH mass spectrometry data. On average we identified 1430 N-glycosites from each sample. Out of those, 220 glycoproteins showed significant quantitative changes associated with diverse biological processes involved in PCa aggressiveness and metastasis and indicated functional relationships. Two glycoproteins, N-acylethanolamine acid amidase and protein tyrosine kinase 7, that were significantly associated with aggressive PCa in the initial sample cohort were further validated in an independent set of patient tissues using tissue microarray analysis. The results suggest that N-acylethanolamine acid amidase and protein tyrosine kinase 7 may be used as potential tissue biomarkers to avoid overtreatment of non-aggressive PCa.
Collapse
Affiliation(s)
- Yansheng Liu
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jing Chen
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Atul Sethi
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Qing K Li
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Lijun Chen
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Ben Collins
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ludovic C J Gillet
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bernd Wollscheid
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Hui Zhang
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231;
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; **Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
18
|
Affiliation(s)
- Hui Zhang
- Institute for Systems Biology, Seattle, WA 98103, USA.
| |
Collapse
|
19
|
Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
20
|
Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
Collapse
Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | | | | | | |
Collapse
|
21
|
Meding S, Martin K, Gustafsson OJR, Eddes JS, Hack S, Oehler MK, Hoffmann P. Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues. J Proteome Res 2012; 12:308-15. [PMID: 23214983 DOI: 10.1021/pr300996x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MALDI imaging mass spectrometry is a powerful tool for morphology-based proteomic tissue analysis. However, peptide identification is still a major challenge due to low S/N ratios, low mass accuracy and difficulties in correlating observed m/z species with peptide identities. To address this, we have analyzed tryptic digests of formalin-fixed paraffin-embedded tissue microarray cores, from 31 ovarian cancer patients, by LC-MS/MS. The sample preparation closely resembled the MALDI imaging workflow in order to create representative reference data sets containing peptides also observable in MALDI imaging experiments. This resulted in 3844 distinct peptide sequences, at a false discovery rate of 1%, for the entire cohort and an average of 982 distinct peptide sequences per sample. From this, a total of 840 proteins and, on average, 297 proteins per sample could be inferred. To support the efforts of the Chromosome-centric Human Proteome Project Consortium, we have annotated these proteins with their respective chromosome location. In the presented work, the benefit of using a large cohort of data sets was exemplified by correct identification of several m/z species observed in a MALDI imaging experiment. The tryptic peptide data sets generated will facilitate peptide identification in future MALDI imaging studies on ovarian cancer.
Collapse
Affiliation(s)
- Stephan Meding
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, SA 5005, Adelaide, Australia
| | | | | | | | | | | | | |
Collapse
|
22
|
Xu M, Yang L, Wang Q. A Way to Probe the Microenvironment of Free Sulfhydryls in Intact Proteins with a Series of Monofunctional Organic Mercurials. Chemistry 2012; 18:13989-93. [DOI: 10.1002/chem.201200901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 08/08/2012] [Indexed: 11/10/2022]
|
23
|
Corso G, Gelzo M, Chambery A, Severino V, Maro AD, Lomoriello FS, D'Apolito O, Russo AD, Gargiulo P, Piccioli C, Arcari P. Characterization of pigments and ligands in a wall painting fragment from Liternum archaeological park (Italy). J Sep Sci 2012; 35:2986-93. [DOI: 10.1002/jssc.201200490] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 07/16/2012] [Accepted: 07/23/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Gaetano Corso
- Dipartimento di Biochimica e Biotecnologie Mediche; Università di Napoli Federico II; Napoli Italy
- Dipartimento di Scienze Biomediche; Università di Foggia; Foggia Italy
| | - Monica Gelzo
- Dipartimento di Biochimica e Biotecnologie Mediche; Università di Napoli Federico II; Napoli Italy
| | - Angela Chambery
- Dipartimento di Scienze per la Vita; Seconda Università di Napoli; Caserta Italy
| | - Valeria Severino
- Dipartimento di Scienze per la Vita; Seconda Università di Napoli; Caserta Italy
| | - Antimo Di Maro
- Dipartimento di Scienze per la Vita; Seconda Università di Napoli; Caserta Italy
| | | | - Oceania D'Apolito
- Dipartimento di Scienze Biomediche; Università di Foggia; Foggia Italy
| | - Antonio Dello Russo
- Dipartimento di Biochimica e Biotecnologie Mediche; Università di Napoli Federico II; Napoli Italy
| | - Patrizia Gargiulo
- Soprintendenza per i beni archeologici di Napoli e Caserta; Napoli Italy
| | | | - Paolo Arcari
- Dipartimento di Biochimica e Biotecnologie Mediche; Università di Napoli Federico II; Napoli Italy
- CEINGE - Biotecnologie Avanzate s.c.a.r.l; Napoli Italy
| |
Collapse
|
24
|
Tan HT, Lee YH, Chung MCM. Cancer proteomics. MASS SPECTROMETRY REVIEWS 2012; 31:583-605. [PMID: 22422534 DOI: 10.1002/mas.20356] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/16/2011] [Accepted: 11/16/2011] [Indexed: 05/31/2023]
Abstract
Cancer presents high mortality and morbidity globally, largely due to its complex and heterogenous nature, and lack of biomarkers for early diagnosis. A proteomics study of cancer aims to identify and characterize functional proteins that drive the transformation of malignancy, and to discover biomarkers to detect early-stage cancer, predict prognosis, determine therapy efficacy, identify novel drug targets, and ultimately develop personalized medicine. The various sources of human samples such as cell lines, tissues, and plasma/serum are probed by a plethora of proteomics tools to discover novel biomarkers and elucidate mechanisms of tumorigenesis. Innovative proteomics technologies and strategies have been designed for protein identification, quantitation, fractionation, and enrichment to delve deeper into the oncoproteome. In addition, there is the need for high-throughput methods for biomarker validation, and integration of the various platforms of oncoproteome data to fully comprehend cancer biology.
Collapse
Affiliation(s)
- Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | | |
Collapse
|
25
|
Pröfrock D, Prange A. Inductively coupled plasma-mass spectrometry (ICP-MS) for quantitative analysis in environmental and life sciences: a review of challenges, solutions, and trends. APPLIED SPECTROSCOPY 2012; 66:843-68. [PMID: 22800465 DOI: 10.1366/12-06681] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This focal point review provides an overview of recent developments and capabilities of inductively coupled plasma mass spectrometry (ICP-MS) coupled with different separation techniques for applications in the fields of quantitative environmental and bio-analysis. Over the past years numerous technical improvements, which are highlighted in this review, have helped to promote the evolution of ICP-MS to one of the most versatile tools for elemental quantification. In particular, the benefits and possibilities of using state-of-the-art hyphenated ICP-MS approaches for quantitative analysis are demonstrated with a focus on environmental and bio-analytical applications.
Collapse
Affiliation(s)
- Daniel Pröfrock
- Helmholtz Zentrum Geesthacht-Zentrum für Material und Küstenforschung, Department Marine Bioanalytical Chemistry, Max-Planck Str. 1, 21502 Geesthacht, Germany.
| | | |
Collapse
|
26
|
Abstract
A newcomer to the -omics era, proteomics, is a broad instrument-intensive research area that has advanced rapidly since its inception less than 20 years ago. Although the 'wet-bench' aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techniques, including various improvements in two-dimensional gel electrophoresis and gel-free or off-gel protein focusing, it has been the seminal advances in MS that have led to the ascension of this field. Recent improvements in sensitivity, mass accuracy and fragmentation have led to achievements previously only dreamed of, including whole-proteome identification, and quantification and extensive mapping of specific PTMs (post-translational modifications). With such capabilities at present, one might conclude that proteomics has already reached its zenith; however, 'capability' indicates that the envisioned goals have not yet been achieved. In the present review we focus on what we perceive as the areas requiring more attention to achieve the improvements in workflow and instrumentation that will bridge the gap between capability and achievement for at least most proteomes and PTMs. Additionally, it is essential that we extend our ability to understand protein structures, interactions and localizations. Towards these ends, we briefly focus on selected methods and research areas where we anticipate the next wave of proteomic advances.
Collapse
|
27
|
Baracat-Pereira MC, de Oliveira Barbosa M, Magalhães MJ, Carrijo LC, Games PD, Almeida HO, Sena Netto JF, Pereira MR, de Barros EG. Separomics applied to the proteomics and peptidomics of low-abundance proteins: Choice of methods and challenges - A review. Genet Mol Biol 2012; 35:283-91. [PMID: 22802713 PMCID: PMC3392880 DOI: 10.1590/s1415-47572012000200009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The enrichment and isolation of proteins are considered limiting steps in proteomic studies. Identification of proteins whose expression is transient, those that are of low-abundance, and of natural peptides not described in databases, is still a great challenge. Plant extracts are in general complex, and contaminants interfere with the identification of proteins involved in important physiological processes, such as plant defense against pathogens. This review discusses the challenges and strategies of separomics applied to the identification of low-abundance proteins and peptides in plants, especially in plants challenged by pathogens. Separomics is described as a group of methodological strategies for the separation of protein molecules for proteomics. Several tools have been used to remove highly abundant proteins from samples and also non-protein contaminants. The use of chromatographic techniques, the partition of the proteome into subproteomes, and an effort to isolate proteins in their native form have allowed the isolation and identification of rare proteins involved in different processes.
Collapse
Affiliation(s)
- Maria Cristina Baracat-Pereira
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Meire de Oliveira Barbosa
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcos Jorge Magalhães
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Lanna Clicia Carrijo
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Patrícia Dias Games
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Hebréia Oliveira Almeida
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José Fabiano Sena Netto
- Departamento de Bioquímica e Biologia Molecular, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | |
Collapse
|
28
|
Wu Q, Yuan H, Zhang L, Zhang Y. Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review. Anal Chim Acta 2012; 731:1-10. [PMID: 22652259 DOI: 10.1016/j.aca.2012.04.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/09/2012] [Accepted: 04/09/2012] [Indexed: 02/08/2023]
Abstract
With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.
Collapse
Affiliation(s)
- Qi Wu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | | | | | | |
Collapse
|
29
|
Polar and non-polar organic binder characterization in Pompeian wall paintings: comparison to a simulated painting mimicking an “a secco” technique. Anal Bioanal Chem 2012; 402:3011-6. [DOI: 10.1007/s00216-012-5746-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/28/2011] [Accepted: 01/13/2012] [Indexed: 10/14/2022]
|
30
|
Qiao L, Su F, Bi H, Girault HH, Liu B. Ga2O3 photocatalyzed on-line tagging of cysteine to facilitate peptide mass fingerprinting. Proteomics 2011; 11:3501-9. [DOI: 10.1002/pmic.201100208] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 04/20/2011] [Accepted: 06/08/2011] [Indexed: 11/06/2022]
|
31
|
Hartlova A, Krocova Z, Cerveny L, Stulik J. A proteomic view of the host-pathogen interaction: The host perspective. Proteomics 2011; 11:3212-20. [PMID: 21726044 DOI: 10.1002/pmic.201000767] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 04/05/2011] [Accepted: 04/19/2011] [Indexed: 01/25/2023]
Abstract
The host-pathogen interaction represents a complex and dynamic biological system. The outcome of this interaction is dependent on the microbial pathogen properties to establish infection and the ability of the host to control infection. Although bacterial pathogens have evolved a variety of strategies to subvert host defense functions, several general mechanisms have been shown to be shared among these pathogens. As a result, host effectors that are critical for pathogen entry, survival and replication inside the host cells have become a new paradigm for antimicrobial targeting. This review focuses on the potential utility of a proteomics approach in defining the host-pathogen interaction from the host's perspective.
Collapse
Affiliation(s)
- Anetta Hartlova
- Centre of Advanced Studies, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | | | | | | |
Collapse
|
32
|
Giron P, Dayon L, Sanchez JC. Cysteine tagging for MS-based proteomics. MASS SPECTROMETRY REVIEWS 2011; 30:366-395. [PMID: 21500242 DOI: 10.1002/mas.20285] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 05/30/2023]
Abstract
Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.
Collapse
Affiliation(s)
- Priscille Giron
- Biomedical Proteomics Research Group, Structural Biology and Bioinformatics Department, University of Geneva, Geneva, Switzerland
| | | | | |
Collapse
|
33
|
Gallien S, Duriez E, Domon B. Selected reaction monitoring applied to proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:298-312. [PMID: 21394846 DOI: 10.1002/jms.1895] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Selected reaction monitoring (SRM) performed on triple quadrupole mass spectrometers has been the reference quantitative technique to analyze small molecules for several decades. It is now emerging in proteomics as the ideal tool to complement shotgun qualitative studies; targeted SRM quantitative analysis offers high selectivity, sensitivity and a wide dynamic range. However, SRM applied to proteomics presents singularities that distinguish it from small molecules analysis. This review is an overview of SRM technology and describes the specificities and the technical aspects of proteomics experiments. Ongoing developments aiming at increasing multiplexing capabilities of SRM are discussed; they dramatically improve its throughput and extend its field of application to directed or supervised discovery experiments.
Collapse
Affiliation(s)
- Sebastien Gallien
- Luxembourg Clinical Proteomics center (LCP), Centre de Recherche Public de la Santé, 1 B rue Thomas Edison, L-1445 Strassen, Luxembourg
| | | | | |
Collapse
|
34
|
Helsens K, Martens L, Vandekerckhove J, Gevaert K. Mass spectrometry-driven proteomics: an introduction. Methods Mol Biol 2011; 753:1-27. [PMID: 21604112 DOI: 10.1007/978-1-61779-148-2_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Proteins are reckoned to be the key actors in a living organism. By studying proteins, one engages into deciphering a complex series of events occurring during a protein's life span. This starts at the creation of a protein, which is tightly controlled on both a transcriptional (Williams and Tyler, 2007, Curr Opin Genet Dev 17, 88-93) and a translational level (Van Der Kelen et al., 2009, Crit Rev Biochem Mol Biol 44, 143-168). During translation, a primary strand of amino acids undergoes a complex folding process in order to obtain a native three-dimensional protein structure (Gross et al., 2003, Cell 115, 739-750). Proteins take on a plethora of functions, such as complex formation, receptor activity, and signal transduction, which ultimately adds up to a cellular phenotype. Consequently, protein analysis is of major interest in molecular biology and involves annotating their presence and localization, as well as their modification state and biochemical context. To accomplish this, many methods have been developed over the last decades, and their general principles and important recent advances in large-scale protein analysis or proteomics are discussed in this review.
Collapse
Affiliation(s)
- Kenny Helsens
- Department of Medical Protein Research, VIB, Ghent University, B-9000, Ghent, Belgium.
| | | | | | | |
Collapse
|
35
|
Pröfrock D. Progress and possible applications of miniaturised separation techniques and elemental mass spectrometry for quantitative, heteroatom-tagged proteomics. Anal Bioanal Chem 2010; 398:2383-401. [PMID: 20582698 DOI: 10.1007/s00216-010-3901-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 06/03/2010] [Accepted: 06/06/2010] [Indexed: 12/23/2022]
Abstract
The application of miniaturised separation techniques such as capillary LC, nano LC or capillary electrophoresis offers a number of advantages in terms of analytical performance, solvent consumption and the ability to analyse very small sample amounts. These features make them attractive for various bioanalytical tasks, in particular those related to the analysis of proteins and peptides. The skillful combination of such techniques with inductively coupled plasma mass spectrometry (ICP-MS) has recently permitted the design of combined analytical approaches utilising either elemental or molecule-specific detection techniques such as electrospray ionisation (ESI) or matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry in a highly complementary manner for, as an example, proteomics-orientated research (heteroatom-tagged proteomics). Such hybrid approaches are, in particular, providing promising new options for the fast screening of complex samples for specific metal-containing or--more generally speaking--heteroatom-containing biomolecules, as well as the accurate absolute quantification of biomolecules, which is still an unsolved problem in bioanalysis. Here, progress in as well as the potential and the special requirements of hyphenating miniaturised separation techniques with ICP-MS are reviewed and critically discussed. In addition, selected applications are highlighted to indicate current and possible future trends within this emerging area of research.
Collapse
Affiliation(s)
- Daniel Pröfrock
- GKSS Forschungszentrum GmbH, Department Marine Bioanalytical Chemistry, Institute for Coastal Research, Max-Planck Str. 1, 21502 Geesthacht, Germany.
| |
Collapse
|
36
|
Zeng X, Hood BL, Sun M, Conrads TP, Day RS, Weissfeld JL, Siegfried JM, Bigbee WL. Lung cancer serum biomarker discovery using glycoprotein capture and liquid chromatography mass spectrometry. J Proteome Res 2010; 9:6440-9. [PMID: 20931982 DOI: 10.1021/pr100696n] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeted glycoproteomics represents an attractive approach for conducting peripheral blood based cancer biomarker discovery due to the well-known altered pattern of protein glycosylation in cancer and the reduced complexity of the resultant glycoproteome. Here we report its application to a set of pooled nonsmall cell lung cancer (NSCLC) case sera (9 adenocarcinoma and 6 squamous cell carcinoma pools from 54 patients) and matched controls pools, including 8 clinical control pools with computed tomography detected nodules but being nonmalignant as determined by biopsy from 54 patients, and 8 matched healthy control pools from 106 cancer-free subjects. The goal of the study is to discover biomarkers that may enable improved early detection and diagnosis of lung cancer. Immunoaffinity subtraction was used to first deplete the topmost abundant serum proteins; the remaining serum proteins were then subjected to hydrazide chemistry based glycoprotein capture and enrichment. Hydrazide resin in situ trypsin digestion was used to release nonglycosylated peptides. Formerly N-linked glycosylated peptides were released by peptide-N-glycosidase F (PNGase F) treatment and were subsequently analyzed by liquid chromatography (LC)-tandem mass spectrometry (MS/MS). A MATLAB based in-house tool was developed to facilitate retention time alignment across different LC-MS/MS runs, determination of precursor ion m/z values and elution profiles, and the integration of mass chromatograms based on determined parameters for identified peptides. A total of 38 glycopeptides from 22 different proteins were significantly differentially abundant across the case/control pools (P < 0.01, Student's t test) and their abundances led to a near complete separation of case and control pools based on hierarchical clustering. The differential abundances of three of these candidate proteins were verified by commercially available ELISAs applied in the pools. Strong positive correlations between glycopeptide mass chromatograms and ELISA-measured protein abundance was observed for all of the selected glycoproteins.
Collapse
Affiliation(s)
- Xuemei Zeng
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Salih E, Siqueira WL, Helmerhorst EJ, Oppenheim FG. Large-scale phosphoproteome of human whole saliva using disulfide-thiol interchange covalent chromatography and mass spectrometry. Anal Biochem 2010; 407:19-33. [PMID: 20659418 DOI: 10.1016/j.ab.2010.07.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 07/19/2010] [Accepted: 07/19/2010] [Indexed: 12/01/2022]
Abstract
To date, only a handful of phosphoproteins with important biological functions have been identified and characterized in oral fluids, and these include some of the abundant protein constituents of saliva. Whole saliva (WS) samples were trypsin digested, followed by chemical derivatization using dithiothreitol (DTT) of the phospho-serine/threonine-containing peptides. The DTT-phosphopeptides were enriched by covalent disulfide-thiol interchange chromatography and analysis by nanoflow liquid chromatography and electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). The specificity of DTT chemical derivatization was evaluated separately under different base-catalyzed conditions with NaOH and Ba(OH)(2), blocking cysteine residues by iodoacetamide and enzymatic O-deglycosylation prior to DTT reaction. Further analysis of WS samples that were subjected to either of these conditions provided supporting evidence for phosphoprotein identifications. The combined chemical strategies and mass spectrometric analyses identified 65 phosphoproteins in WS; of these, 28 were based on two or more peptide identification criteria with high confidence and 37 were based on a single phosphopeptide identification. Most of the identified proteins (∼80%) were previously unknown phosphoprotein components. This study represents the first large-scale documentation of phosphoproteins of WS. The origins and identity of WS phosphoproteome suggest significant implications for both basic science and the development of novel biomarkers/diagnostic tools for systemic and oral disease states.
Collapse
Affiliation(s)
- Erdjan Salih
- Department of Periodontology and Oral Biology, Henry M. Goldman School of Dental Medicine, Boston University Medical Center, Boston, MA 02118, USA.
| | | | | | | |
Collapse
|
38
|
Abstract
Automated multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) is routinely applied in large scale proteome profiling. However global proteome analysis remains a technical challenge due to the issues associated with sample complexity by tryptic digestion. The application of tag containing peptide enrichment approach for sample pre-separation could reduce the complexity of protein digest. Here, we demonstrated a simple and highly efficient cysteine-containing peptide enrichment method using a thiol specific covalent resin. The cysteine-containing peptides from the tryptic digests of the complex protein mixtures were selected by covalent chromatography based on thiol-disulfide exchange, identified by mass spectrometry. The strategy was firstly optimized and evaluated by using the tryptic peptides of bovine serum albumin (BSA). Then the method was applied with a relatively complicated sample from a five standard protein mixture. The results of these studies show that the enrichment method of cysteine-containing peptides is highly specific, efficient and reproducible. The effectiveness of this method in reducing the sample complexity and improving the identification of peptides by mass spectrometry has enabled high-throughput, automatic and large-scale qualitative and quantitative proteome analyses.
Collapse
|
39
|
Chandramouli K, Qian PY. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. HUMAN GENOMICS AND PROTEOMICS : HGP 2009; 2009. [PMID: 20948568 PMCID: PMC2950283 DOI: 10.4061/2009/239204] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 08/28/2009] [Indexed: 01/12/2023]
Abstract
Proteomics is the large-scale study of the structure and function of proteins in complex biological sample. Such an approach has the potential value to understand the complex nature of the organism. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. Advances in protein fractionation and labeling techniques have improved protein identification to include the least abundant proteins. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration paved with various difficulties and pitfalls. The quantity of data that is acquired with new techniques places new challenges on data processing and analysis. This article provides a brief overview of currently available proteomic techniques and their applications, followed by detailed description of advantages and technical challenges. Some solutions to circumvent technical difficulties are proposed.
Collapse
|
40
|
Tebbe A, Schmidt A, Konstantinidis K, Falb M, Bisle B, Klein C, Aivaliotis M, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D. Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics 2009; 9:3843-55. [PMID: 19670246 DOI: 10.1002/pmic.200800944] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Quantitative proteomics based on isotopic labeling has become the method of choice to accurately determine changes in protein abundance in highly complex mixtures. Isotope-coded protein labeling (ICPL), which is based on the nicotinoylation of proteins at lysine residues and free N-termini was used as a simple, reliable and fast method for the comparative analysis of three different cellular states of the halophilic archaeon Halobacterium salinarum through pairwise comparison. The labeled proteins were subjected to SDS-PAGE, in-gel digested and the proteolytic peptides were separated by LC and analyzed by MALDI-TOF/TOF MS. Automated quantitation was performed by comparing the MS peptide signals of (12)C and (13)C nicotinoylated isotopic peptide pairs. The transitions between (i) aerobic growth in complex versus synthetic medium and (ii) aerobic versus anaerobic/phototrophic growth, both in complex medium, provide a wide span in nutrient and energy supply for the cell and thus allowed optimal studies of proteome changes. In these two studies, 559 and 643 proteins, respectively, could be quantified allowing a detailed analysis of the adaptation of H. salinarum to changes of its living conditions. The subtle cellular response to a wide variation of nutrient and energy supply demonstrates a fine tuning of the cellular protein inventory.
Collapse
Affiliation(s)
- Andreas Tebbe
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Bettmer J, Montes Bayón M, Ruiz Encinar J, Fernández Sánchez ML, Fernández de la Campa MDR, Sanz Medel A. The emerging role of ICP-MS in proteomic analysis. J Proteomics 2009; 72:989-1005. [DOI: 10.1016/j.jprot.2009.05.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/08/2009] [Accepted: 05/17/2009] [Indexed: 12/13/2022]
|
42
|
Pereira Navaza A, Encinar JR, Ballesteros A, González JM, Sanz-Medel A. Capillary HPLC−ICPMS and Tyrosine Iodination for the Absolute Quantification of Peptides Using Generic Standards. Anal Chem 2009; 81:5390-9. [DOI: 10.1021/ac9005606] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Ana Pereira Navaza
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain, and Instituto Universitario de Química Organometálica “Enrique Moles”, Unidad Asociada al CSIC, Julián Clavería, 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain, and Instituto Universitario de Química Organometálica “Enrique Moles”, Unidad Asociada al CSIC, Julián Clavería, 8, 33006 Oviedo, Spain
| | - Alfredo Ballesteros
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain, and Instituto Universitario de Química Organometálica “Enrique Moles”, Unidad Asociada al CSIC, Julián Clavería, 8, 33006 Oviedo, Spain
| | - José M. González
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain, and Instituto Universitario de Química Organometálica “Enrique Moles”, Unidad Asociada al CSIC, Julián Clavería, 8, 33006 Oviedo, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain, and Instituto Universitario de Química Organometálica “Enrique Moles”, Unidad Asociada al CSIC, Julián Clavería, 8, 33006 Oviedo, Spain
| |
Collapse
|
43
|
Domon B. Glycosylation as means of reducing sample complexity to enable quantitative proteomics. Proteomics 2009; 9:1488-91. [DOI: 10.1002/pmic.200800545] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
44
|
Abstract
Determination of the protein amount and of the extent of protein phosphorylation is crucial for a variety of research fields, but is not always straightforward. We describe the application of capillary LC-ICP-MS (liquid chromatography-inductively coupled plasma-mass spectrometry) for quantification of phospho-proteins and their phosphorylation degree. Element mass spectrometry is ideally suited for monitor ing and quantification of compounds with heteroelements such as phosphorus and sulphur, particularly because the ICP-MS response is virtually independent from the chemical form of the element. Determination of the phosphorylation stoichiometry, i.e. the relative abundance of the phosphorylated isoforms, can be assessed by the relative abundance of phosphorus compared with sulphur as a marker for the protein amount. Moreover, isotope dilution analysis by post-column addition of a 34S-Spike provides absolute protein quantification with exceptionally high accuracy. Phosphoprotein analysis by capillary LC-ICP-MS may be applied to isolated proteins or protein digests and may include separation of impurities by 1D-SDS-PAGE followed by enzymatic digestion. Alternatively, digestion of complex protein mixtures such as cellular protein extracts allows determination of global, tissue-specific phosphorylation degrees.
Collapse
Affiliation(s)
- Ralf Krüger
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Mainz, Mainz, Germany
| | | | | |
Collapse
|
45
|
Linscheid MW, Ahrends R, Pieper S, Kühn A. Liquid chromatography-mass spectrometry-based quantitative proteomics. Methods Mol Biol 2009; 564:189-205. [PMID: 19544024 DOI: 10.1007/978-1-60761-157-8_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
During the last decades, molecular sciences revolutionized biomedical research and gave rise to the biotechnology industry. During the next decades, the application of the quantitative sciences--informatics, physics, chemistry, and engineering--to biomedical research brings about the next revolution that will improve human healthcare and certainly create new technologies, since there is no doubt that small changes can have great effects. It is not a question of "yes" or "no," but of "how much," to make best use of the medical options we will have. In this context, the development of accurate analytical methods must be considered a cornerstone, since the understanding of biological processes will be impossible without information about the minute changes induced in cells by interactions of cell constituents with all sorts of endogenous and exogenous influences and disturbances. The first quantitative techniques, which were developed, allowed monitoring relative changes only, but they clearly showed the significance of the information obtained. The recent advent of techniques claiming to quantify proteins and peptides not only relative to each other, but also in an absolute fashion, promised another quantum leap, since knowing the absolute amount will allow comparing even unrelated species and the definition of parameters will permit to model biological systems much more accurate than before. To bring these promises to life, several approaches are under development at this point in time and this review is focused on those developments.
Collapse
Affiliation(s)
- Michael W Linscheid
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | | | | | | |
Collapse
|
46
|
Diez-Orejas R, Fernández-Arenas E. Candida albicans–macrophage interactions: genomic and proteomic insights. Future Microbiol 2008; 3:661-81. [DOI: 10.2217/17460913.3.6.661] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Candida albicans infection is a significant cause of morbidity and mortality in immunocompromised patients. In vivo and in vitro models have been developed to study both the fungal and the mammalian immune responses. Phagocytic cells (i.e., macrophages) play a key role in innate immunity against C. albicans by capturing, killing and processing the pathogen for presentation to T cells. The use of microarray technology to study global fungal transcriptional changes after interaction with different host cells has revealed how C. albicans adapts to its environment. Proteomic tools complement molecular approaches and computational methods enable the formulation of relevant biological hypotheses. Therefore, the combination of genomics, proteomics and bioinformatics tools (i.e., network analyses) is a powerful strategy to better understand the biological situation of the fungus inside macrophages; part of the fungal population is killed while a significantly high percentage survives.
Collapse
Affiliation(s)
- Rosalía Diez-Orejas
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain
| | - Elena Fernández-Arenas
- Centro de Biología Molecular Severo Ochoa (CBM-SO), Consejo Superior de Investigaciones Científicas (CSIC), Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
47
|
Lee EY, Choi DS, Kim KP, Gho YS. Proteomics in gram-negative bacterial outer membrane vesicles. MASS SPECTROMETRY REVIEWS 2008; 27:535-555. [PMID: 18421767 DOI: 10.1002/mas.20175] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Gram-negative bacteria constitutively secrete outer membrane vesicles (OMVs) into the extracellular milieu. Recent research in this area has revealed that OMVs may act as intercellular communicasomes in polyspecies communities by enhancing bacterial survival and pathogenesis in hosts. However, the mechanisms of vesicle formation and the pathophysiological roles of OMVs have not been clearly defined. While it is obvious that mass spectrometry-based proteomics offers great opportunities for improving our knowledge of bacterial OMVs, limited proteomic data are available for OMVs. The present review aims to give an overview of the previous biochemical, biological, and proteomic studies in the emerging field of bacterial OMVs, and to give future directions for high-throughput and comparative proteomic studies of OMVs that originate from diverse Gram-negative bacteria under various environmental conditions. This article will hopefully stimulate further efforts to construct a comprehensive proteome database of bacterial OMVs that will help us not only to elucidate the biogenesis and functions of OMVs but also to develop diagnostic tools, vaccines, and antibiotics effective against pathogenic bacteria.
Collapse
Affiliation(s)
- Eun-Young Lee
- Department of Life Science and Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | | | | | | |
Collapse
|
48
|
Abstract
Plasma has been the focus of testing different proteomic technologies for the identification of biomarkers due to its ready accessibility. However, it is not clear if direct proteomic analysis of plasma can be used to discover new marker proteins from tumor that are associated with tumor progression. Here, we reported that such proteins can be detected in plasma in a chemical induced skin cancer mouse model. We analyzed glycoproteins from both benign papillomas and malignant carcinomas from mice using our recently developed platform, solid-phase extraction of glycopeptides (SPEG) and mass spectrometry, and identified 463 unique N-linked glycosites from 318 unique glycoproteins. These include most known extracellular proteins that have been reported to play roles in skin cancer development such as thrombospondin, cathepsins, epidermal growth factor receptor, cell adhesion molecules, cadherins, integrins, tuberin, fibulin, TGFβ receptor, etc. We further investigated whether these tumor proteins could be detected in plasma from tumor bearing mice using isotope labeling and 2D-LC-MALDI-MS/MS. Two tumor glycoproteins, Tenascin-C and Arylsulfatase B, were identified and quantified successfully in plasma from tumor bearing mice. This result indicates that analysis of tumor associated proteins in tumors and plasma by method using glycopeptide capture, isotopic labeling, and mass spectrometry can be used as a discovery tool to identify candidate tumor proteins that may be detected in plasma.
Collapse
|
49
|
Gundry RL, Boheler KR, Van Eyk JE, Wollscheid B. A novel role for proteomics in the discovery of cell-surface markers on stem cells: Scratching the surface. Proteomics Clin Appl 2008; 2:892-903. [PMID: 19526049 DOI: 10.1002/prca.200780122] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The concept of cell-based therapy has been advocated as a novel approach for treating diseases or conditions where regeneration of cells, tissue and/or potentially organs is required. A promising source for cell-replacement therapies is provided by stem cells, but the success of this approach will ultimately rely on the ability to isolate primary stem or progenitor cells. Cell-surface protein markers will play a critical role in this step. Current methodologies for the identification of cell-surface protein markers rely primarily on antibody availability and flow cytometry, but many cell-surface proteins remain undetectable. Proteomic technologies now offer the possibility to specifically identify and investigate the cell-surface subproteome in a quantitative and discovery-driven manner. Once a cell surface protein marker panel has been identified by MS and the antibodies become available, the panel should permit the identification, tracking, and/or isolation of stem or progenitor cells that may be appropriate for therapeutics. This review provides a context for the use of proteomics in discovering new cell-surface markers for stem cells.
Collapse
Affiliation(s)
- Rebekah L Gundry
- Johns Hopkins School of Medicine, Department of Medicine, Baltimore, MD, USA
| | | | | | | |
Collapse
|
50
|
Sanz-Medel A. Heteroatom(isotope)-tagged proteomics via ICP-MS: screening and quantification of proteins and their post-translational modifications. Anal Bioanal Chem 2008; 391:885-94. [DOI: 10.1007/s00216-008-2083-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 03/16/2008] [Accepted: 03/19/2008] [Indexed: 11/27/2022]
|