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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 2023. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Escudero-Cernuda S, García de Pablos C, Celis FC, Fernández-Sánchez ML, Encinar JR. Certification of protein biomarker standards using element MS and generic standards: Application to human cytokines. Anal Chim Acta 2023; 1251:341002. [PMID: 36925291 DOI: 10.1016/j.aca.2023.341002] [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: 12/20/2022] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
The availability of protein standards and methods for their characterization, quantification, and purity assessment are currently a bottleneck in absolute quantitative proteomics. In this work, we introduce an absolute quantitative analytical strategy based on ICP-MS sulfur detection that uses sulfate as generic standard to quantify and certify the mass purity of protein standards. The methodology combines capillary chromatographic separation with parallel detection with ICP-MS and ESI-MS to determine proteoforms concentration and identity, respectively. The workability of the methodology was demonstrated using recombinant human cytokine standards IP-10 and Flt3L (2 batches), which are relevant biomarkers for carcinoma or inflammatory diseases. Every key factor (transport efficiency, column recovery, signal stability and internal standard suitability) was taken into account and certified BSA standard was used as quality control for validation purposes. Protein quantification values and resulting mass purity certification of IP-10 and one batch of Flt3L were very high (100 and 86%, respectively). Lower mass purity obtained for another batch of Flt3L (<70%) concurred with the finding of significant proteoforms resulted from oxidation processes as observed by parallel ESI-MS.
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Affiliation(s)
- Sara Escudero-Cernuda
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain
| | - Carlos García de Pablos
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain
| | - Francisco Calderón Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain.
| | - M Luisa Fernández-Sánchez
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain.
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain
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van Thiel J, Alonso LL, Slagboom J, Dunstan N, Wouters RM, Modahl CM, Vonk FJ, Jackson TNW, Kool J. Highly Evolvable: Investigating Interspecific and Intraspecific Venom Variation in Taipans ( Oxyuranus spp.) and Brown Snakes ( Pseudonaja spp.). Toxins (Basel) 2023; 15:74. [PMID: 36668892 PMCID: PMC9864820 DOI: 10.3390/toxins15010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
Snake venoms are complex mixtures of toxins that differ on interspecific (between species) and intraspecific (within species) levels. Whether venom variation within a group of closely related species is explained by the presence, absence and/or relative abundances of venom toxins remains largely unknown. Taipans (Oxyuranus spp.) and brown snakes (Pseudonaja spp.) represent medically relevant species of snakes across the Australasian region and provide an excellent model clade for studying interspecific and intraspecific venom variation. Using liquid chromatography with ultraviolet and mass spectrometry detection, we analyzed a total of 31 venoms covering all species of this monophyletic clade, including widespread localities. Our results reveal major interspecific and intraspecific venom variation in Oxyuranus and Pseudonaja species, partially corresponding with their geographical regions and phylogenetic relationships. This extensive venom variability is generated by a combination of the absence/presence and differential abundance of venom toxins. Our study highlights that venom systems can be highly dynamical on the interspecific and intraspecific levels and underscores that the rapid toxin evolvability potentially causes major impacts on neglected tropical snakebites.
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Affiliation(s)
- Jory van Thiel
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Luis L. Alonso
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | - Julien Slagboom
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | | | - Roel M. Wouters
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Cassandra M. Modahl
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Freek J. Vonk
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | - Timothy N. W. Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jeroen Kool
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
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Rangel DL, Melani RD, Carvalho EL, Boldo JT, Gomes Dos Santos T, Kelleher NL, Pinto PM. Venom characterization of the Brazilian Pampa snake Bothrops pubescens by top-down and bottom-up proteomics. Toxicon 2022; 220:106937. [PMID: 36228757 PMCID: PMC9901210 DOI: 10.1016/j.toxicon.2022.106937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
The envenomation from the Bothrops genus is characterized by systemic and local effects caused by the main toxin families in the venom. In Bothrops pubescens venom we were able to identify 89 protein groups belonging to 13 toxin families with the bottom-up proteomics approach and 40 unique proteoforms belonging to 6 toxin families with the top-down proteomics approach. We also identified multi-proteoform complexes of dimeric L-amino acid oxidase using native top-down mass spectrometry.
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Affiliation(s)
- Darlene Lopes Rangel
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil; Pos Graduation in Biological Sciences, Federal University of Pampa, São Gabriel, Brazil
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, United States
| | - Evelise Leis Carvalho
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil; Pos Graduation in Biological Sciences, Federal University of Pampa, São Gabriel, Brazil
| | | | - Tiago Gomes Dos Santos
- Pampa Biodiversity Studies Laboratory (LEBIP), Federal University of Pampa, São Gabriel, Brazil
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, United States
| | - Paulo Marcos Pinto
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil; Pos Graduation in Biological Sciences, Federal University of Pampa, São Gabriel, Brazil.
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Tasoulis T, Pukala TL, Isbister GK. Investigating Toxin Diversity and Abundance in Snake Venom Proteomes. Front Pharmacol 2022; 12:768015. [PMID: 35095489 PMCID: PMC8795951 DOI: 10.3389/fphar.2021.768015] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
Understanding snake venom proteomes is becoming increasingly important to understand snake venom biology, evolution and especially clinical effects of venoms and approaches to antivenom development. To explore the current state of snake venom proteomics and transcriptomics we investigated venom proteomic methods, associations between methodological and biological variability and the diversity and abundance of protein families. We reviewed available studies on snake venom proteomes from September 2017 to April 2021. This included 81 studies characterising venom proteomes of 79 snake species, providing data on relative toxin abundance for 70 species and toxin diversity (number of different toxins) for 37 species. Methodologies utilised in these studies were summarised and compared. Several comparative studies showed that preliminary decomplexation of crude venom by chromatography leads to increased protein identification, as does the use of transcriptomics. Combining different methodological strategies in venomic approaches appears to maximize proteome coverage. 48% of studies used the RP-HPLC →1D SDS-PAGE →in-gel trypsin digestion → ESI -LC-MS/MS pathway. Protein quantification by MS1-based spectral intensity was used twice as commonly as MS2-based spectral counting (33–15 studies). Total toxin diversity was 25–225 toxins/species, with a median of 48. The relative mean abundance of the four dominant protein families was for elapids; 3FTx–52%, PLA2–27%, SVMP–2.8%, and SVSP–0.1%, and for vipers: 3FTx–0.5%, PLA2–24%, SVMP–27%, and SVSP–12%. Viper venoms were compositionally more complex than elapid venoms in terms of number of protein families making up most of the venom, in contrast, elapid venoms were made up of fewer, but more toxin diverse, protein families. No relationship was observed between relative toxin diversity and abundance. For equivalent comparisons to be made between studies, there is a need to clarify the differences between methodological approaches and for acceptance of a standardised protein classification, nomenclature and reporting procedure. Correctly measuring and comparing toxin diversity and abundance is essential for understanding biological, clinical and evolutionary implications of snake venom composition.
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Affiliation(s)
- Theo Tasoulis
- Clinical Toxicology Research Group, University of Newcastle, Callaghan, NSW, Australia
| | - Tara L Pukala
- Department of Chemistry, University of Adelaide, Adelaide, SA, Australia
| | - Geoffrey K Isbister
- Clinical Toxicology Research Group, University of Newcastle, Callaghan, NSW, Australia
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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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Calvete JJ, Pla D, Els J, Carranza S, Damm M, Hempel BF, John EBO, Petras D, Heiss P, Nalbantsoy A, Göçmen B, Süssmuth RD, Calderón-Celis F, Nosti AJ, Encinar JR. Combined Molecular and Elemental Mass Spectrometry Approaches for Absolute Quantification of Proteomes: Application to the Venomics Characterization of the Two Species of Desert Black Cobras, Walterinnesia aegyptia and Walterinnesia morgani. J Proteome Res 2021; 20:5064-5078. [PMID: 34606723 PMCID: PMC8576837 DOI: 10.1021/acs.jproteome.1c00608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
We report a novel hybrid, molecular
and elemental mass spectrometry
(MS) setup for the absolute quantification of snake venom proteomes
shown here for two desert black cobra species within the genus Walterinnesia, Walterinnesia aegyptia and Walterinnesia morgani. The experimental
design includes the decomplexation of the venom samples by reverse-phase
chromatography independently coupled to four mass spectrometry systems:
the combined bottom-up and top-down molecular MS for protein identification
and a parallel reverse-phase microbore high-performance liquid chromatograph
(RP-μHPLC) on-line to inductively coupled plasma (ICP-MS/MS)
elemental mass spectrometry and electrospray ionization quadrupole
time-of-flight mass spectrometry (ESI-QToF MS). This allows to continuously
record the absolute sulfur concentration throughout the chromatogram
and assign it to the parent venom proteins separated in the RP-μHPLC-ESI-QToF
parallel run via mass profiling. The results provide a locus-resolved
and quantitative insight into the three desert black cobra venom proteome
samples. They also validate the units of measure of our snake venomics
strategy for the relative quantification of snake venom proteomes
as % of total venom peptide bonds as a proxy for the % by weight of
the venom toxins/toxin families. In a more general context, our work
may pave the way for broader applications of hybrid elemental/molecular
MS setups in diverse areas of proteomics.
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Affiliation(s)
- Juan J Calvete
- Laboratorio de Venómica Evolutiva y Traslational, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain
| | - Davinia Pla
- Laboratorio de Venómica Evolutiva y Traslational, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain
| | - Johannes Els
- Environment and Protected Areas Authority, 82828 Sharjah, United Arab Emirates
| | - Salvador Carranza
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Maik Damm
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | - Benjamin-Florian Hempel
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.,BIH Center for Regenerative Therapies BCRT, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Elisa B O John
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Daniel Petras
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Túbingen, 72076 Tübingen, Germany
| | - Paul Heiss
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - Bayram Göçmen
- Zoology Section, Department of Biology, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | | | - Alicia Jiménez Nosti
- Department of Physical and Analytical Chemistry, University of Oviedo, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, 33006 Oviedo, Spain
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Chen F, Qin M, Liu W, Wang F, Ren W, Xu H, Li F. Snake Venom Identification via Fluorescent Discrimination. Anal Chem 2021; 93:14025-14030. [PMID: 34528790 DOI: 10.1021/acs.analchem.1c02804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The identification and discrimination of snake venom are highly desired for timely clinical treatment. However, the complex components in snake venom make it a great challenge to achieve rapid and accurate identification. Inspired by the organism's taste sensing system, a fluorescent sensor array that could differentiate snake venoms was fabricated. The interaction of snake venoms with different fluorescent dyes in the sensor array gave rich information, based on which efficient detection of complex snake venom was achieved. The main six proteins of snake venom in the same concentration, different concentrations, and their mixtures were identified with 100% accuracy. Furthermore, seven snake venoms belonging to different snake families were discriminated in PBS buffer and human plasma. Interferents of bovine serum albumin (BSA), thrombin, and transferrin (TRF) demonstrated the practicability of the fluorescent sensor array. This strategy of a multiresponse sensor array provides an effective method for accurate and rapid venom toxicology analysis, benefiting early and timely clinical diagnosis and treatment.
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Affiliation(s)
- Fei Chen
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Meng Qin
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Wei Liu
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453000, China
| | - Fan Wang
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453000, China
| | - Wanjie Ren
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Huihua Xu
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Fengyu Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
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Calvete JJ, Lomonte B, Saviola AJ, Bonilla F, Sasa M, Williams DJ, Undheim EA, Sunagar K, Jackson TN. Mutual enlightenment: A toolbox of concepts and methods for integrating evolutionary and clinical toxinology via snake venomics and the contextual stance. Toxicon X 2021; 9-10:100070. [PMID: 34195606 PMCID: PMC8234350 DOI: 10.1016/j.toxcx.2021.100070] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Snakebite envenoming is a neglected tropical disease that may claim over 100,000 human lives annually worldwide. Snakebite occurs as the result of an interaction between a human and a snake that elicits either a defensive response from the snake or, more rarely, a feeding response as the result of mistaken identity. Snakebite envenoming is therefore a biological and, more specifically, an ecological problem. Snake venom itself is often described as a "cocktail", as it is a heterogenous mixture of molecules including the toxins (which are typically proteinaceous) responsible for the pathophysiological consequences of envenoming. The primary function of venom in snake ecology is pre-subjugation, with defensive deployment of the secretion typically considered a secondary function. The particular composition of any given venom cocktail is shaped by evolutionary forces that include phylogenetic constraints associated with the snake's lineage and adaptive responses to the snake's ecological context, including the taxa it preys upon and by which it is predated upon. In the present article, we describe how conceptual frameworks from ecology and evolutionary biology can enter into a mutually enlightening relationship with clinical toxinology by enabling the consideration of snakebite envenoming from an "ecological stance". We detail the insights that may emerge from such a perspective and highlight the ways in which the high-fidelity descriptive knowledge emerging from applications of -omics era technologies - "venomics" and "antivenomics" - can combine with evolutionary explanations to deliver a detailed understanding of this multifactorial health crisis.
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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, CO, USA
| | - Fabián Bonilla
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Mahmood Sasa
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Museo de Zoología, Centro de Investigaciones en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, Costa Rica
| | | | - Eivind A.B. Undheim
- Centre for Biodiversity Dynamics, Department of Biology, NTNU, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Timothy N.W. Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
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11
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Ehnert S, Seehase J, Müller-Renno C, Hannig M, Ziegler C. Simultaneous quantification of total carbohydrate and protein amounts from aqueous solutions by the sulfuric acid ultraviolet absorption method (SA-UV method). Anal Chim Acta 2021; 1174:338712. [PMID: 34247739 DOI: 10.1016/j.aca.2021.338712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/03/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Based on the sulfuric acid-ultraviolet assay (SA-UV, developed by Albalasmeh et al., 2013), we have further expanded this method for the simultaneous quantification of saccharides (carbohydrates) and proteins by ultraviolet spectrophotometry. The absorbance of saccharides depends on the formation of furfurals by dehydration in the presence of concentrated sulfuric acid, whereas proteins are unaffected and can be quantified by UV active peptide bonds and aromatic amino acid residues. In saccharide/protein mixtures the SA-UV assay offers a good alternative and substitutes the need for two different methods, like the phenol-sulfuric acid (PSA, developed by DuBois et al., 1951) and bicinchoninic acid (BCA, developed by Smith et al., 1985) assays. For the development of this method, we used glucose and BSA as model substrates and performed a method validation in terms of linearity, LOD, LOQ, accuracy, and precision. Simultaneous quantification in glucose/BSA mixtures is possible down to 20 mg/L from 30 μL sample volumes, and even low content mixtures with concentrations down to 2 mg/L can appropriately be quantified from higher volumes by an evaporation technique.
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Affiliation(s)
- Swen Ehnert
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Jürgen Seehase
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Christine Müller-Renno
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Hospital, 66421 Homburg, Germany
| | - Christiane Ziegler
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
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Larraga-Urdaz AL, Sanchez MLF, Encinar JR, Costa-Fernandez JM. Signal amplification strategies for clinical biomarker quantification using elemental mass spectrometry. Anal Bioanal Chem 2021; 414:53-62. [PMID: 33674934 DOI: 10.1007/s00216-021-03251-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 11/29/2022]
Abstract
The current trends in modern medicine towards early diagnosis, or even prognosis, of different diseases have brought about the need for the corresponding biomarker detection at ever lower levels in really complex matrices. To do so, it is necessary to use proper extremely sensitive detection techniques such as elemental mass spectrometry. However, target labelling with metals for subsequent sensitive ICP-MS detection falls short nowadays even if resorting to inorganic nanoparticles containing a high number of detectable elements. Thus, new amplification strategies are being proposed to face this analytical challenge that will be critically discussed in this paper. Fundamentals of different novel strategies developed to achieve signal amplification and sensitive elemental mass spectrometry detection are here discussed. Some representative examples of relevant clinical applications are highlighted, along with future prospects and challenges.
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Affiliation(s)
- Andrea L Larraga-Urdaz
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julian Claveria, 8, 33006, Oviedo, Spain
| | - Maria L Fernandez Sanchez
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julian Claveria, 8, 33006, Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julian Claveria, 8, 33006, Oviedo, Spain.
| | - Jose M Costa-Fernandez
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julian Claveria, 8, 33006, Oviedo, Spain.
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Cid-Barrio L, Calderón-Celis F, Costa-Fernández JM, Encinar JR. Assessment of the Potential and Limitations of Elemental Mass Spectrometry in Life Sciences for Absolute Quantification of Biomolecules Using Generic Standards. Anal Chem 2020; 92:13500-13508. [PMID: 32842726 DOI: 10.1021/acs.analchem.0c02942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inductively coupled plasma-mass spectrometry (ICP-MS) has been widely used in Life Sciences for the absolute quantification of biomolecules without specific standards, assuming the same response for generic compounds including complex biomolecules. However, contradictory results have been published on this regard. We present the first critical statistical comparison of the ICP-MS response factors obtained for 14 different relevant S-containing biomolecules (three peptides, four proteins, one amino acid, two cofactors, three polyethylene glycol (PEG) derivatives, and sulfate standard), covering a wide range of hydrophobicities and molecular sizes. Two regular flow nebulizers and a total consumption nebulizer (TCN) were tested. ICP-MS response factors were determined though calibration curves, and isotope dilution analysis was used to normalize the results. No statistical differences have been found for low-molecular-weight biocompounds, PEGs, and nonhydrophobic peptides using any of the nebulizers tested. Interestingly, while statistical differences were still found negligible (96-104%) for the proteins and hydrophobic peptide using the TCN, significantly lower response factors (87-40%) were obtained using regular flow nebulizers. Such differential behavior seems to be related mostly to hydrophobicity and partially to the molecular weight. Findings were validated using IDA in intact and digested bovine serum albumin solutions using the TCN (98 and 100%, respectively) and the concentric nebulizer (73 and 97%, respectively). Additionally, in the case of a phosphoprotein, results were corroborated using the P trace in parallel to the S trace used along the manuscript. This work seems to suggest that ICP-MS operated with regular nebulizers can offer absolute quantification using generic standards for most biomolecules except proteins and hydrophobic peptides.
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Affiliation(s)
- Laura Cid-Barrio
- Department of Physical and Analytical Chemistry, University of Oviedo, Av. Julian Clavería 8, 33006 Oviedo, Spain
| | - Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Av. Julian Clavería 8, 33006 Oviedo, Spain
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Av. Julian Clavería 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Av. Julian Clavería 8, 33006 Oviedo, Spain
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14
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Resano M, Aramendía M, Nakadi FV, García-Ruiz E, Alvarez-Llamas C, Bordel N, Pisonero J, Bolea-Fernández E, Liu T, Vanhaecke F. Breaking the boundaries in spectrometry. Molecular analysis with atomic spectrometric techniques. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115955] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Bocian A, Sławek S, Jaromin M, Hus KK, Buczkowicz J, Łysiak D, Petrílla V, Petrillova M, Legáth J. Comparison of Methods for Measuring Protein Concentration in Venom Samples. Animals (Basel) 2020; 10:E448. [PMID: 32182656 PMCID: PMC7142616 DOI: 10.3390/ani10030448] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 01/15/2023] Open
Abstract
Snake venom is an extremely interesting natural mixture of proteins and peptides, characterized by both high diversity and high pharmacological potential. Much attention has been paid to the study of venom composition of different species and also detailed analysis of the properties of individual components. Since proteins and peptides are the active ingredients in venom, rapidly developing proteomic techniques are used to analyze them. During such analyses, one of the routine operations is to measure the protein concentration in the sample. The aim of this study was to compare five methods used to measure protein content in venoms of two snake species: the Viperids representative, Agkistrodon contortrix, and the Elapids representative, Naja ashei. The study showed that for A. contortrix venom, the concentration of venom protein measured by four methods is very similar and only the NanoDrop method clearly stands out from the rest. However, in the case of N. ashei venom, each technique yields significantly different results. We hope that this report will help to draw attention to the problem of measuring protein concentration, especially in such a complex mixture as animal venoms.
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Affiliation(s)
- Aleksandra Bocian
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Sonja Sławek
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Marcin Jaromin
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Konrad K. Hus
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Justyna Buczkowicz
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Dawid Łysiak
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
| | - Vladimir Petrílla
- Department of Anatomy, Histology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia;
- Zoological Department, Zoological Garden Košice, Široká 31, 040 06 Košice-Kavečany, Slovakia
| | - Monika Petrillova
- Department of General Education Subjects, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia;
| | - Jaroslav Legáth
- Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland; (S.S.); (M.J.); (K.K.H.); (J.B.); (D.Ł.)
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia
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16
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Raab A, Feldmann J. Biological sulphur-containing compounds – Analytical challenges. Anal Chim Acta 2019; 1079:20-29. [DOI: 10.1016/j.aca.2019.05.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/25/2019] [Accepted: 05/27/2019] [Indexed: 01/19/2023]
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17
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Spider Venom: Components, Modes of Action, and Novel Strategies in Transcriptomic and Proteomic Analyses. Toxins (Basel) 2019; 11:toxins11100611. [PMID: 31652611 PMCID: PMC6832493 DOI: 10.3390/toxins11100611] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/18/2019] [Indexed: 12/19/2022] Open
Abstract
This review gives an overview on the development of research on spider venoms with a focus on structure and function of venom components and techniques of analysis. Major venom component groups are small molecular mass compounds, antimicrobial (also called cytolytic, or cationic) peptides (only in some spider families), cysteine-rich (neurotoxic) peptides, and enzymes and proteins. Cysteine-rich peptides are reviewed with respect to various structural motifs, their targets (ion channels, membrane receptors), nomenclature, and molecular binding. We further describe the latest findings concerning the maturation of antimicrobial, and cysteine-rich peptides that are in most known cases expressed as propeptide-containing precursors. Today, venom research, increasingly employs transcriptomic and mass spectrometric techniques. Pros and cons of venom gland transcriptome analysis with Sanger, 454, and Illumina sequencing are discussed and an overview on so far published transcriptome studies is given. In this respect, we also discuss the only recently described cross contamination arising from multiplexing in Illumina sequencing and its possible impacts on venom studies. High throughput mass spectrometric analysis of venom proteomes (bottom-up, top-down) are reviewed.
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18
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Freije-Carrelo L, García-Bellido J, Calderón-Celis F, Moldovan M, Encinar JR. GC-ICP-MS/MS Instrumental Setup for Total and Speciation Sulfur Analysis in Gasolines using Generic Standards. Anal Chem 2019; 91:7019-7024. [PMID: 31083916 DOI: 10.1021/acs.analchem.9b01199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative characterization of sulfur-containing petroleum derivatives is mainly limited by the large number of potential targets present and the matrix effects suffered due to the high-carbon-containing matrices. Herein we describe the instrumental modifications required in a commercial GC-ICP-MS/MS instrument, and their corresponding optimization, for turning it into a compound-independent quantitative technique for both total and speciation sulfur analysis in gasolines. Additionally, carbon-derived matrix effects were made negligible for direct and fast total S analysis, making the use of relatively complex isotope-dilution strategies not necessary anymore. An absolute detection limit of 0.3 pg of S was achieved, which is, to the best of our knowledge, more than 1 order of magnitude below the ones reported for other sulfur GC selective detectors. The precision was below 3% RSD. Total analysis was performed by flow-injection analysis through a transfer line and external calibration, whereas speciation analysis was carried out by chromatographic separation and internal standardization. In both cases, simple generic standards were used, which enabled us to get rid of specific S-containing standards, which were sometimes not available or unstable. The proposed method was successfully applied to total and speciation sulfur analysis of a commercial gasoline sample and validated with a certified-reference-material (ERM-EF213) gasoline. The approach has proved to be simple, fast, robust, and convenient for implementation in routine laboratories, as demonstrated by the successive analyses of 50 gasoline samples in 3 h without any instrumental drift.
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Affiliation(s)
- Laura Freije-Carrelo
- Department of Physical and Analytical Chemistry , University of Oviedo , Julián Clavería 8 , 33006 Oviedo , Spain
| | - Javier García-Bellido
- Department of Physical and Analytical Chemistry , University of Oviedo , Julián Clavería 8 , 33006 Oviedo , Spain
| | - Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry , University of Oviedo , Julián Clavería 8 , 33006 Oviedo , Spain
| | - Mariella Moldovan
- 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
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19
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Ghezellou P, Garikapati V, Kazemi SM, Strupat K, Ghassempour A, Spengler B. A perspective view of top-down proteomics in snake venom research. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 1:20-27. [PMID: 30076652 DOI: 10.1002/rcm.8255] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/25/2018] [Accepted: 07/29/2018] [Indexed: 06/08/2023]
Abstract
The venom produced by snakes contains complex mixtures of pharmacologically active proteins and peptides which play a crucial role in the pathophysiology of snakebite diseases. The deep understanding of venom proteomes can help to improve the treatment of this "neglected tropical disease" (as expressed by the World Health Organization [WHO]) and to develop new drugs. The most widely used technique for venom analysis is liquid chromatography/tandem mass spectrometry (LC/MS/MS)-based bottom-up (BU) proteomics. Considering the fact that multiple multi-locus gene families encode snake venom proteins, the major challenge for the BU proteomics is the limited sequence coverage and also the "protein inference problem" which result in a loss of information for the identification and characterization of toxin proteoforms (genetic variation, alternative mRNA splicing, single nucleotide polymorphism [SNP] and post-translational modifications [PTMs]). In contrast, intact protein measurements with top-down (TD) MS strategies cover almost complete protein sequences, and prove the ability to identify venom proteoforms and to localize their modifications and sequence variations.
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Affiliation(s)
- Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Germany
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | | | - Seyed Mahdi Kazemi
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | | | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Germany
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20
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Simultaneous extraction and analysis of multiple cystine-dense peptides by μSPE and microflow-MS/MS from plasma. Bioanalysis 2019; 11:485-493. [DOI: 10.4155/bio-2018-0276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aim: Develop a universal extraction and liquid chromatography-mass spectrometer method to simultaneously analyze cystine-dense peptide (CDP) miniproteins from rat and human plasma. The results of the analysis will be used to assist selection of therapeutic drug candidates from the vast CDP library. Methods & results: A micro-elution solid-phase extraction method was developed for the sample preparation of the CDP peptides in rat and human plasma followed by analysis by microflow liquid chromatography MS/MS. The methods developed for drug discovery were found to be accurate (±≤15.2% from nominal concentrations) and precise (≤13.4% CV), with a dynamic range of 1.00–500 ng/ml and extraction recoveries of 47.2–99.0%. Conclusion: This bioanalytical method can be utilized to screen CDP proteins and other miniproteins for drug discovery, candidate selection and further drug development.
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21
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Bouzas-Ramos D, García-Alonso JI, Costa-Fernández JM, Ruiz Encinar J. Quantitative Assessment of Individual Populations Present in Nanoparticle-Antibody Conjugate Mixtures Using AF4-ICP-MS/MS. Anal Chem 2019; 91:3567-3574. [PMID: 30727735 DOI: 10.1021/acs.analchem.8b05482] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A current remaining challenge in nanotechnology is the fast and reliable determination of the ratios between engineered nanoparticles and the species attached to their surface after chemical functionalization. The approach proposed herein based on the online coupling of asymmetric flow field-flow fractionation (AF4) with inductively coupled plasma-tandem mass spectrometry (ICP-MS/MS) allows for the first time the direct determination of such ratios in CdSe/ZnS core-shell quantum dot:rat monoclonal IgG2a antibody (QD:Ab) conjugate mixtures in a single run without any previous sample preparation (i.e., derivatization). AF4 provides full recovery and adequate resolution of the resulting bioconjugate from the excess of nanoparticles and proteins used in the different bioconjugation mixtures (1:1, 2:1, and 3:1 QD:Ab molar ratios were assessed). The point-by-point determination by ICP-MS/MS of the metal to sulfur ratios along the bioconjugate fractographic peak allowed disclosing the mixture of the different species in the bioconjugated sample, providing not only the limits of the range of QD:Ab ratios in the different bioconjugate species resulting after functionalization but also a good estimation of their individual relative abundance in the mixture. Interestingly, a wide variety of compositions were observed for the different bioconjugate mixtures studied (QD:Ab molar ratios ranging from 0.27 to 4.6). The resulting weighted QD:Ab ratio computed in this way for each bioconjugate peak matches well with both the global (average) QD:Ab ratio experimentally obtained by the simpler peak area ratio computation and the theoretical QD:Ab molar ratios assayed, which internally validates the procedure developed.
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Affiliation(s)
- Diego Bouzas-Ramos
- Department of Physical and Analytical Chemistry , University of Oviedo , Avda. Julián Clavería 8 , 33006 Oviedo , Spain
| | - Jose Ignacio García-Alonso
- Department of Physical and Analytical Chemistry , University of Oviedo , Avda. Julián Clavería 8 , 33006 Oviedo , Spain
| | - Jose Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry , University of Oviedo , Avda. Julián Clavería 8 , 33006 Oviedo , Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry , University of Oviedo , Avda. Julián Clavería 8 , 33006 Oviedo , Spain
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22
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Ouyang F, Yu T, Gu C, Wang G, Shi R, Lv R, Wu E, Ma C, Guo R, Li J, Zaczek A, Liu J. Sensitive detection of caspase-3 enzymatic activities and inhibitor screening by mass spectrometry with dual maleimide labelling quantitation. Analyst 2019; 144:6751-6759. [DOI: 10.1039/c9an01458f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is a great need to develop sensitive and specific methods for quantitative analysis of caspase-3 activities in cell apoptosis.
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23
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Calderón-Celis F, Sugiyama N, Yamanaka M, Sakai T, Diez-Fernández S, Calvete JJ, Sanz-Medel A, Encinar JR. Enhanced Universal Quantification of Biomolecules Using Element MS and Generic Standards: Application to Intact Protein and Phosphoprotein Determination. Anal Chem 2018; 91:1105-1112. [DOI: 10.1021/acs.analchem.8b04731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Naoki Sugiyama
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Michiko Yamanaka
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Tetsushi Sakai
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Silvia Diez-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Juan J. Calvete
- Instituto de Biomedicina de Valencia, IBV-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
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
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24
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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.
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Affiliation(s)
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Spain.
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25
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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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26
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Contreras-Martos S, Nguyen HH, Nguyen PN, Hristozova N, Macossay-Castillo M, Kovacs D, Bekesi A, Oemig JS, Maes D, Pauwels K, Tompa P, Lebrun P. Quantification of Intrinsically Disordered Proteins: A Problem Not Fully Appreciated. Front Mol Biosci 2018; 5:83. [PMID: 30234128 PMCID: PMC6131523 DOI: 10.3389/fmolb.2018.00083] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Protein quantification is essential in a great variety of biochemical assays, yet the inherent systematic errors associated with the concentration determination of intrinsically disordered proteins (IDPs) using classical methods are hardly appreciated. Routinely used assays for protein quantification, such as the Bradford assay or ultraviolet absorbance at 280 nm, usually seriously misestimate the concentrations of IDPs due to their distinct and variable amino acid composition. Therefore, dependable method(s) have to be worked out/adopted for this task. By comparison to elemental analysis as the gold standard, we show through the example of four globular proteins and nine IDPs that the ninhydrin assay and the commercial QubitTM Protein Assay provide reliable data on IDP quantity. However, as IDPs can show extreme variation in amino acid composition and physical features not necessarily covered by our examples, even these techniques should only be used for IDPs following standardization. The far-reaching implications of these simple observations are demonstrated through two examples: (i) circular dichroism spectrum deconvolution, and (ii) receptor-ligand affinity determination. These actual comparative examples illustrate the potential errors that can be incorporated into the biophysical parameters of IDPs, due to systematic misestimation of their concentration. This leads to inaccurate description of IDP functions.
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Affiliation(s)
- Sara Contreras-Martos
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hung H Nguyen
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Phuong N Nguyen
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nevena Hristozova
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mauricio Macossay-Castillo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Denes Kovacs
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Angela Bekesi
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jesper S Oemig
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kris Pauwels
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Institute of Enzymology, Budapest, Hungary
| | - Pierre Lebrun
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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Calvete JJ. Snake venomics – from low-resolution toxin-pattern recognition to toxin-resolved venom proteomes with absolute quantification. Expert Rev Proteomics 2018; 15:555-568. [DOI: 10.1080/14789450.2018.1500904] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Juan J. Calvete
- Evolutionary and Translational Venomics Laboratory, CSIC, Valencia, Spain
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Cid-Barrio L, Calderón-Celis F, Abásolo-Linares P, Fernández-Sánchez ML, Costa-Fernández JM, Encinar JR, Sanz-Medel A. Advances in absolute protein quantification and quantitative protein mapping using ICP-MS. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.09.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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29
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Applications of liquid chromatography-inductively coupled plasma-mass spectrometry in the biosciences: A tutorial review and recent developments. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.09.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Calvete JJ, Rodríguez Y, Quesada-Bernat S, Pla D. Toxin-resolved antivenomics-guided assessment of the immunorecognition landscape of antivenoms. Toxicon 2018; 148:107-122. [PMID: 29704534 DOI: 10.1016/j.toxicon.2018.04.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/26/2018] [Accepted: 04/22/2018] [Indexed: 01/23/2023]
Abstract
Snakebite envenoming represents a major issue in rural areas of tropical and subtropical regions across sub-Saharan Africa, South to Southeast Asia, Latin America and Oceania. Antivenoms constitute the only scientifically validated therapy for snakebite envenomings, provided they are safe, effective, affordable, accessible and administered appropriately. However, the lack of financial incentives in a technology that has remained relatively unchanged for more than a century, has contributed to some manufacturers leaving the market and others downscaling production or increasing the prices, leading to a decline in the availability and accessibility for these life-saving antidotes to millions of rural poor most at risk from snakebites in low income countries. The shortage of antivenoms can be significantly alleviated by optimizing the use of current antivenoms (through the assessment of their specific and paraspecific efficacy against the different medically relevant homologous and heterologous snake venoms) and by generating novel polyspecific antivenoms exhibiting broad clinical spectrum and wide geographic distribution range. Research on venoms has been continuously enhanced by advances in technology. Particularly, the last decade has witnessed the development of omics strategies for unravelling the toxin composition of venoms ("venomics") and to assess the immunorecognition profile of antivenoms ("antivenomics"). Here, we review recent developments and reflect on near future innovations that promise to revolutionize the mutually enlightening relationship between evolutionary and translational venomics.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain.
| | - Yania Rodríguez
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Sarai Quesada-Bernat
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Davinia Pla
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain.
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31
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Hempel BF, Damm M, Göçmen B, Karis M, Oguz MA, Nalbantsoy A, Süssmuth RD. Comparative Venomics of the Vipera ammodytes transcaucasiana and Vipera ammodytes montandoni from Turkey Provides Insights into Kinship. Toxins (Basel) 2018; 10:toxins10010023. [PMID: 29301241 PMCID: PMC5793110 DOI: 10.3390/toxins10010023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022] Open
Abstract
The Nose-horned Viper (Vipera ammodytes) is one of the most widespread and venomous snakes in Europe, which causes high frequent snakebite accidents. The first comprehensive venom characterization of the regional endemic Transcaucasian Nose-horned Viper (Vipera ammodytes transcaucasiana) and the Transdanubian Sand Viper (Vipera ammodytes montandoni) is reported employing a combination of intact mass profiling and bottom-up proteomics. The bottom-up analysis of both subspecies identified the major snake protein families of viper venoms. Furthermore, intact mass profiling revealed the presence of two tripeptidic metalloprotease inhibitors and their precursors. While previous reports applied multivariate analysis techniques to clarify the taxonomic status of the subspecies, an accurate classification of Vipera ammodytestranscaucasiana is still part of the ongoing research. The comparative analysis of the viper venoms on the proteome level reveals a close relationship between the Vipera ammodytes subspecies, which could be considered to clarify the classification of the Transcaucasian Nose-horned Viper. However, the slightly different ratio of some venom components could be indicating interspecific variations of the two studied subspecies or intraspecies alternations based on small sample size. Additionally, we performed a bioactivity screening with the crude venoms against several human cancerous and non-cancerous cell lines, which showed interesting results against a human breast adenocarcinoma epithelial cell line. Several fractions of Vipera a. transcaucasiana demonstrated a strong cytotoxic effect on triple negative MDA MB 231 breast cancer cells.
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Affiliation(s)
| | - Maik Damm
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Bayram Göçmen
- Department of Biology, Ege University, 35100 Izmir, Turkey.
| | - Mert Karis
- Department of Biology, Ege University, 35100 Izmir, Turkey.
| | | | - Ayse Nalbantsoy
- Department of Bioengineering, Ege University, 35100 Izmir, Turkey.
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
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32
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Calderón-Celis F, Sanz-Medel A, Encinar JR. Universal absolute quantification of biomolecules using element mass spectrometry and generic standards. Chem Commun (Camb) 2018; 54:904-907. [DOI: 10.1039/c7cc09059e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Standardless highly sensitive ICP-MS approach for the absolute and simultaneous quantification of important target biomolecules in life sciences.
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Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry
- University of Oviedo
- Julián Clavería 8
- 33006 Oviedo
- Spain
| | - Alfredo Sanz-Medel
- 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
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33
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Melani RD, Nogueira FCS, Domont GB. It is time for top-down venomics. J Venom Anim Toxins Incl Trop Dis 2017; 23:44. [PMID: 29075288 PMCID: PMC5648493 DOI: 10.1186/s40409-017-0135-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/21/2017] [Indexed: 12/19/2022] Open
Abstract
The protein composition of animal venoms is usually determined by peptide-centric proteomics approaches (bottom-up proteomics). However, this technique cannot, in most cases, distinguish among toxin proteoforms, herein called toxiforms, because of the protein inference problem. Top-down proteomics (TDP) analyzes intact proteins without digestion and provides high quality data to identify and characterize toxiforms. Denaturing top-down proteomics is the most disseminated subarea of TDP, which performs qualitative and quantitative analyzes of proteoforms up to ~30 kDa in high-throughput and automated fashion. On the other hand, native top-down proteomics provides access to information on large proteins (> 50 kDA) and protein interactions preserving non-covalent bonds and physiological complex stoichiometry. The use of native and denaturing top-down venomics introduced novel and useful techniques to toxinology, allowing an unprecedented characterization of venom proteins and protein complexes at the toxiform level. The collected data contribute to a deep understanding of venom natural history, open new possibilities to study the toxin evolution, and help in the development of better biotherapeutics.
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Affiliation(s)
- Rafael D. Melani
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Fabio C. S. Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Gilberto B. Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
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Abstract
Snakebite envenoming is a neglected tropical disease that kills >100,000 people and maims >400,000 people every year. Impoverished populations living in the rural tropics are particularly vulnerable; snakebite envenoming perpetuates the cycle of poverty. Snake venoms are complex mixtures of proteins that exert a wide range of toxic actions. The high variability in snake venom composition is responsible for the various clinical manifestations in envenomings, ranging from local tissue damage to potentially life-threatening systemic effects. Intravenous administration of antivenom is the only specific treatment to counteract envenoming. Analgesics, ventilator support, fluid therapy, haemodialysis and antibiotic therapy are also used. Novel therapeutic alternatives based on recombinant antibody technologies and new toxin inhibitors are being explored. Confronting snakebite envenoming at a global level demands the implementation of an integrated intervention strategy involving the WHO, the research community, antivenom manufacturers, regulatory agencies, national and regional health authorities, professional health organizations, international funding agencies, advocacy groups and civil society institutions.
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Affiliation(s)
- José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, PO Box 11501-2060, San José, Costa Rica
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | | | - Robert A Harrison
- Alistair Reid Venom Research Unit, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David J Williams
- Charles Campbell Toxinology Centre, School of Medicine &Health Sciences, University of Papua New Guinea, Boroko, National Capital District, Papua New Guinea
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia
| | - David A Warrell
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
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35
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Liu Z, Li X, Xiao G, Chen B, He M, Hu B. Application of inductively coupled plasma mass spectrometry in the quantitative analysis of biomolecules with exogenous tags: A review. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.05.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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36
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Nalbantsoy A, Hempel BF, Petras D, Heiss P, Göçmen B, Iğci N, Yildiz MZ, Süssmuth RD. Combined venom profiling and cytotoxicity screening of the Radde's mountain viper (Montivipera raddei) and Mount Bulgar Viper (Montivipera bulgardaghica) with potent cytotoxicity against human A549 lung carcinoma cells. Toxicon 2017. [PMID: 28625888 DOI: 10.1016/j.toxicon.2017.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here we report the first characterization of the endemic Mount Bulgar Viper (Montivipera bulgardaghica) and Radde's mountain viper (Montivipera raddei) venom by a combined approach using intact mass profiling and bottom-up proteomics. The cytotoxicity screening of crude venom as well as isolated serine proteases revealed a high activity against A549 human lung carcinoma cells. By means of intact mass profiling of native and reduced venom we observed basic and acidic phospholipases type A2. Moreover, the analysis revealed snake venom metalloproteases, cysteine-rich secretory proteins, disintegrins, snake venom serine proteases, C-type lectins, a vascular endothelial growth factor and an L-amino acid oxidase.
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Affiliation(s)
- Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, 35100, Izmir, Turkey
| | - Benjamin-Florian Hempel
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Daniel Petras
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany; University of California - San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences, PSB 4231, 9500, Gilman Drive, La Jolla, CA, USA
| | - Paul Heiss
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Bayram Göçmen
- Zoology Section, Department of Biology, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Nasit Iğci
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Nevşehir Hacı Bektaş Veli University, Nevşehir, Turkey
| | - Mehmet Zülfü Yildiz
- Zoology Section, Department of Biology, Faculty of Arts and Science, Adıyaman University, Adıyaman, Turkey
| | - Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany.
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Calderón-Celis F, Cid-Barrio L, Encinar JR, Sanz-Medel A, Calvete JJ. Absolute venomics: Absolute quantification of intact venom proteins through elemental mass spectrometry. J Proteomics 2017; 164:33-42. [PMID: 28579478 DOI: 10.1016/j.jprot.2017.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 12/17/2022]
Abstract
We report the application of a hybrid element and molecular MS configuration for the parallel absolute quantification of μHPLC-separated intact sulfur-containing venom proteins, via ICP triple quadrupole MS and 32S/34S isotope dilution analysis, and identification by ESI-QToF-MS of the toxins of the medically important African black-necked spitting cobra, Naja nigricollis (Tanzania); New Guinea small-eyed snake, Micropechis ikaheka; and Papuan black snake, Pseudechis papuanus. The main advantage of this approach is that only one generic sulfur-containing standard is required to quantify each and all intact Cys- and/or Met-containing toxins of the venom proteome. The results of absolute quantification are in reasonably good agreement with previously reported relative quantification of the most abundant protein families. However, both datasets depart in the quantification of the minor ones, showing a tendency for this set of proteins to be underestimated in standard peptide-centric venomics approaches. The molecular identity, specific toxic activity, and concentration in the venom, are the pillars on which the toxicovenomics-aimed discovery of the most medically-relevant venom toxins, e.g. those that need to be neutralized by an effective therapeutic antivenom, should be based. The pioneering venom proteome-wide absolute quantification shown in this paper represents thus a significant advance towards this goal. The potential of ICP triple quadrupole MS in proteomics in general, and venomics in particular, is critically discussed. BIOLOGICAL SIGNIFICANCE Animal venoms provide excellent model systems for investigating interactions between predators and prey, and the molecular mechanisms that contribute to adaptive protein evolution. On the other hand, numerous cases of snake bites occur yearly by encounters of humans and snakes in their shared natural environment. Snakebite envenoming is a serious global public health issue that affects the most impoverished and geopolitically disadvantaged rural communities in many tropical and subtropical countries. Unveiling the temporal and spatial patterns of venom variability is of fundamental importance to understand the molecular basis of envenoming, a prerequisite for developing therapeutic strategies against snakebite envenoming. Research on venoms has been continuously enhanced by advances in technology. The combined application of next-generation transcriptomic and venomic workflows has demonstrated unparalleled capabilities for venom characterization in unprecedented detail. However, mass spectrometry is not inherently quantitative, and this analytical limitation has sparked the development of methods to determine absolute abundance of proteins in biological samples. Here we show the potential of a hybrid element and molecular MS configuration for the parallel ESI-QToF-MS and ICP-QQQ detection and absolute quantification of intact sulfur-containing venom proteins via 32S/34S isotope dilution analysis. This configuration has been applied to quantify the toxins of the medically important African snake Naja nigricollis (Tanzania), and the Papuan species Micropechis ikaheka and Pseudechis papuanus.
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Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Laura Cid-Barrio
- 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.
| | - Alfredo Sanz-Medel
- 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.
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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.
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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
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Venomics: integrative venom proteomics and beyond*. Biochem J 2017; 474:611-634. [DOI: 10.1042/bcj20160577] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/31/2016] [Accepted: 01/03/2017] [Indexed: 01/15/2023]
Abstract
Venoms are integrated phenotypes that evolved independently in, and are used for predatory and defensive purposes by, a wide phylogenetic range of organisms. The same principles that contribute to the evolutionary success of venoms, contribute to making the study of venoms of great interest in such diverse fields as evolutionary ecology and biotechnology. Evolution is profoundly contingent, and nature also reinvents itself continuosly. Changes in a complex phenotypic trait, such as venom, reflect the influences of prior evolutionary history, chance events, and selection. Reconstructing the natural history of venoms, particularly those of snakes, which will be dealt with in more detail in this review, requires the integration of different levels of knowledge into a meaningful and comprehensive evolutionary framework for separating stochastic changes from adaptive evolution. The application of omics technologies and other disciplines have contributed to a qualitative and quantitative advance in the road map towards this goal. In this review we will make a foray into the world of animal venoms, discuss synergies and complementarities of the different approaches used in their study, and identify current bottlenecks that prevent inferring the evolutionary mechanisms and ecological constraints that molded snake venoms to their present-day variability landscape.
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