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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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Tanaka T, Kojo K, Nagumo Y, Ikeda A, Shimizu T, Fujimoto S, Kakinuma T, Uchida M, Kimura T, Kandori S, Negoro H, Nishiyama H. A new clustering model based on the seminal plasma/serum ratios of multiple trace element concentrations in male patients with subfertility. Reprod Med Biol 2024; 23:e12584. [PMID: 38807752 PMCID: PMC11131575 DOI: 10.1002/rmb2.12584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024] Open
Abstract
Purpose To investigate whether seminal plasma (SP)/serum ratios of multiple trace elements (TEs) can classify patients with male subfertility. Methods SP/serum ratios of 20 TEs (lithium, sodium, magnesium, phosphorus, sulfur, potassium, calcium, manganese, iron, cobalt, copper, zinc, arsenic, selenium, rubidium, strontium, molybdenum, cesium, barium, and thallium) were calculated for healthy volunteers (n = 4) and those consulting for male subfertility (n = 245). Volunteer semen samples were collected by split ejaculation into early and subsequent fractions, and SP/serum ratio data were compared between fractions. The patients' SP/serum ratio data were used in an unsupervised clustering analysis and qualitatively compared with the data from the fractions of ejaculation from the volunteers. Semen quality parameters and pregnancy outcomes were compared between patient clusters. Results The early fraction of volunteers was characterized by lower phosphorus and arsenic and 18 other higher TEs than the subsequent fraction. Cluster analysis classified patients into four distinct clusters, one sharing characteristics with the early fraction and another with the subsequent fraction. One cluster with the early fraction characteristics had significantly lower semen volume and higher pregnancy rates from spontaneous pregnancies or intrauterine insemination. Conclusions Classification of patients based on SP/serum ratios of multiple TEs represents the dominance of fractions of ejaculation samples.
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Affiliation(s)
- Takazo Tanaka
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
| | - Kosuke Kojo
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
- Center for Human ReproductionInternational University of Health and Welfare HospitalNasushiobaraTochigiJapan
| | - Yoshiyuki Nagumo
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
| | - Atsushi Ikeda
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
| | - Takuya Shimizu
- Health Care Analysis CenterRenatech Co., Ltd.IseharaKanagawaJapan
| | | | - Toshiyuki Kakinuma
- Center for Human ReproductionInternational University of Health and Welfare HospitalNasushiobaraTochigiJapan
| | - Masahiro Uchida
- Department of UrologyTsukuba Gakuen HospitalTsukubaIbarakiJapan
| | - Tomokazu Kimura
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
| | - Shuya Kandori
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
| | - Hiromitsu Negoro
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
| | - Hiroyuki Nishiyama
- Department of Urology, Faculty of MedicineUniversity of TsukubaTsukubaIbarakiJapan
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3
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Lemke N, El-Khatib AH, Tchipilov T, Jakubowski N, Weller MG, Vogl J. Procedure providing SI-traceable results for the calibration of protein standards by sulfur determination and its application on tau. Anal Bioanal Chem 2022; 414:4441-4455. [PMID: 35316347 PMCID: PMC9142460 DOI: 10.1007/s00216-022-03974-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 11/20/2022]
Abstract
Quantitative proteomics is a growing research area and one of the most important tools in the life sciences. Well-characterized and quantified protein standards are needed to achieve accurate and reliable results. However, only a limited number of sufficiently characterized protein standards are currently available. To fill this gap, a method for traceable protein quantification using sulfur isotope dilution inductively coupled plasma mass spectrometry (ICP-MS) was developed in this study. Gel filtration and membrane filtration were tested for the separation of non-protein-bound sulfur in the protein solution. Membrane filtration demonstrated a better performance due to the lower workload and the very low sulfur blanks of 11 ng, making it well suited for high-purity proteins such as NIST SRM 927, a bovine serum albumin (BSA). The method development was accomplished with NIST SRM 927e and a commercial avidin. The quantified mass fraction of NIST SRM 927e agreed very well with the certified value and showed similar uncertainties (3.6%) as established methods while requiring less sample preparation and no species-specific standards. Finally, the developed procedure was applied to the tau protein, which is a biomarker for a group of neurodegenerative diseases denoted “tauopathies” including, e.g., Alzheimer’s disease and frontotemporal dementia. For the absolute quantification of tau in the brain of transgenic mice overexpressing human tau, a well-defined calibration standard was needed. Therefore, a pure tau solution was quantified, yielding a protein mass fraction of (0.328 ± 0.036) g/kg, which was confirmed by amino acid analysis.
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Affiliation(s)
- Nora Lemke
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Hessische Str. 3-4, 10115, Berlin, Germany
| | - Ahmed H El-Khatib
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.,Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Teodor Tchipilov
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | | | - Michael G Weller
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Jochen Vogl
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.
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4
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Xia LY, Tang YN, Zhang J, Dong TY, Zhou RX. Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications. Semin Cancer Biol 2022; 86:1105-1119. [PMID: 34979273 DOI: 10.1016/j.semcancer.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.
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Affiliation(s)
- Ling-Ying Xia
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ya-Nan Tang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jie Zhang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Tian-Yu Dong
- College of Chemistry, Sichuan University Chengdu, Sichuan 610064, PR China
| | - Rong-Xing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China.
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5
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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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6
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Torregrosa D, Grindlay G, Gras L, Mora J. Immunoassays based on inductively coupled plasma mass spectrometry detection: So far so good, so what? Microchem J 2021. [DOI: 10.1016/j.microc.2021.106200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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Ramírez-Acosta S, Arias-Borrego A, Navarro-Roldán F, Selma-Royo M, Calatayud M, Collado MC, Huertas-Abril PV, Abril N, Barrera TG. Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review. Anal Chim Acta 2021; 1176:338620. [PMID: 34399890 DOI: 10.1016/j.aca.2021.338620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/12/2021] [Accepted: 04/01/2021] [Indexed: 02/08/2023]
Abstract
Omic methodologies have become key analytical tools in a wide number of research topics such as systems biology, environmental analysis, biomedicine or food analysis. They are especially useful when they are combined providing a new perspective and a holistic view of the analytical problem. Methodologies for microbiota analysis have been mostly focused on genome sequencing. However, information provided by these metagenomic studies is limited to the identification of the presence of genes, taxa and their inferred functionality. To achieve a deeper knowledge of microbial functionality in health and disease, especially in dysbiosis conditions related to metal and metalloid exposure, the introduction of additional meta-omic approaches including metabolomics, metallomics, metatranscriptomics and metaproteomics results essential. The possible impact of metals and metalloids on the gut microbiota and their effects on gut-brain axis (GBA) only begin to be figured out. To this end new analytical workflows combining powerful tools are claimed such as high resolution mass spectrometry and heteroatom-tagged proteomics for the absolute quantification of metal-containing biomolecules using the metal as a "tag" in a sensitive and selective detector (e.g. ICP-MS). This review focus on current analytical methodologies related with the analytical techniques and procedures available for metallomics and microbiota analysis with a special attention on their advantages and drawbacks.
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Affiliation(s)
- Sara Ramírez-Acosta
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
| | - Ana Arias-Borrego
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
| | - Francisco Navarro-Roldán
- Department of Integrated Sciences, Cell Biology, Faculty of Experimental Sciences, University of Huelva, Spain
| | - Marta Selma-Royo
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Marta Calatayud
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Paula V Huertas-Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain.
| | - Tamara García Barrera
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain.
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Jin X, Yang L, Yan X, Wang Q. Screening Platform Based on Inductively Coupled Plasma Mass Spectrometry for β-Site Amyloid Protein Cleaving Enzyme 1 (BACE1) Inhibitors. ACS Chem Neurosci 2021; 12:1093-1099. [PMID: 33764738 DOI: 10.1021/acschemneuro.0c00816] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
β-Site amyloid protein cleaving enzyme 1 (BACE1) is a promising therapeutic target for developing inhibitors to alleviate Alzheimer's disease (AD). Herein, we established an inductively coupled plasma mass spectrometry (ICPMS)-based inhibitor screening platform. A biotin-labeled lanthanide-coded peptide probe (LCPP; biotin-PEG2-EVNLDAEC-DOTA-Ln) was designed to determine the activity of BACE1 and evaluate the degree of inhibition of inhibitors. The platform was first validated with two commercially available inhibitors (BSI I and BSI IV) in terms of IC50 values and then applied to two newly designed inhibitors (inhibitors II and III) based on the crystal structure of BACE1 interacting with inhibitor I, and each of them contained an acylguanidine core structure. We found that their inhibition effects were improved as evaluated by the sensitive and accurate LCPP-ICPMS platform, demonstrating its ability for new drug screening.
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Affiliation(s)
- Xin Jin
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Limin Yang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaowen Yan
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Qiuquan Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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9
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Abstract
Inductively coupled plasma mass spectrometry (ICP-MS) is a sensitive instrumental analysis technique used for multielemental and isotopic determination. Here we provide a sample preparation and circadian ICP-MS analysis protocol for use with mammalian tissues and cells, using mouse fibroblasts as a case study.
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10
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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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11
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Knoll S, Rösch T, Huhn C. Trends in sample preparation and separation methods for the analysis of very polar and ionic compounds in environmental water and biota samples. Anal Bioanal Chem 2020; 412:6149-6165. [PMID: 32710277 PMCID: PMC7442764 DOI: 10.1007/s00216-020-02811-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/29/2020] [Accepted: 07/08/2020] [Indexed: 12/25/2022]
Abstract
Recent years showed a boost in knowledge about the presence and fate of micropollutants in the environment. Instrumental and methodological developments mainly in liquid chromatography coupled to mass spectrometry hold a large share in this success story. These techniques soon complemented gas chromatography and enabled the analysis of more polar compounds including pesticides but also household chemicals, food additives, and pharmaceuticals often present as traces in surface waters. In parallel, sample preparation techniques evolved to extract and enrich these compounds from biota and water samples. This review article looks at very polar and ionic compounds using the criterion log P ≤ 1. Considering about 240 compounds, we show that (simulated) log D values are often even lower than the corresponding log P values due to ionization of the compounds at our reference pH of 7.4. High polarity and charge are still challenging characteristics in the analysis of micropollutants and these compounds are hardly covered in current monitoring strategies of water samples. The situation is even more challenging in biota analysis given the large number of matrix constituents with similar properties. Currently, a large number of sample preparation and separation approaches are developed to meet the challenges of the analysis of very polar and ionic compounds. In addition to reviewing them, we discuss some trends: for sample preparation, preconcentration and purification efforts by SPE will continue, possibly using upcoming mixed-mode stationary phases and mixed beds in order to increase comprehensiveness in monitoring applications. For biota analysis, miniaturization and parallelization are aspects of future research. For ionic or ionizable compounds, we see electromembrane extraction as a method of choice with a high potential to increase throughput by automation. For separation, predominantly coupled to mass spectrometry, hydrophilic interaction liquid chromatography applications will increase as the polarity range ideally complements reversed phase liquid chromatography, and instrumentation and expertise are available in most laboratories. Two-dimensional applications have not yet reached maturity in liquid-phase separations to be applied in higher throughput. Possibly, the development and commercial availability of mixed-mode stationary phases make 2D applications obsolete in semi-targeted applications. An interesting alternative will enter routine analysis soon: supercritical fluid chromatography demonstrated an impressive analyte coverage but also the possibility to tailor selectivity for targeted approaches. For ionic and ionizable micropollutants, ion chromatography and capillary electrophoresis are amenable but may be used only for specialized applications such as the analysis of halogenated acids when aspects like desalting and preconcentration are solved and the key advantages are fully elaborated by further research. Graphical abstract.
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Affiliation(s)
- Sarah Knoll
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, Tübingen, Germany
| | - Tobias Rösch
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, Tübingen, Germany
| | - Carolin Huhn
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, Tübingen, Germany.
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12
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Xu B, Zhang Y, Chen Y, Zeng M, Feng J, Tang J, Yu L. Simultaneous multielement analysis by ICP-MS with simple whole blood sample dilution and its application to uremic patients undergoing long-term hemodialysis. Scandinavian Journal of Clinical and Laboratory Investigation 2020; 80:247-255. [PMID: 32077771 DOI: 10.1080/00365513.2020.1729401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Few studies were reported on trace elements' alterations in uremic patients undergoing long-term (>24 months) hemodialysis (HD), especially by using the whole blood as the biological fluid for the measuring purpose. Our objective was to develop an improved micro-sampling inductively coupled plasma-mass spectrometry (ICP-MS) method to determine the levels of Ca, Mg, Cu, Zn, Fe, Mn, Se and Pb in uremic patients receiving long-term HD. A ICP-MS method with a modified whole blood sample preparation procedure with small volumes was established and applied for the simultaneous quantification of the various elements in uremic patients undergoing long-term HD. 124 eligible uremic patients receiving long-term HD (75 males and 49 females) and 77 healthy subjects (54 males and 23 females) were recruited and Ca, Mg, Cu, Zn, Fe, Mn, Se and Pb levels were further determined. Our results revealed that uremic patients with HD had significantly higher blood levels of Ca, Mg, Zn and Pb and lower Cu, Fe, Se and Mn concentrations than healthy controls. In conclusion, a reproducible and reliable ICP-MS method using minimal whole blood sample volume (50 μL) with a simple dilution-based preparation procedure was successfully improved, validated and applied. Uremic patients undergoing long-term HD might be at increased risk of some essential trace elements deficiency (especially for Cu, Fe and Se) or toxic trace element excess (Pb) in respect to healthy subjects. Monitoring of blood levels and supplementation of some trace elements may be indicated in uremic patients undergoing long-term HD.
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Affiliation(s)
- Bei Xu
- Department of Clinical Laboratory, Mianyang Central Hospital, Mianyang, Sichuan, China
| | - Yamei Zhang
- Department of Clinical Laboratory, Mianyang Central Hospital, Mianyang, Sichuan, China
| | - Yan Chen
- Department of Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Min Zeng
- Department of Pharmacy, Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiafu Feng
- Department of Clinical Laboratory, Mianyang Central Hospital, Mianyang, Sichuan, China
| | - Jie Tang
- Department of Clinical Laboratory, Mianyang Central Hospital, Mianyang, Sichuan, China
| | - Lin Yu
- Department of Clinical Laboratory, Mianyang Central Hospital, Mianyang, Sichuan, China
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13
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Benda D, Lüttgert N, Beck S. Peptide quantification in elemental mass spectrometry using a photoclevable metal-coded affinity tag (MeCAT) reagent. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:978-980. [PMID: 30835904 DOI: 10.1002/rcm.8425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/14/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Affiliation(s)
- David Benda
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Nils Lüttgert
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Sebastian Beck
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
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14
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Yuan R, Ge F, Liang Y, Zhou Y, Yang L, Wang Q. Viruslike Element-Tagged Nanoparticle Inductively Coupled Plasma Mass Spectrometry Signal Multiplier: Membrane Biomarker Mediated Cell Counting. Anal Chem 2019; 91:4948-4952. [DOI: 10.1021/acs.analchem.9b00749] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Rong Yuan
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fuchun Ge
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yong Liang
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yang Zhou
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Limin Yang
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Qiuquan Wang
- Department of Chemistry & the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- State Key Lab of Marine Environmental Science, Xiamen University, Xiamen 361005, China
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15
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Krasnići N, Dragun Z, Kazazić S, Muharemović H, Erk M, Jordanova M, Rebok K, Kostov V. Characterization and identification of selected metal-binding biomolecules from hepatic and gill cytosols of Vardar chub (Squalius vardarensis Karaman, 1928) using various techniques of liquid chromatography and mass spectrometry. Metallomics 2019; 11:1060-1078. [DOI: 10.1039/c9mt00036d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Metals play crucial physiological roles, but they can also cause irreparable toxic effects through binding to important cellular biomolecules in aquatic organisms.
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Affiliation(s)
- Nesrete Krasnići
- Ruđer Bošković Institute
- Division for Marine and Environmental Research
- Laboratory for Biological Effects of Metals
- 10002 Zagreb
- Croatia
| | - Zrinka Dragun
- Ruđer Bošković Institute
- Division for Marine and Environmental Research
- Laboratory for Biological Effects of Metals
- 10002 Zagreb
- Croatia
| | - Snježana Kazazić
- Ruđer Bošković Institute
- Division of Physical Chemistry
- Laboratory for Mass Spectrometry and Functional Proteomics
- 10002 Zagreb
- Croatia
| | - Hasan Muharemović
- Ruđer Bošković Institute
- Division of Physical Chemistry
- Laboratory for Mass Spectrometry and Functional Proteomics
- 10002 Zagreb
- Croatia
| | - Marijana Erk
- Ruđer Bošković Institute
- Division for Marine and Environmental Research
- Laboratory for Biological Effects of Metals
- 10002 Zagreb
- Croatia
| | - Maja Jordanova
- Faculty of Natural Sciences and Mathematics
- Ss. Cyril and Methodius University in Skopje
- 1000 Skopje
- Macedonia
| | - Katerina Rebok
- Faculty of Natural Sciences and Mathematics
- Ss. Cyril and Methodius University in Skopje
- 1000 Skopje
- Macedonia
| | - Vasil Kostov
- Institute of Animal Sciences
- 1000 Skopje
- Macedonia
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16
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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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17
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Pérez E, Marco FM, Martínez-Peinado P, Mora J, Grindlay G. Evaluation of different competitive immunoassays for aflatoxin M 1 determination in milk samples by means of inductively coupled plasma mass spectrometry. Anal Chim Acta 2018; 1049:10-19. [PMID: 30612640 DOI: 10.1016/j.aca.2018.11.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/29/2022]
Abstract
Haptens (i.e. biomolecules which molecular weight is lower than 10 kDa) determination by inductively coupled plasma mass spectrometry (ICP-MS) is usually performed by means of competitive immunoassays. In these immunoassays, analyte quantification is indirectly carried out using two different tracer species (i.e. antibodies or antigen-protein conjugates). However, the benefits (and drawbacks) derived from using a given tracer species have not been systematically investigated so far. The goal of this work is to evaluate the influence of the tracer species employed in competitive immunoassays on the analytical figures of merit for aflatoxin M1 (AFM1) determination in milk samples. To this end, three different strategies have been developed and evaluated, namely: (i) antibody binding inhibition assay (ABIA); (ii) capture inhibition assay (CIA); and (iii) capture bridge inhibition assay (CBIA). Experimental results show that the use of the antibody as tracer species (as in the ABIA approach) affords better analytical figures of merit for AFM1 determination than using the antigen-protein conjugate as the tracer one (as in the CIA and CBIA strategies). The limit of detection afforded by ABIA strategy (i.e. 0.1 ng kg-1) for AFM1 determination was 1000-fold and 50-fold lower regarding the CIA and CBIA strategies, respectively. In the case of the ABIA approach, the characteristics of the metal nanoparticle label employed to detect the tracer species is critical on the analytical figures of merit. However, when the hapten-protein conjugates are used as tracer species, immunocomplex formation is severely hampered by steric effects caused by the protein moiety and, consequently, the characteristics of the metal nanoparticle label is not critical in the immunoassay performance. The different immunoassay strategies were successfully validated for AFM1 determination in milk samples using a certified reference material of whole milk powder (ERM-BD283) according to European Conformity guidelines for analytical methods of food contaminants and mycotoxins. Compared to ELISA, the immunoassay developed for AFM1 determination in milk samples improve limits of detection up to 10-fold.
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Affiliation(s)
- Emma Pérez
- Department of Analytical Chemistry, Nutrition and Food Sciences, University of Alicante, PO Box 99, 03080, Alicante, Spain
| | - Francisco M Marco
- Department of Biotechnology, University of Alicante, PO Box 99, 03080, Alicante, Spain
| | | | - Juan Mora
- Department of Analytical Chemistry, Nutrition and Food Sciences, University of Alicante, PO Box 99, 03080, Alicante, Spain
| | - Guillermo Grindlay
- Department of Analytical Chemistry, Nutrition and Food Sciences, University of Alicante, PO Box 99, 03080, Alicante, Spain.
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18
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Cheignon C, Cordeau E, Prache N, Cantel S, Martinez J, Subra G, Arnaudguilhem C, Bouyssiere B, Enjalbal C. Receptor-Ligand Interaction Measured by Inductively Coupled Plasma Mass Spectrometry and Selenium Labeling. J Med Chem 2018; 61:10173-10184. [PMID: 30395477 DOI: 10.1021/acs.jmedchem.8b01320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the search for an alternative strategy to the radioactivity measurement conventionally performed to probe receptor-ligand interactions in pharmacological assays, we demonstrated that selenium labeling of the studied ligand combined with elemental mass spectrometry was as efficient and robust as the reference method but devoid of its environmental and health hazards. The proof-of-concept was illustrated on two GPCR receptors, vasopressin (V1A) and cholecystokinin B (CCK-B), involving peptides as endogenous ligands. We proposed several methodologies to produce selenium-labeled ligands according to peptide sequences along with binding affinity constraints. A selection of selenopeptides that kept high affinities toward the targeted receptor were engaged in saturation and competitive binding experiments with subsequent sensitive RP-LC-ICP-MS measurements. Experimental values of affinity constant ( Ki) were perfectly correlated to literature data, illustrating the general great potency of replacing radioactive iodine by selenium for ligand labeling to further undergo unaffected pharmacology experiments efficiently monitored by elemental mass spectrometry.
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Affiliation(s)
- Clémence Cheignon
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Emmanuelle Cordeau
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Nolween Prache
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Sonia Cantel
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Jean Martinez
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Gilles Subra
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Carine Arnaudguilhem
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Brice Bouyssiere
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Christine Enjalbal
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
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19
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Galvez L, Theiner S, Grabarics M, Kowol CR, Keppler BK, Hann S, Koellensperger G. Critical assessment of different methods for quantitative measurement of metallodrug-protein associations. Anal Bioanal Chem 2018; 410:7211-7220. [PMID: 30155703 PMCID: PMC6208971 DOI: 10.1007/s00216-018-1328-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/13/2018] [Accepted: 08/15/2018] [Indexed: 01/18/2023]
Abstract
Quantitative screening for potential drug-protein binding is an essential step in developing novel metal-based anticancer drugs. ICP-MS approaches are at the core of this task; however, many applications lack in the capability of large-scale high-throughput screenings and proper validation. In this work, we critically discuss the analytical figures of merit and the potential method-based quantitative differences applying four different ICP-MS strategies to ex vivo drug-serum incubations. Two candidate drugs, more specifically, two Pt(IV) complexes with known differences of binding affinity towards serum proteins were selected. The study integrated centrifugal ultrafiltration followed by flow injection analysis, turbulent flow chromatography (TFC), and size exclusion chromatography (SEC), all combined with inductively coupled plasma-mass spectrometry (ICP-MS). As a novelty, for the first time, UHPLC SEC-ICP-MS was implemented to enable rapid protein separation to be performed within a few minutes at > 90% column recovery for protein adducts and small molecules. Graphical abstract Quantitative screening for potential drug-protein binding is an essential step in developingnovel metal-based anticancer drugs.
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Affiliation(s)
- Luis Galvez
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Sarah Theiner
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Márkó Grabarics
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Christian R Kowol
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 42, 1090, Vienna, Austria
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 42, 1090, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences - BOKU Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria.
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20
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Pérez E, Bierla K, Grindlay G, Szpunar J, Mora J, Lobinski R. Lanthanide polymer labels for multiplexed determination of biomarkers in human serum samples by means of size exclusion chromatography-inductively coupled plasma mass spectrometry. Anal Chim Acta 2018; 1018:7-15. [DOI: 10.1016/j.aca.2018.02.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 11/27/2022]
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21
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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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22
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Yan X, He B, Wang D, Hu L, Liu L, Liao C, Jiang G. Two-dimensional (weak anion exchange chromatography-gel electrophoresis) separations coupling to inductively coupled plasma mass spectrometry strategy for analysis of metalloproteins. Talanta 2018; 184:404-410. [DOI: 10.1016/j.talanta.2018.03.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/02/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
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23
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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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24
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Kaur R, Mudgal R, Narwal M, Tomar S. Development of an ELISA assay for screening inhibitors against divalent metal ion dependent alphavirus capping enzyme. Virus Res 2018; 256:209-218. [PMID: 29958924 DOI: 10.1016/j.virusres.2018.06.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 11/24/2022]
Abstract
Alphavirus non-structural protein, nsP1 has a distinct molecular mechanism of capping the viral RNAs than the conventional capping mechanism of host. Thus, alphavirus capping enzyme nsP1 is a potential drug target. nsP1 catalyzes the methylation of guanosine triphosphate (GTP) by transferring the methyl group from S-adenosylmethionine (SAM) to a GTP molecule at its N7 position with the help of nsP1 methyltransferase (MTase) followed by guanylylation (GT) reaction which involves the formation of m7GMP-nsP1 covalent complex by nsP1 guanylyltransferase (GTase). In subsequent reactions, m7GMP moiety is added to the 5' end of the viral ppRNA by nsP1 GTase resulting in the formation of cap0 structure. In the present study, chikungunya virus (CHIKV) nsP1 MTase and GT reactions were confirmed by an indirect non-radioactive colorimetric assay and western blot assay using an antibody specific for the m7G cap, respectively. The purified recombinant CHIKV nsP1 has been used for the development of a rapid and sensitive non-radioactive enzyme linked immunosorbent assay (ELISA) to identify the inhibitors of CHIKV nsP1. The MTase reaction is followed by GT reaction and resulted in m7GMP-nsP1 covalent complex formation. The developed ELISA nsP1 assay measures this m7GMP-nsP1 complex by utilizing anti-m7G cap monoclonal antibody. The mutation of a conserved residue Asp63 to Ala revealed its role in nsP1 enzyme reaction. Inductively coupled plasma mass spectroscopy (ICP-MS) was used to determine the presence of magnesium ions (Mg2+) in the purified nsP1 protein. The divalent metal ion selectivity and investigation show preference for Mg2+ ion by CHIKV nsP1. Additionally, using the developed ELISA nsP1 assay, the inhibitory effects of sinefungin, aurintricarboxylic acid (ATA) and ribavirin were determined and the IC50 values were estimated to be 2.69 μM, 5.72 μM and 1.18 mM, respectively.
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Affiliation(s)
- Ramanjit Kaur
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Rajat Mudgal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Manju Narwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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Montes-Bayón M, Bettmer J. The Use of Stable Isotopic Tracers in Metallomics Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1055:111-137. [DOI: 10.1007/978-3-319-90143-5_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Pérez E, Martínez-Peinado P, Marco F, Gras L, Sempere JM, Mora J, Grindlay G. Determination of aflatoxin M1 in milk samples by means of an inductively coupled plasma mass spectrometry-based immunoassay. Food Chem 2017; 230:721-727. [DOI: 10.1016/j.foodchem.2017.03.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 01/24/2017] [Accepted: 03/13/2017] [Indexed: 11/17/2022]
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27
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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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28
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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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29
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Yang B, Zhang Y, Chen B, He M, Hu B. Elemental-tagged immunoassay combined with inductively coupled plasma mass spectrometry for the detection of tumor cells using a lead sulfide nanoparticle label. Talanta 2017; 167:499-505. [DOI: 10.1016/j.talanta.2017.02.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 02/20/2017] [Accepted: 02/26/2017] [Indexed: 12/22/2022]
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30
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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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31
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Coufalíková K, Benešová I, Vaculovič T, Kanický V, Preisler J. LC coupled to ESI, MALDI and ICP MS - A multiple hyphenation for metalloproteomic studies. Anal Chim Acta 2017; 968:58-65. [PMID: 28395775 DOI: 10.1016/j.aca.2017.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022]
Abstract
A new multiple detection arrangement for liquid chromatography (LC) that supplements conventional electrospray ionization (ESI) mass spectrometry (MS) detection with two complementary detection techniques, matrix-assisted laser desorption/ionization (MALDI) MS and substrate-assisted laser desorption inductively coupled plasma (SALD ICP) MS has been developed. The combination of the molecular and elemental detectors in a single separation run is accomplished by utilizing a commercial MALDI target made of conductive plastic. The proposed platform provides a number of benefits in today's metalloproteomic applications, which are demonstrated by analysis of a metallothionein mixture. To maintain metallothionein complexes, separation is carried out at a neutral pH. The effluent is split; a major portion is directed to ESI MS while the remaining 1.8% fraction is deposited onto a plastic MALDI target. Dried droplets are overlaid with MALDI matrix and analysed consecutively by MALDI MS and SALD ICP MS. In the ESI MS spectra, the MT isoform complexes with metals and their stoichiometry are determined; the apoforms are revealed in the MALDI MS spectra. Quantitative determination of metallothionein isoforms is performed via determination of metals in the complexes of the individual protein isoforms using SALD ICP MS.
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Affiliation(s)
- Kateřina Coufalíková
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Iva Benešová
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic
| | - Tomáš Vaculovič
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic
| | - Viktor Kanický
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic
| | - Jan Preisler
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, CEITEC MU, Masaryk University, Brno, Czech Republic.
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Protein Quantification and Quantitative Phosphorylation Analysis by the Determination of Hetero Atoms (S and P) by Means of nanoHPLC-ICPMS. Metallomics 2017. [DOI: 10.1007/978-4-431-56463-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Choi R, Sun J, Yoo H, Kim S, Cho YY, Kim HJ, Kim SW, Chung JH, Oh SY, Lee SY. A Prospective Study of Serum Trace Elements in Healthy Korean Pregnant Women. Nutrients 2016; 8:nu8110749. [PMID: 27886083 PMCID: PMC5133131 DOI: 10.3390/nu8110749] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/22/2023] Open
Abstract
This prospective study sought to investigate serum levels of trace elements (cobalt, copper, zinc, and selenium) and to assess their effects on pregnancy and neonatal outcomes. Serum levels of trace elements in 245 Korean pregnant women (median gestational age at delivery was 39 + 4 weeks and interquartile range was 38 + 4–40 + 1 weeks) were compared with those of 527 general adults and those of previous studies in other ethnic groups. Pregnancy and neonatal outcomes including gestational diabetes, preeclampsia, neonatal birth weight, and congenital abnormalities were assessed. The median serum trace element concentrations of all pregnant women were: cobalt: 0.39 μg/L (interquartile range, IQR 0.29–0.53), copper: 165.0 μg/dL (IQR 144.0–187.0), zinc: 57.0 μg/dL (IQR 50.0–64.0), and selenium: 94.0 μg/L (IQR 87.0–101.0). Serum cobalt and copper concentrations were higher in pregnant women than in the general population, whereas zinc and selenium levels were lower (p < 0.01). Concentrations of all four trace elements varied significantly during the three trimesters (p < 0.05), and seasonal variation was found in copper, zinc, and selenium, but was not observed for cobalt. The prevalence of preeclampsia was significantly lower with high copper (p = 0.03). Trace element levels varied by pregnancy trimester and season, and alteration in copper status during pregnancy might influence pregnancy outcomes such as preeclampsia.
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Affiliation(s)
- Rihwa Choi
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Jiyu Sun
- Statistics and Data Center, Research Institute for Future Medicine, Samsung Medical Center, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Heejin Yoo
- Statistics and Data Center, Research Institute for Future Medicine, Samsung Medical Center, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Seonwoo Kim
- Statistics and Dater Center, Samsung Biomedical Research Institute, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Yoon Young Cho
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Hye Jeong Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Sun Wook Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Jae Hoon Chung
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Soo-Young Oh
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
| | - Soo-Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
- Department of Clinical Pharmacology & Therapeutics, Samsung Medical Center, 81 Irwon-Ro, Gangnam-Gu, Seoul 06351, Korea.
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Tang N, Li Z, Yang L, Wang Q. ICPMS-Based Specific Quantification of Phosphotyrosine: A Gallium-Tagging and Tyrosine-Phosphatase Mediated Strategy. Anal Chem 2016; 88:9890-9896. [DOI: 10.1021/acs.analchem.6b02979] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nannan Tang
- Department
of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis
and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhaoxin Li
- Department
of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis
and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Limin Yang
- Department
of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis
and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qiuquan Wang
- Department
of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis
and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- State
Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China
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Calderón-Celis F, Diez-Fernández S, Costa-Fernández JM, Encinar JR, Calvete JJ, Sanz-Medel A. Elemental Mass Spectrometry for Absolute Intact Protein Quantification without Protein-Specific Standards: Application to Snake Venomics. Anal Chem 2016; 88:9699-9706. [PMID: 27593495 DOI: 10.1021/acs.analchem.6b02585] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Absolute protein quantification methods based on molecular mass spectrometry usually require stable isotope-labeled analogous standards for each target protein or peptide under study, which in turn must be certified using natural standards. In this work, we report a direct and accurate methodology based on capLC-ICP-QQQ and online isotope dilution analysis for the absolute and sensitive quantification of intact proteins. The combination of the postcolumn addition of 34S and a generic S-containing internal standard spiked to the sample provides full compound independent detector response and thus protein quantification without the need for specific standards. Quantitative recoveries, using a chromatographic core-shell C4 column for the various protein species assayed were obtained (96-100%). Thus, the proposed strategy enables the accurate quantification of proteins even if no specific standards are available for them. In addition, to the best of our knowledge, we obtained the lowest detection limits reported in the quantitative analysis of intact proteins by direct measurement of sulfur with ICPMS (358 fmol) and protein (ranging from 7 to 15 fmol depending on the assayed protein). The quantitative results for individual and simple mixtures of model proteins were statistically indistinguishable from the manufacturer's values. Finally, the suitability of the strategy for real sample analysis (including quantitative protein recovery from the column) was illustrated for the individual absolute quantification of the proteins and whole protein content in a venom sample. Parallel capLC-ESI-QTOF analysis was employed to identify the proteins, a prerequisite to translate the mass of quantified S for each chromatographic peak into individual protein mass.
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Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Silvia Diez-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
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Pröfrock D. Coupling Techniques and Orthogonal Combination of Mass Spectrometric Techniques. Metallomics 2016. [DOI: 10.1002/9783527694907.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Pröfrock
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research; Department Marine Bioanalytical Chemistry, Institute of Coastal Research/Biogeochemistry in Coastal Seas; Max-Planck Str.1 21502 Geesthacht Germany
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37
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Eichberg S, Sanz L, Calvete JJ, Pla D. Constructing comprehensive venom proteome reference maps for integrative venomics. Expert Rev Proteomics 2016; 12:557-73. [PMID: 26400467 DOI: 10.1586/14789450.2015.1073590] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Understanding the molecular basis of complex adaptive traits, such as snake venom, demands qualitative and quantitative comparisons of the temporal and spatial patterns of venom variation. Here, we assessed the proof-of-concept that locus-resolved reference venom proteome maps can be achieved through efficient pre-MS venom proteome decomplexation, peptide-centric MS/MS analysis and species-specific database searching. METHODS Venom proteome components were fractionated and quantified by RP-HPLC, SDS-PAGE and 2DE prior to LC-MS/MS matching against a species-specific transcriptomic dataset. RESULTS Combination of RP-HPLC/SDS-PAGE and 2DE followed by LC-MS/MS showed the existence of ∼178-180 venom protein species generated from ∼48 unique transcripts. CONCLUSIONS Our results underscore that if sufficient pre-MS and MS efforts are applied, comprehensive venom maps can be achieved. And - equally important - dissociating the venom decomplexing steps from the protein identification process represents the key to achieving a quantitative and locus-resolved insight of the venom proteome.
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Affiliation(s)
- Susann Eichberg
- a 1 Beuth Hochschule für Technik Berlin, Luxemburger Straße 10, 13353 Berlin, Germany
| | - Libia Sanz
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Juan J Calvete
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Davinia Pla
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
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38
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Ropero MP, Fariñas NR, Krupp E, Mateo R, Nevado JB, Martín-Doimeadios RR. Mercury and selenium binding biomolecules in terrestrial mammals (Cervus elaphus and Sus scrofa) from a mercury exposed area. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1022:159-166. [DOI: 10.1016/j.jchromb.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 10/22/2022]
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Maes E, Tirez K, Baggerman G, Valkenborg D, Schoofs L, Encinar JR, Mertens I. The use of elemental mass spectrometry in phosphoproteomic applications. MASS SPECTROMETRY REVIEWS 2016; 35:350-360. [PMID: 25139451 DOI: 10.1002/mas.21440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/14/2014] [Accepted: 05/14/2014] [Indexed: 06/03/2023]
Abstract
Reversible phosphorylation is one of the most important post-translational modifications in mammalian cells. Because this molecular switch is an important mechanism that diversifies and regulates proteins in cellular processes, knowledge about the extent and quantity of phosphorylation is very important to understand the complex cellular interplay. Although phosphoproteomics strategies are applied worldwide, they mainly include only molecular mass spectrometry (like MALDI or ESI)-based experiments. Although identification and relative quantification of phosphopeptides is straightforward with these techniques, absolute quantification is more complex and usually requires for specific isotopically phosphopeptide standards. However, the use of elemental mass spectrometry, and in particular inductively coupled plasma mass spectrometry (ICP-MS), in phosphoproteomics-based experiments, allow one to absolutely quantify phosphopeptides. Here, these phosphoproteomic applications with ICP-MS as elemental detector are reviewed. Pioneering work and recent developments in the field are both described. Additionally, the advantage of the parallel use of molecular and elemental mass spectrometry is stressed.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Kristof Tirez
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Liliane Schoofs
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
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40
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de Bang TC, Husted S. Lanthanide elements as labels for multiplexed and targeted analysis of proteins, DNA and RNA using inductively-coupled plasma mass spectrometry. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Amaral CD, Amais RS, Fialho LL, Schiavo D, Nogueira ARA, Nóbrega JA. Determination of carbon in digested samples and amino acids by inductively coupled plasma tandem mass spectrometry. Microchem J 2015. [DOI: 10.1016/j.microc.2015.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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XU M, YANG LM, WANG QQ. Se-Hg Dual-element Labeling Strategy for Selectively Recognizing Selenoprotein and Selenopeptide. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Elucidation of the defence mechanism in microalgae Chlorella sorokiniana under mercury exposure. Identification of Hg–phytochelatins. Chem Biol Interact 2015; 238:82-90. [DOI: 10.1016/j.cbi.2015.06.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/30/2015] [Accepted: 06/05/2015] [Indexed: 11/18/2022]
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44
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de Bang TC, Petersen J, Pedas PR, Rogowska-Wrzesinska A, Jensen ON, Schjoerring JK, Jensen PE, Thelen JJ, Husted S. A laser ablation ICP-MS based method for multiplexed immunoblot analysis: applications to manganese-dependent protein dynamics of photosystem II in barley (Hordeum vulgare L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:555-565. [PMID: 26095749 DOI: 10.1111/tpj.12906] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/04/2015] [Indexed: 06/04/2023]
Abstract
Manganese (Mn) constitutes an essential co-factor in the oxygen-evolving complex of photosystem II (PSII). Consequently, Mn deficiency reduces photosynthetic efficiency and leads to changes in PSII composition. In order to study these changes, multiplexed protein assays are advantageous. Here, we developed a multiplexed antibody-based assay and analysed selected PSII subunits in barley (Hordeum vulgare L.). A selection of antibodies were labelled with specific lanthanides and immunoreacted with thylakoids exposed to Mn deficiency after western blotting. Subsequently, western blot membranes were analysed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), which allowed selective and relative quantitative analysis via the different lanthanides. The method was evaluated against established liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) methods, based on data-dependent acquisition (DDA) and selected reaction monitoring (SRM). Manganese deficiency resulted in a general decrease in PSII protein abundances, an effect that was shown to be reversible upon Mn re-supplementation. Specifically, the extrinsic proteins PsbP and PsbQ showed Mn-dependent changes in abundances. Similar trends in the response to Mn deficiency at the protein level were observed when comparing DDA, SRM and LA-ICP-MS results. A biologically important exception to this trend was the loss of PsbO in the SRM analysis, which highlights the necessity of validating protein changes by more than one technique. The developed method enables a higher number of proteins to be multiplexed in comparison to existing immunoassays. Furthermore, multiplexed protein analysis by LA-ICP-MS provides an analytical platform with high throughput appropriate for screening large collections of plants.
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Affiliation(s)
- Thomas Christian de Bang
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Jørgen Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark, Denmark
| | - Pai Rosager Pedas
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark, Denmark
| | - Ole Noerregaard Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark, Denmark
| | - Jan Kofod Schjoerring
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Jay J Thelen
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO 65211, USA
| | - Søren Husted
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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Serum Concentrations of Trace Elements in Patients with Tuberculosis and Its Association with Treatment Outcome. Nutrients 2015. [PMID: 26197334 PMCID: PMC4517040 DOI: 10.3390/nu7075263] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Deficiencies in essential trace elements are associated with impaired immunity in tuberculosis infection. However, the trace element concentrations in the serum of Korean patients with tuberculosis have not yet been investigated. This study aimed to compare the serum trace element concentrations of Korean adult patients with tuberculosis with noninfected controls and to assess the impact of serum trace element concentration on clinical outcome after antituberculosis treatment. The serum concentrations of four trace elements in 141 consecutively recruited patients with tuberculosis and 79 controls were analyzed by inductively coupled plasma-mass spectrometry. Demographic characteristics were also analyzed. Serum cobalt and copper concentrations were significantly higher in patients with tuberculosis compared with controls, while zinc and selenium concentrations were significantly lower (p < 0.01). Moreover, serum selenium and zinc concentrations were positively correlated (ρ = 0.41, p < 0.05). A high serum copper concentration was associated with a worse clinical outcome, as assessed after one month of antituberculosis therapy. Specifically, culture-positive patients had higher serum copper concentrations than culture-negative patients (p < 0.05). Patients with tuberculosis had altered serum trace element concentrations. Further research is needed to elucidate the roles of individual trace elements and to determine their clinical impact on patients with tuberculosis.
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46
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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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47
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Abstract
Metallomics is newly coined terms and defined as a comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type. Then, metallome is defined as the entire category of metalloproteins and any other metal-containing biomolecules. Metallomics and research on metallome require analytical techniques that can provide information on the identification and quantification of metal/metalloid-containing biomolecules. This concept has been called speciation, and the acquisition of data according to the concept is performed using hyphenated techniques involving both separation and detection methods. In this review, the author intends to present several applications of complementary use of HPLC-inductively coupled plasma mass spectrometry (ICP-MS) and HPLC-electrospray ionization tandem mass spectrometry for identification of unknown selenium-containing metabolites, and also to present a newly developed technique, capillary LC-ICP-MS to be used for the analysis of metal-binding proteins.
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Affiliation(s)
- Yasumitsu Ogra
- Laboratory of Chemical Toxicology and Environmental Health, Showa Pharmaceutical University
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García-Sevillano M, Rodríguez-Moro G, García-Barrera T, Navarro F, Gómez-Ariza J. Biological interactions between mercury and selenium in distribution and detoxification processes in mice under controlled exposure. Effects on selenoprotein. Chem Biol Interact 2015; 229:82-90. [DOI: 10.1016/j.cbi.2015.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/24/2015] [Accepted: 02/01/2015] [Indexed: 02/06/2023]
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Selective analysis of human serum albumin based on SEC-ICP-MS after labelling with iophenoxic acid. Anal Bioanal Chem 2015; 407:2829-36. [DOI: 10.1007/s00216-015-8507-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 11/25/2022]
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50
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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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