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Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2024; 43:977-997. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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2
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Chen J, Wang R, Ma M, Gao L, Zhao B, Xu M. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS)-based strategies applied for the analysis of metal-binding protein in biological samples: an update on recent advances. Anal Bioanal Chem 2022; 414:7023-7033. [PMID: 35790569 DOI: 10.1007/s00216-022-04185-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/21/2022] [Accepted: 06/17/2022] [Indexed: 11/01/2022]
Abstract
New analytical strategies for metal-binding protein facilitate researchers learning about how metals play a significant role in life. Laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS) offers many advantages for the metal analysis of biological samples and shows a promising future in protein analysis, but recent advances in LA-ICP-MS-based strategies for identifying metal-binding proteins via endogenous metals remain less updated yet. To present the current status in this field, the main analytical strategies for metal-binding proteins with LA-ICP-MS are reviewed here, including in situ analysis of biospecimens and ex situ analysis with gel electrophoresis. A critical discussion of challenges and future perspectives is also given. Multifarious laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS)-based strategies have been developed and applied to investigate the metal-binding proteins in biospecimens in situ or through gel electrophoresis ex situ over the past decades, facilitating researchers disclosing how essential metals are implicated in life or what proteins toxic metals will target.
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Affiliation(s)
- Jiahao Chen
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruixia Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghao Ma
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lirong Gao
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Zhao
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Xu
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China. .,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Ghose A, Gullapalli SVN, Chohan N, Bolina A, Moschetta M, Rassy E, Boussios S. Applications of Proteomics in Ovarian Cancer: Dawn of a New Era. Proteomes 2022; 10:proteomes10020016. [PMID: 35645374 PMCID: PMC9150001 DOI: 10.3390/proteomes10020016] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/01/2022] [Accepted: 05/06/2022] [Indexed: 12/11/2022] Open
Abstract
The ability to identify ovarian cancer (OC) at its earliest stages remains a challenge. The patients present an advanced stage at diagnosis. This heterogeneous disease has distinguishable etiology and molecular biology. Next-generation sequencing changed clinical diagnostic testing, allowing assessment of multiple genes, simultaneously, in a faster and cheaper manner than sequential single gene analysis. Technologies of proteomics, such as mass spectrometry (MS) and protein array analysis, have advanced the dissection of the underlying molecular signaling events and the proteomic characterization of OC. Proteomics analysis of OC, as well as their adaptive responses to therapy, can uncover new therapeutic choices, which can reduce the emergence of drug resistance and potentially improve patient outcomes. There is an urgent need to better understand how the genomic and epigenomic heterogeneity intrinsic to OC is reflected at the protein level, and how this information could potentially lead to prolonged survival.
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Affiliation(s)
- Aruni Ghose
- Department of Medical Oncology, Barts Cancer Centre, St. Bartholomew’s Hospital, Barts Health NHS Trust, London EC1A 7BE, UK; (A.G.); (N.C.)
- Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Hertfordshire NHS Trust, Northwood HA6 2RN, UK
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK
- Division of Research, Academics and Cancer Control, Saroj Gupta Cancer Centre and Research Institute, Kolkata 700063, India
| | | | - Naila Chohan
- Department of Medical Oncology, Barts Cancer Centre, St. Bartholomew’s Hospital, Barts Health NHS Trust, London EC1A 7BE, UK; (A.G.); (N.C.)
| | - Anita Bolina
- Department of Haematology, Clatterbridge Cancer Centre Liverpool, The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool L7 8YA, UK;
| | - Michele Moschetta
- Novartis Institutes for BioMedical Research, 4033 Basel, Switzerland;
| | - Elie Rassy
- Department of Medical Oncology, Gustave Roussy Institut, 94805 Villejuif, France;
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London WC2R 2LS, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
- Correspondence: or or
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4
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Jiang-Long DU, Meng-Yao FU, Ying-Hua YAN, Chuan-Fan DING. A complementary bimetal synergized with polyethyleneimine functionalized affinity chromatography nanosphere for enrichment of global phosphopeptides. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2021.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Nosti AJ, Barrio LC, Calderón-Celis F, Soldado A, Encinar JR. Absolute quantification of proteins using element mass spectrometry and generic standards. J Proteomics 2022; 256:104499. [DOI: 10.1016/j.jprot.2022.104499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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6
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YAMAMOTO S. <i>In Situ </i>Photopolymerization of Functionalized Polyacrylamide-Based Preconcentrators for Highly Sensitive Specific Detection of Various Analytes by Microchip Electrophoresis. CHROMATOGRAPHY 2021. [DOI: 10.15583/jpchrom.2020.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Du J, Yan Y, Tang K, Ding C. Modified Carbon Nanotubes Decorated with ZIFs as New Immobilized Metal Ion Affinity Chromatography Platform for Enrichment of Phosphopeptides. ChemistrySelect 2021. [DOI: 10.1002/slct.202004650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jianglong Du
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
| | - Yinghua Yan
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
| | - Keqi Tang
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
| | - Chuan‐Fan Ding
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry Ningbo University Ningbo 315211 China
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8
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Finamore F, Ucciferri N, Signore G, Cecchettini A, Ceccherini E, Vitiello M, Poliseno L, Rocchiccioli S. Proteomics pipeline for phosphoenrichment and its application on a human melanoma cell model. Talanta 2020; 220:121381. [PMID: 32928406 DOI: 10.1016/j.talanta.2020.121381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 11/25/2022]
Abstract
Cell signalling is tightly regulated by post-translational modification of proteins. Among them, phosphorylation is one of the most interesting and important. Identifying phosphorylation sites on proteins is challenging and requires strategies for pre-separation and enrichment of the phosphorylated species. We applied four different methods for phospho-enrichment involving TiO2 and IMAC matrix to human melanoma cell lysates of starved A375 induced for 1 h with 1% FBS. Comparison of protocol efficiency was evaluated through peptide concentration, sulphur and phosphorus content and peptide analysis by LC-MS in the collected fractions. Our results underlined that each single method is not sufficient for a comprehensive phosphoproteome analysis. In fact, each methodology permits to identify only a fraction of the phosphoproteome contained in a whole cell lysate. The selection of the most efficient protocols and a combination of two phospho-enrichment methods allowed the assessment of this workflow able to pinpoint the main actors in the phospho-proteome cascade of A375 human melanoma cells treated with Vemurafenib.
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Affiliation(s)
- Francesco Finamore
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy
| | - Nadia Ucciferri
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy
| | - Giovanni Signore
- NEST, Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, 56127, Italy; Fondazione Pisana per la Scienza ONLUS, via Ferruccio Giovannini 13, San Giuliano Terme, 56017, Italy
| | - Antonella Cecchettini
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy; Dept of Clinical and Experimental Medicine, Pisa University, via Volta 4, 56126, Pisa, Italy
| | - Elisa Ceccherini
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy
| | - Marianna Vitiello
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy; Oncogenomics Unit, ISPRO, via Moruzzi 1, Pisa, 56124, Italy
| | - Laura Poliseno
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy; Oncogenomics Unit, ISPRO, via Moruzzi 1, Pisa, 56124, Italy
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9
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Phosphoproteomic and bioinformatic methods for analyzing signaling in vertebrate axon growth and regeneration. J Neurosci Methods 2020; 339:108723. [DOI: 10.1016/j.jneumeth.2020.108723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 02/07/2023]
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10
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Facciuolo A, Denomy C, Lipsit S, Kusalik A, Napper S. From Beef to Bees: High-Throughput Kinome Analysis to Understand Host Responses of Livestock Species to Infectious Diseases and Industry-Associated Stress. Front Immunol 2020; 11:765. [PMID: 32499776 PMCID: PMC7243914 DOI: 10.3389/fimmu.2020.00765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
Within human health research, the remarkable utility of kinase inhibitors as therapeutics has motivated efforts to understand biology at the level of global cellular kinase activity (the kinome). In contrast, the diminished potential for using kinase inhibitors in food animals has dampened efforts to translate this research approach to livestock species. This, in our opinion, was a lost opportunity for livestock researchers given the unique potential of kinome analysis to offer insight into complex biology. To remedy this situation, our lab developed user-friendly, cost-effective approaches for kinome analysis that can be readily incorporated into most research programs but with a specific priority to enable the technology to livestock researchers. These contributions include the development of custom software programs for the creation of species-specific kinome arrays as well as comprehensive deconvolution and analysis of kinome array data. Presented in this review are examples of the application of kinome analysis to highlight the utility of the technology to further our understanding of two key complex biological events of priority to the livestock industry: host immune responses to infectious diseases and animal stress responses. These advances and examples of application aim to provide both mechanisms and motivation for researchers, particularly livestock researchers, to incorporate kinome analysis into their research programs.
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Affiliation(s)
- Antonio Facciuolo
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Connor Denomy
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Lipsit
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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11
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Hu J, Li Z, Zhang H, Liu R, Lv Y. Tag-Free Methodology for Ultrasensitive Biosensing of miRNA Based on Intrinsic Isotope Detection. Anal Chem 2020; 92:8523-8529. [PMID: 32340438 DOI: 10.1021/acs.analchem.0c01295] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
MicroRNA (miRNA), of which the abnormal intracellular expression highly associates with numerous pathological diseases, is considered as an important biomarker for early diagnosis and state monitoring of cancer. To avoid the tedious and vunerable labeling process, a series of novel label-free quantification methods for miRNA have been proposed. However, current label-free miRNA assays still require the presynthesis of a sensing unit as tags. Herein, we propose a "tag-free" methodology for miRNA quantification to realize the removal of sensing labels. Combining a concatenated-HCR (C-HCR) strategy and high-resolution inductive couple plasma mass spectrometry (HR-ICPMS) detection, we utilize phosphorus as a characteristic element to quantify the concentration of nucleotides. Benefiting from the excellent amplification performance of C-HCR and element analysis capacity of HR-ICPMS, a 13 fM limit of detection (LOD) was obtained. Ulteriorly, we verify the anti-interference performance of the proposed tag-free miRNA assay with a phosphate substrate-contained cell culture medium or nontarget miRNA. Furthermore, two cell lines of human cancer were chosen to evaluate the real biological sample analysis capacity. The good correlation data indicate promising prospects of the proposed tag-free methodology for the quantification of miRNA in tumor cells and further clinical applications.
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Affiliation(s)
- Jianyu Hu
- College of Architecture & Environment, Sichuan University, Chengdu 610064, China.,Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Ziyan Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Hu Zhang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
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12
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Huang YL, Wang J, Jiang YH, Yang PY, Wang GW, Liu F. Development of amphiphile 4-armed PEO-based Ti4+ complex for highly selective enrichment of phosphopeptides. Talanta 2019; 204:670-676. [DOI: 10.1016/j.talanta.2019.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/24/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022]
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13
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Hussain D, Najam-ul-Haq M, Majeed S, Musharraf SG, Lu Q, He X, Feng YQ. Facile liquid-phase deposition synthesis of titania-coated magnetic sporopollenin for the selective capture of phosphopeptides. Anal Bioanal Chem 2019; 411:3373-3382. [DOI: 10.1007/s00216-019-01811-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/24/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022]
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14
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Calderón-Celis F, Encinar JR, Sanz-Medel A. Standardization approaches in absolute quantitative proteomics with mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:715-737. [PMID: 28758227 DOI: 10.1002/mas.21542] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 05/10/2023]
Abstract
Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers. However, the physico-chemical environment of the analyte species affects strongly the ionization efficiency in most mass spectrometry (MS) types, which thereby require the use of specially designed standardization approaches to provide absolute quantifications. Most common of such approaches nowadays include (i) the use of stable isotope-labeled peptide standards, isotopologues to the target proteotypic peptides expected after tryptic digestion of the target protein; (ii) use of stable isotope-labeled protein standards to compensate for sample preparation, sample loss, and proteolysis steps; (iii) isobaric reagents, which after fragmentation in the MS/MS analysis provide a final detectable mass shift, can be used to tag both analyte and standard samples; (iv) label-free approaches in which the absolute quantitative data are not obtained through the use of any kind of labeling, but from computational normalization of the raw data and adequate standards; (v) elemental mass spectrometry-based workflows able to provide directly absolute quantification of peptides/proteins that contain an ICP-detectable element. A critical insight from the Analytical Chemistry perspective of the different standardization approaches and their combinations used so far for absolute quantitative MS-based (molecular and elemental) proteomics is provided in this review.
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Affiliation(s)
| | - 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
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15
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Swiatly A, Plewa S, Matysiak J, Kokot ZJ. Mass spectrometry-based proteomics techniques and their application in ovarian cancer research. J Ovarian Res 2018; 11:88. [PMID: 30270814 PMCID: PMC6166298 DOI: 10.1186/s13048-018-0460-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/20/2018] [Indexed: 12/26/2022] Open
Abstract
Ovarian cancer has emerged as one of the leading cause of gynecological malignancies. So far, the measurement of CA125 and HE4 concentrations in blood and transvaginal ultrasound examination are essential ovarian cancer diagnostic methods. However, their sensitivity and specificity are still not sufficient to detect disease at the early stage. Moreover, applied treatment may appear to be ineffective due to drug-resistance. Because of a high mortality rate of ovarian cancer, there is a pressing need to develop innovative strategies leading to a full understanding of complicated molecular pathways related to cancerogenesis. Recent studies have shown the great potential of clinical proteomics in the characterization of many diseases, including ovarian cancer. Therefore, in this review, we summarized achievements of proteomics in ovarian cancer management. Since the development of mass spectrometry has caused a breakthrough in systems biology, we decided to focus on studies based on this technique. According to PubMed engine, in the years 2008-2010 the number of studies concerning OC proteomics was increasing, and since 2010 it has reached a plateau. Proteomics as a rapidly evolving branch of science may be essential in novel biomarkers discovery, therapy decisions, progression predication, monitoring of drug response or resistance. Despite the fact that proteomics has many to offer, we also discussed some limitations occur in ovarian cancer studies. Main difficulties concern both complexity and heterogeneity of ovarian cancer and drawbacks of the mass spectrometry strategies. This review summarizes challenges, capabilities, and promises of the mass spectrometry-based proteomics techniques in ovarian cancer management.
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Affiliation(s)
- Agata Swiatly
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Szymon Plewa
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Zenon J. Kokot
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
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16
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Zhang Y, Zhao C, Li L, Hsu CC, Zhu JK, Iliuk A, Tao WA. High-Throughput Phosphorylation Screening and Validation through Ti(IV)-Nanopolymer Functionalized Reverse Phase Phosphoprotein Array. Anal Chem 2018; 90:10263-10270. [PMID: 30103608 DOI: 10.1021/acs.analchem.8b01843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Protein phosphorylation is one of the most important and widespread molecular regulatory mechanisms that controls almost all aspects of cellular functions in animals and plants. Here, we introduce a novel chemically functionalized reverse phase phosphoprotein array (RP3A) to capture and measure phosphoproteomes. RP3A uses polyamidoamine (PAMAM) dendrimer immobilized with Ti(IV) ions to functionalize nitrocellulose membrane, facilitating specific chelation of phosphoproteins from complex protein samples on the array. Globular, water-soluble Ti(IV)-dendrimer allows the RP3A surface to be highly accessible to phosphoproteins multidimensionally, and the captured phosphoproteins were subsequently detected using the same validated antibodies as in regular reverse-phase protein arrays. The novel chemical strategy demonstrated superior specificity (1:10 000), high sensitivity (fg level), and good quantitative nature ( R2 = 0.99) for measuring phosphoproteins. We further applied quantitative phosphoproteomics followed by RP3A to validate the phosphorylation status of a panel of phosphoproteins in response to environmental stresses in Arabidopsis.
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Affiliation(s)
- Ying Zhang
- Shanghai Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , P. R. China
| | - Chunzhao Zhao
- Department of Horticulture and Landscape Architecture , Purdue University , West Lafayette , Indiana 47907 , United States.,Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Li Li
- Tymora Analytical Operations , West Lafayette , Indiana 47906 , United States
| | - Chuan-Chih Hsu
- Department of Biochemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture , Purdue University , West Lafayette , Indiana 47907 , United States.,Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Anton Iliuk
- Tymora Analytical Operations , West Lafayette , Indiana 47906 , United States
| | - W Andy Tao
- Department of Biochemistry , Purdue University , West Lafayette , Indiana 47907 , United States
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17
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Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress. Mol Genet Genomics 2017; 292:1307-1322. [PMID: 28710562 DOI: 10.1007/s00438-017-1348-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/03/2017] [Indexed: 01/09/2023]
Abstract
Drought stress is a major problem around the world and there is still little molecular mechanism about how fruit crops deal with moderate drought stress. Here, the physiological and phosphoproteomic responses of drought-sensitive genotype (M26) and drought-tolerant genotype (MBB) under moderate drought stress were investigated. Our results of the physiology analysis indicated that the MBB genotype could produce more osmosis-regulating substances. Furthermore, phosphoproteins from leaves of both genotypes under moderate drought stress were analyzed using the isobaric tags for relative and absolute quantification technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites, and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Five and thirty-five phosphoproteins with the phosphorylation levels significantly changed (PLSC) were identified in M26 and MBB, respectively. Among these, four PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlap of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins represent a unique combination of metabolism, transcription, translation, and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new and unique homeostasis of major cellular processes. The basic trend was an increase in protein and organic molecules abundance related to drought. These increases were higher in MBB than in M26. Our study is the first to address the phosphoproteome of apple rootstocks in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.
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Solari FA, Dell'Aica M, Sickmann A, Zahedi RP. Why phosphoproteomics is still a challenge. MOLECULAR BIOSYSTEMS 2016; 11:1487-93. [PMID: 25800119 DOI: 10.1039/c5mb00024f] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite continuous improvements phosphoproteomics still faces challenges that are often neglected, e.g. partially poor recovery of phosphopeptide enrichment, assessment of phosphorylation stoichiometry, label-free quantification, poor behavior during chromatography, and general limitations of peptide-centric proteomics. Here we critically discuss current limitations that need consideration in both qualitative and quantitative studies.
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Affiliation(s)
- Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.
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Nitric Oxide-Mediated Posttranslational Modifications: Impacts at the Synapse. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2016:5681036. [PMID: 26635909 PMCID: PMC4655263 DOI: 10.1155/2016/5681036] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/28/2015] [Indexed: 11/18/2022]
Abstract
Nitric oxide (NO) is an important gasotransmitter molecule that is involved in numerous physiological processes throughout the nervous system. In addition to its involvement in physiological plasticity processes (long-term potentiation, LTP; long-term depression, LTD) which can include NMDAR-mediated calcium-dependent activation of neuronal nitric oxide synthase (nNOS), new insights into physiological and pathological consequences of nitrergic signalling have recently emerged. In addition to the canonical cGMP-mediated signalling, NO is also implicated in numerous pathways involving posttranslational modifications. In this review we discuss the multiple effects of S-nitrosylation and 3-nitrotyrosination on proteins with potential modulation of function but limit the analyses to signalling involved in synaptic transmission and vesicular release. Here, crucial proteins which mediate synaptic transmission can undergo posttranslational modifications with either pre- or postsynaptic origin. During normal brain function, both pathways serve as important cellular signalling cascades that modulate a diverse array of physiological processes, including synaptic plasticity, transcriptional activity, and neuronal survival. In contrast, evidence suggests that aging and disease can induce nitrosative stress via excessive NO production. Consequently, uncontrolled S-nitrosylation/3-nitrotyrosination can occur and represent pathological features that contribute to the onset and progression of various neurodegenerative diseases, including Parkinson's, Alzheimer's, and Huntington's.
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Chahrour O, Cobice D, Malone J. Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. J Pharm Biomed Anal 2015; 113:2-20. [PMID: 25956803 DOI: 10.1016/j.jpba.2015.04.013] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 02/04/2023]
Abstract
Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.
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Affiliation(s)
| | - Diego Cobice
- Spectroscopy Group, Analytical Services, Almac, UK
| | - John Malone
- Spectroscopy Group, Analytical Services, Almac, UK
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Maes E, Brusten W, Beutels F, Baggerman G, Mertens I, Valkenborg D, Landuyt B, Schoofs L, Tirez K. The benefits and limitations of reaction cell and sector field inductively coupled plasma mass spectrometry in the detection and quantification of phosphopeptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:35-44. [PMID: 25462361 DOI: 10.1002/rcm.7079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 10/16/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE The phosphorylation of proteins is one of the most important post-translational modifications in nature. Knowledge of the quantity or degree of protein phosphorylation in biological samples is extremely important. A combination of liquid chromatography (LC) and inductively coupled plasma mass spectrometry (ICP-MS) allows the absolute and relative quantification of the phosphorus signal. METHODS A comparison between dynamic reaction cell quadrupole ICP-MS (DRC-Q-ICP-MS) and high-resolution sector field ICP-MS (SF-ICP-MS) in detecting signals of phosphorus-containing species using identical capillary LC (reversed-phase technology) and nebulizer settings was performed. RESULTS A method to diminish the reversed-phase gradient-related signal instability in phosphorus detection with LC/ICP-MS applications was developed. Bis(4-nitrophenyl)phosphate (BNPP) was used as a standard to compare signal-to-noise ratios and limits of detection (LODs) between the two instrumental setups. The LOD reaches a value of 0.8 µg L(-1) when applying the DRC technology in Q-ICP-MS and an LOD of 0.09 µg L(-1) was found with the SF-ICP-MS setup. This BNPP standard was further used to compare the absolute quantification possibilities of phosphopeptides in these two setups. CONCLUSIONS This one-to-one comparison of two interference-reducing ICP-MS instruments demonstrates that absolute quantification of individual LC-separated phosphopeptides is possible. However, based on the LOD values, SF-ICP-MS has a higher sensitivity in detecting phosphorus signals and thus is preferred in phosphopeptide analysis.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium; KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
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