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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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Arapidi GP, Urban AS, Osetrova MS, Shender VO, Butenko IO, Bukato ON, Kuznetsov AA, Saveleva TM, Nos GA, Ivanova OM, Lopukhov LV, Laikov AV, Sharova NI, Nikonova MF, Mitin AN, Martinov AI, Grigorieva TV, Ilina EN, Ivanov VT, Govorun VM. Non-human peptides revealed in blood reflect the composition of intestinal microbiota. BMC Biol 2024; 22:178. [PMID: 39183269 PMCID: PMC11346180 DOI: 10.1186/s12915-024-01975-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/07/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND The previously underestimated effects of commensal gut microbiota on the human body are increasingly being investigated using omics. The discovery of active molecules of interaction between the microbiota and the host may be an important step towards elucidating the mechanisms of symbiosis. RESULTS Here, we show that in the bloodstream of healthy people, there are over 900 peptides that are fragments of proteins from microorganisms which naturally inhabit human biotopes, including the intestinal microbiota. Absolute quantitation by multiple reaction monitoring has confirmed the presence of bacterial peptides in the blood plasma and serum in the range of approximately 0.1 nM to 1 μM. The abundance of microbiota peptides reaches its maximum about 5 h after a meal. Most of the peptides correlate with the bacterial composition of the small intestine and are likely obtained by hydrolysis of membrane proteins with trypsin, chymotrypsin and pepsin - the main proteases of the gastrointestinal tract. The peptides have physicochemical properties that likely allow them to selectively pass the intestinal mucosal barrier and resist fibrinolysis. CONCLUSIONS The proposed approach to the identification of microbiota peptides in the blood, after additional validation, may be useful for determining the microbiota composition of hard-to-reach intestinal areas and monitoring the permeability of the intestinal mucosal barrier.
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Affiliation(s)
- Georgij P Arapidi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation.
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation.
| | - Anatoly S Urban
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
| | - Maria S Osetrova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Victoria O Shender
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
| | - Ivan O Butenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
- Research Institute for Systems Biology and Medicine, Nauchny Proezd 18, Moscow, 117246, Russian Federation
| | - Olga N Bukato
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
| | - Alexandr A Kuznetsov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
| | - Tatjana M Saveleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Grigorii A Nos
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Olga M Ivanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
| | - Leonid V Lopukhov
- Kazan Federal University, Kremlyovskaya Str. 18, Kazan, 420008, Russian Federation
| | - Alexander V Laikov
- Kazan Federal University, Kremlyovskaya Str. 18, Kazan, 420008, Russian Federation
| | - Nina I Sharova
- National Research Center-Institute of Immunology Federal Medical-Biological Agency of Russia, Kashirskoe Highway 24, Moscow, 115522, Russian Federation
| | - Margarita F Nikonova
- National Research Center-Institute of Immunology Federal Medical-Biological Agency of Russia, Kashirskoe Highway 24, Moscow, 115522, Russian Federation
| | - Alexander N Mitin
- National Research Center-Institute of Immunology Federal Medical-Biological Agency of Russia, Kashirskoe Highway 24, Moscow, 115522, Russian Federation
| | - Alexander I Martinov
- National Research Center-Institute of Immunology Federal Medical-Biological Agency of Russia, Kashirskoe Highway 24, Moscow, 115522, Russian Federation
| | - Tatiana V Grigorieva
- Kazan Federal University, Kremlyovskaya Str. 18, Kazan, 420008, Russian Federation
| | - Elena N Ilina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
- Research Institute for Systems Biology and Medicine, Nauchny Proezd 18, Moscow, 117246, Russian Federation
| | - Vadim T Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Vadim M Govorun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, 119435, Russian Federation
- Research Institute for Systems Biology and Medicine, Nauchny Proezd 18, Moscow, 117246, Russian Federation
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3
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Kline JT, Belford MW, Huang J, Greer JB, Bergen D, Fellers RT, Greer SM, Horn DM, Zabrouskov V, Huguet R, Boeser CL, Durbin KR, Fornelli L. Improved Label-Free Quantification of Intact Proteoforms Using Field Asymmetric Ion Mobility Spectrometry. Anal Chem 2023; 95:9090-9096. [PMID: 37252723 PMCID: PMC11149911 DOI: 10.1021/acs.analchem.3c01534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The high-throughput quantification of intact proteoforms using a label-free approach is typically performed on proteins in the 0-30 kDa mass range extracted from whole cell or tissue lysates. Unfortunately, even when high-resolution separation of proteoforms is achieved by either high-performance liquid chromatography or capillary electrophoresis, the number of proteoforms that can be identified and quantified is inevitably limited by the inherent sample complexity. Here, we benchmark label-free quantification of proteoforms of Escherichia coli by applying gas-phase fractionation (GPF) via field asymmetric ion mobility spectrometry (FAIMS). Recent advances in Orbitrap instrumentation have enabled the acquisition of high-quality intact and fragmentation mass spectra without the need for averaging time-domain transients prior to Fourier transform. The resulting speed improvements allowed for the application of multiple FAIMS compensation voltages in the same liquid chromatography-tandem mass spectrometry experiment without increasing the overall data acquisition cycle. As a result, the application of FAIMS to label-free quantification based on intact mass spectra substantially increases the number of both identified and quantified proteoforms without penalizing quantification accuracy in comparison to traditional label-free experiments that do not adopt GPF.
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Affiliation(s)
- Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | - Jingjing Huang
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Joseph B. Greer
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | - David Bergen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ryan T. Fellers
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | | | - David M. Horn
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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4
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Dafun AS, Živković D, Leon-Icaza SA, Möller S, Froment C, Bonnet D, de Jesus AA, Alric L, Quaranta-Nicaise M, Ferrand A, Cougoule C, Meunier E, Burlet-Schiltz O, Ebstein F, Goldbach-Mansky R, Krüger E, Bousquet MP, Marcoux J. Establishing 20S Proteasome Genetic, Translational and Post-Translational Status from Precious Biological and Patient Samples with Top-Down MS. Cells 2023; 12:cells12060844. [PMID: 36980185 PMCID: PMC10047880 DOI: 10.3390/cells12060844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
The mammalian 20S catalytic core of the proteasome is made of 14 different subunits (α1-7 and β1-7) but exists as different subtypes depending on the cell type. In immune cells, for instance, constitutive catalytic proteasome subunits can be replaced by the so-called immuno-catalytic subunits, giving rise to the immunoproteasome. Proteasome activity is also altered by post-translational modifications (PTMs) and by genetic variants. Immunochemical methods are commonly used to investigate these PTMs whereby protein-tagging is necessary to monitor their effect on 20S assembly. Here, we present a new miniaturized workflow combining top-down and bottom-up mass spectrometry of immunopurified 20S proteasomes that analyze the proteasome assembly status as well as the full proteoform footprint, revealing PTMs, mutations, single nucleotide polymorphisms (SNPs) and induction of immune-subunits in different biological samples, including organoids, biopsies and B-lymphoblastoid cell lines derived from patients with proteasome-associated autoinflammatory syndromes (PRAAS). We emphasize the benefits of using top-down mass spectrometry in preserving the endogenous conformation of protein modifications, while enabling a rapid turnaround (1 h run) and ensuring high sensitivity (1–2 pmol) and demonstrate its capacity to semi-quantify constitutive and immune proteasome subunits.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Dušan Živković
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Stephen Adonai Leon-Icaza
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Sophie Möller
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Carine Froment
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Delphine Bonnet
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Université de Toulouse III—Paul Sabatier (UPS), 31300 Toulouse, France
- Internal Medicine Department of Digestive Disease, Rangueil Hospital, Université de Toulouse III—Paul Sabatier (UPS), 31400 Toulouse, France
| | - Adriana Almeida de Jesus
- Translational Autoinflammatory Diseases Section, LCIM, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laurent Alric
- Internal Medicine Department of Digestive Disease, Rangueil Hospital, Université de Toulouse III—Paul Sabatier (UPS), 31400 Toulouse, France
| | - Muriel Quaranta-Nicaise
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Université de Toulouse III—Paul Sabatier (UPS), 31300 Toulouse, France
| | - Audrey Ferrand
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Université de Toulouse III—Paul Sabatier (UPS), 31300 Toulouse, France
| | - Céline Cougoule
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Etienne Meunier
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
| | - Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, LCIM, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marie-Pierre Bousquet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
- Correspondence: (M.-P.B.); (J.M.)
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UPS), 31077 Toulouse, France
- Correspondence: (M.-P.B.); (J.M.)
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5
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Takemori A, Kaulich PT, Cassidy L, Takemori N, Tholey A. Size-Based Proteome Fractionation through Polyacrylamide Gel Electrophoresis Combined with LC-FAIMS-MS for In-Depth Top-Down Proteomics. Anal Chem 2022; 94:12815-12821. [PMID: 36069571 DOI: 10.1021/acs.analchem.2c02777] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. Here, we present an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, in which a molecular-weight-based proteome fractionation approach using SDS-polyacrylamide gel electrophoresis is performed prior to LC-FAIMS-MS. Since individual bands and their corresponding mass ranges require different compensating voltages (CVs), the MS parameters for each gel band and CV were optimized to increase the number and reliability of proteoform identifications further. We developed an easy-to-implement and inexpensive procedure combining the earlier established Passively Eluting Proteins from Polyacrylamide gels as Intact species (PEPPI) protocol with an optimized Anion-Exchange disk-assisted Sequential sample Preparation (AnExSP) method for the removal of stains and SDS. The protocol was compared with a methanol-chloroform-water (MCW)-based protein precipitation protocol. The results show that the PEPPI-AnExSP procedure is better suited for the identification of low-molecular-weight proteoforms, whereas the MCW-based protocol showed advantages for higher-molecular-weight proteoforms. Moreover, complementary results were observed with the two methods in terms of hydrophobicity and isoelectric points of the identified proteoforms. In total, 8500 proteoforms could be identified in a human proteome standard, showing the effectiveness of the gel-based sample fractionation approaches in combination with LC-FAIMS-MS.
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Affiliation(s)
- Ayako Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Toon 790-8577, Ehime, Japan
| | - Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Nobuaki Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Toon 790-8577, Ehime, Japan
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
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6
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Winkels K, Koudelka T, Kaulich PT, Leippe M, Tholey A. Validation of Top-Down Proteomics Data by Bottom-Up-Based N-Terminomics Reveals Pitfalls in Top-Down-Based Terminomics Workflows. J Proteome Res 2022; 21:2185-2196. [PMID: 35972260 DOI: 10.1021/acs.jproteome.2c00277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide additional information about post-translational modifications and the respective C-termini. To evaluate the potential of TDP for terminomics, two established TDP workflows were employed for the proteome analysis of the nematode Caenorhabditis elegans. The N-termini of the identified proteoforms were validated using a BUP-based N-terminomics approach. The TDP workflows used here identified 1658 proteoforms, the N-termini of which were verified by BUP in 25% of entities only. Caveats in both the BUP- and TDP-based workflows were shown to contribute to this low overlap. In BUP, the use of trypsin prohibits the detection of arginine-rich or arginine-deficient N-termini, while in TDP, the formation of artificially generated termini was observed in particular in a workflow encompassing sample treatment with high acid concentrations. Furthermore, we demonstrate the applicability of reductive dimethylation in TDP to confirm biological N-termini. Overall, our study shows not only the potential but also current limitations of TDP for terminomics studies and also presents suggestions for future developments, for example, for data quality control, allowing improvement of the detection of protein termini by TDP.
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Affiliation(s)
- Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tomas Koudelka
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Matthias Leippe
- Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
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7
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Chen D, Yang Z, Shen X, Sun L. Capillary Zone Electrophoresis-Tandem Mass Spectrometry As an Alternative to Liquid Chromatography-Tandem Mass Spectrometry for Top-down Proteomics of Histones. Anal Chem 2021; 93:4417-4424. [PMID: 33650845 PMCID: PMC8564867 DOI: 10.1021/acs.analchem.0c04237] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Top-down proteomics (TDP) is an ideal approach for deciphering the histone code and it routinely employs reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS). Because of the extreme complexity of histones regarding the number of proteoforms, new analytical tools with high-capacity separation and highly sensitive detection of proteoforms are required for TDP of histones. Here we present capillary zone electrophoresis (CZE)-MS/MS via the electro-kinetically pumped sheath-flow CE-MS interface for large-scale top-down delineation of histone proteoforms. CZE-MS/MS identified a comparable number of proteoforms to RPLC-MS/MS from a calf histone sample with more than 30-fold less sample consumption (75-ng vs. Three μg), indicating its substantially higher sensitivity. We identified about 400 histone proteoforms from the calf histone sample using two-dimensional size-exclusion chromatography (SEC)-CZE-MS/MS with less than 300-ng proteins consumed. We identified histone proteoforms carrying various tentative post-translational modifications (PTMs), for example, acetylation, methylation (mono-, di-, and tri-), phosphorylation, and succinylation. The electrophoretic mobility (μef) of unmodified histone proteoforms can be predicted accurately (R2 = 0.98) with an optimized semiempirical model based on our recent work. The results render CZE-MS/MS as a useful tool for deciphering the histone code in a proteoform-specific manner and on a global scale.
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Affiliation(s)
- Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
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8
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Fenselau C, Ostrand-Rosenberg S. Molecular cargo in myeloid-derived suppressor cells and their exosomes. Cell Immunol 2021; 359:104258. [PMID: 33338939 PMCID: PMC7802618 DOI: 10.1016/j.cellimm.2020.104258] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022]
Abstract
Collaborative research is reviewed in which mass spectrometry-based proteomics and next generation sequencing were used qualitatively and quantitatively to interrogate proteins and RNAs carried in intact myeloid-derived suppressor cells (MDSC) and exosomes shed in vitro by MDSC. In aggregate exosomes more than 4000 proteins were identified, including annexins and immunosuppressive mediators. Bioassays showed that exosomes induce MDSC chemotaxis dependent on S100A8 and S100A9 in their cargo. Surface selective chemistry identified glycoproteins on MDSC and exosome surfaces, including CD47 and thrombospondin 1, which both facilitate exosome-catalyzed chemotaxis. Large numbers of mRNAs and microRNAs were identified in aggregate exosomes, whose potential functions in receptor cells include angiogenesis, and proinflammatory and immunosuppressive activities. Inflammation was found to have asymmetric effects on MDSC and exosomal cargos. Collectively, our findings indicate that the exosomes shed by MDSC provide divergent and complementary functions that support the immunosuppression and tumor promotion activities of MDSC.
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Affiliation(s)
- Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
| | - Suzanne Ostrand-Rosenberg
- Department of Biological Sciences, University of Maryland, Baltimore County, MD 20742, United States; Department of Pathology, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, United States
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9
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Xu T, Shen X, Yang Z, Chen D, Lubeckyj RA, McCool EN, Sun L. Automated Capillary Isoelectric Focusing-Tandem Mass Spectrometry for Qualitative and Quantitative Top-Down Proteomics. Anal Chem 2020; 92:15890-15898. [PMID: 33263984 PMCID: PMC8564864 DOI: 10.1021/acs.analchem.0c03266] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Top-down proteomics (TDP) aims to delineate proteomes in a proteoform-specific manner, which is vital for accurately understanding protein function in cellular processes. It requires high-capacity separation of proteoforms before mass spectrometry (MS) and tandem MS (MS/MS). Capillary isoelectric focusing (cIEF)-MS has been recognized as a useful tool for TDP in the 1990s because cIEF is capable of high-resolution separation of proteoforms. Previous cIEF-MS studies concentrated on measuring the protein's mass without MS/MS, impeding the confident proteoform identification in complex samples and the accurate localization of post-translational modifications on proteoforms. Herein, for the first time, we present automated cIEF-MS/MS-based TDP for large-scale delineation of proteoforms in complex proteomes. Single-shot cIEF-MS/MS identified 711 proteoforms from an Escherichia coli (E. coli) proteome consuming only nanograms of proteins. Coupling two-dimensional size-exclusion chromatography (SEC)-cIEF to ESI-MS/MS enabled the identification of nearly 2000 proteoforms from the E. coli proteome. Label-free quantitative TDP of zebrafish male and female brains using SEC-cIEF-MS/MS quantified thousands of proteoforms and revealed sex-dependent proteoform profiles in brains. Particularly, we discovered several proteolytic proteoforms of pro-opiomelanocortin and prodynorphin with significantly higher abundance in male zebrafish brains as potential endogenous hormone proteoforms. Multilevel quantitative proteomics (TDP and bottom-up proteomics) of the brains revealed that the majority of proteoforms having statistically significant difference in abundance between genders showed no abundance difference at the protein group level. This work represents the first multilevel quantitative proteomics study of sexual dimorphism of the brain.
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Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
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10
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Chen D, Geis-Asteggiante L, Gomes FP, Ostrand-Rosenberg S, Fenselau C. Top-Down Proteomic Characterization of Truncated Proteoforms. J Proteome Res 2019; 18:4013-4019. [PMID: 31545043 DOI: 10.1021/acs.jproteome.9b00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A top-down proteomic strategy with semiautomated analysis of data sets has proven successful for the global identification of truncated proteins without the use of chemical derivatization, enzymatic manipulation, immunoprecipitation, or other enrichment. This approach provides the reliable identification of internal polypeptides formed from precursor gene products by proteolytic cleavage of both the N- and C-termini, as well as truncated proteoforms that retain one or the other termini. The strategy has been evaluated by application to the immunosuppressive extracellular vesicles released by myeloid-derived suppressor cells. More than 1000 truncated proteoforms have been identified, from which binding motifs are derived to allow characterization of the putative proteases responsible for truncation.
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Affiliation(s)
- Dapeng Chen
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Fabio P Gomes
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Suzanne Ostrand-Rosenberg
- Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , Maryland 21250 , United States
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
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11
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Lin Z, Wei L, Cai W, Zhu Y, Tucholski T, Mitchell SD, Guo W, Ford SP, Diffee GM, Ge Y. Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome. Mol Cell Proteomics 2019; 18:594-605. [PMID: 30591534 PMCID: PMC6398208 DOI: 10.1074/mcp.tir118.001086] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Determining changes in protein expression and post-translational modifications (PTMs) is crucial for elucidating cellular signal transduction and disease mechanisms. Conventional antibody-based approaches have inherent problems such as the limited availability of high-quality antibodies and batch-to-batch variation. Top-down mass spectrometry (MS)-based proteomics has emerged as the most powerful method for characterization and quantification of protein modifications. Nevertheless, robust methods to simultaneously determine changes in protein expression and PTMs remain lacking. Herein, we have developed a straightforward and robust top-down liquid chromatography (LC)/MS-based targeted proteomics platform for simultaneous quantification of protein expression and PTMs with high throughput and high reproducibility. We employed this method to analyze the sarcomeric subproteome from various muscle types of different species, which successfully revealed skeletal muscle heterogeneity and cardiac developmental changes in sarcomeric protein isoform expression and PTMs. As demonstrated, this targeted top-down proteomics platform offers an excellent 'antibody-independent' alternative for the accurate quantification of sarcomeric protein expression and PTMs concurrently in complex mixtures, which is generally applicable to different species and various tissue types.
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Affiliation(s)
- Ziqing Lin
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Liming Wei
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ¶Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Yanlong Zhu
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Trisha Tucholski
- **Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Stanford D Mitchell
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Wei Guo
- ‡‡Department of Animal Science, Fetal Programming Center, University of Wyoming, Laramie, Wyoming 82071
| | - Stephen P Ford
- ‡‡Department of Animal Science, Fetal Programming Center, University of Wyoming, Laramie, Wyoming 82071
| | - Gary M Diffee
- §§Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53705
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705;
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
- **Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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12
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Lazar IM, Deng J, Stremler MA, Ahuja S. Microfluidic reactors for advancing the MS analysis of fast biological responses. MICROSYSTEMS & NANOENGINEERING 2019; 5:7. [PMID: 31057934 PMCID: PMC6369226 DOI: 10.1038/s41378-019-0048-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/08/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
The response of cells to physical or chemical stimuli is complex, unfolding on time-scales from seconds to days, with or without de novo protein synthesis, and involving signaling processes that are transient or sustained. By combining the technology of microfluidics that supports fast and precise execution of a variety of cell handling operations, with that of mass spectrometry detection that facilitates an accurate and complex characterization of the protein complement of cells, in this work, we developed a platform that supports (near) real-time sampling and proteome-level capturing of cellular responses to a perturbation such as treatment with mitogens. The geometric design of the chip supports three critical features: (a) capture of a sufficient number of cells to meet the detection limit requirements of mass spectrometry instrumentation, (b) fluid delivery for uniform stimulation of the resident cells, and (c) fast cell recovery, lysis and processing for accurate sampling of time-sensitive cellular responses to a stimulus. COMSOL simulations and microscopy were used to predict and evaluate the flow behavior inside the microfluidic device. Proteomic analysis of the cellular extracts generated by the chip experiments revealed that the identified proteins were representative of all cellular locations, exosomes, and major biological processes related to proliferation and signaling, demonstrating that the device holds promising potential for integration into complex lab-on-chip work-flows that address systems biology questions. The applicability of the chips to study time-sensitive cellular responses is discussed in terms of technological challenges and biological relevance.
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Affiliation(s)
- Iulia M. Lazar
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA 24061 USA
- Virginia Tech Carilion School of Medicine, Virginia Tech, 2 Riverside Circle, Roanoke, VA 24016 USA
| | - Jingren Deng
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA 24061 USA
| | - Mark A. Stremler
- Department of Mechanical Engineering, Virginia Tech, 780 Drillfield Drive, Room 333P, Blacksburg, VA 24061 USA
| | - Shreya Ahuja
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA 24061 USA
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13
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Ostrand-Rosenberg S, Fenselau C. Myeloid-Derived Suppressor Cells: Immune-Suppressive Cells That Impair Antitumor Immunity and Are Sculpted by Their Environment. THE JOURNAL OF IMMUNOLOGY 2018; 200:422-431. [PMID: 29311384 DOI: 10.4049/jimmunol.1701019] [Citation(s) in RCA: 362] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
Abstract
Myeloid-derived suppressor cells (MDSC) are a diverse population of immature myeloid cells that have potent immune-suppressive activity. Studies in both mice and humans have demonstrated that MDSC accumulate in most individuals with cancer, where they promote tumor progression, inhibit antitumor immunity, and are an obstacle to many cancer immunotherapies. As a result, there has been intense interest in understanding the mechanisms and in situ conditions that regulate and sustain MDSC, and the mechanisms MDSC use to promote tumor progression. This article reviews the characterization of MDSC and how they are distinguished from neutrophils, describes the suppressive mechanisms used by MDSC to mediate their effects, and explains the role of proinflammatory mediators and the tumor microenvironment in driving MDSC accumulation, suppressive potency, and survival.
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Affiliation(s)
- Suzanne Ostrand-Rosenberg
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250; and
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
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14
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Adams KR, Chauhan S, Patel DB, Clements VK, Wang Y, Jay SM, Edwards NJ, Ostrand-Rosenberg S, Fenselau C. Ubiquitin Conjugation Probed by Inflammation in Myeloid-Derived Suppressor Cell Extracellular Vesicles. J Proteome Res 2018; 17:315-324. [PMID: 29061044 PMCID: PMC6137330 DOI: 10.1021/acs.jproteome.7b00585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ubiquitinated proteins carried by the extracellular vesicles (EV) released by myeloid-derived suppressor cells (MDSC) have been investigated using proteomic strategies to examine the effect of tumor-associated inflammation. EV were collected from MDSC directly following isolation from tumor-bearing mice with low and high inflammation. Among the 1092 proteins (high inflammation) and 925 proteins (low inflammation) identified, more than 50% were observed as ubiquitinated proteoforms. More than three ubiquitin-attachment sites were characterized per ubiquitinated protein, on average. Multiple ubiquitination sites were identified in the pro-inflammatory proteins S100 A8 and S100 A9, characteristic of MDSC and in histones and transcription regulators among other proteins. Spectral counting and pathway analysis suggest that ubiquitination occurs independently of inflammation. Some ubiquitinated proteins were shown to cause the migration of MDSC, which has been previously connected with immune suppression and tumor progression. Finally, MDSC EV are found collectively to carry all the enzymes required to catalyze ubiquitination, and the hypothesis is presented that a portion of the ubiquitinated proteins are produced in situ.
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Affiliation(s)
- Katherine R. Adams
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Sitara Chauhan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Divya B. Patel
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Virginia K. Clements
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Yan Wang
- Proteomic Core Facility, College of Mathematics and Natural Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Steven M. Jay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Nathan J. Edwards
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington D.C. 20057, United States
| | - Suzanne Ostrand-Rosenberg
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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15
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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16
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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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