1
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Griffiths D, Anderson M, Richardson K, Inaba-Inoue S, Allen WJ, Collinson I, Beis K, Morris M, Giles K, Politis A. Cyclic Ion Mobility for Hydrogen/Deuterium Exchange-Mass Spectrometry Applications. Anal Chem 2024; 96:5869-5877. [PMID: 38561318 PMCID: PMC11024883 DOI: 10.1021/acs.analchem.3c05753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localization of dynamic changes. Consequently, the HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase the data quality by providing an orthogonal mode of peptide ion separation in the gas phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multipass IM separations. Using one-pass and multipass cIM routines, we use the recently commercialized SELECT SERIES Cyclic IM spectrometer for HDX-MS analyses of four detergent solubilized IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multipass cIM data. Interestingly, use of one-pass and multipass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM that has the potential to enable the analysis of more complex systems with greater accuracy and speed.
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Affiliation(s)
- Damon Griffiths
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Keith Richardson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Satomi Inaba-Inoue
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
- Diffraction
and Scattering Division, Japan Synchrotron
Radiation Research Institute, SPring-8, 1-1-1, Kouto, Sayo, Hyogo 679-5198, Japan
| | - William J. Allen
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Ian Collinson
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Konstantinos Beis
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Kevin Giles
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Argyris Politis
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
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2
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Little AS, Younker IT, Schechter MS, Bernardino PN, Méheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramanswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH. Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nat Microbiol 2024; 9:55-69. [PMID: 38177297 PMCID: PMC11055453 DOI: 10.1038/s41564-023-01560-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.
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Affiliation(s)
- Alexander S Little
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Isaac T Younker
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Matthew S Schechter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Paola Nol Bernardino
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Joshua Stemczynski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Kaylie Scorza
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | | | - Deepti Sharan
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - William Leiter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Matthew A Odenwald
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Section of Infectious Diseases & Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenbug, Germany
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
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3
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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4
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Di Trani JM, Gheorghita AA, Turner M, Brzezinski P, Ädelroth P, Vahidi S, Howell PL, Rubinstein JL. Structure of the bc1- cbb3 respiratory supercomplex from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2023; 120:e2307093120. [PMID: 37751552 PMCID: PMC10556555 DOI: 10.1073/pnas.2307093120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/14/2023] [Indexed: 09/28/2023] Open
Abstract
Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that enables ATP synthesis and membrane transport. These protein complexes can also form higher order assemblies known as respiratory supercomplexes (SCs). The electron transport chain of the opportunistic pathogen Pseudomonas aeruginosa is closely linked with its ability to invade host tissue, tolerate harsh conditions, and resist antibiotics but is poorly characterized. Here, we determine the structure of a P. aeruginosa SC that forms between the quinol:cytochrome c oxidoreductase (cytochrome bc1) and one of the organism's terminal oxidases, cytochrome cbb3, which is found only in some bacteria. Remarkably, the SC structure also includes two intermediate electron carriers: a diheme cytochrome c4 and a single heme cytochrome c5. Together, these proteins allow electron transfer from ubiquinol in cytochrome bc1 to oxygen in cytochrome cbb3. We also present evidence that different isoforms of cytochrome cbb3 can participate in formation of this SC without changing the overall SC architecture. Incorporating these different subunit isoforms into the SC would allow the bacterium to adapt to different environmental conditions. Bioinformatic analysis focusing on structural motifs in the SC suggests that cytochrome bc1-cbb3 SCs also exist in other bacterial pathogens.
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Affiliation(s)
- Justin M. Di Trani
- Molecular Medicine program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
| | - Andreea A. Gheorghita
- Molecular Medicine program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Madison Turner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, StockholmSE-106 91, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, StockholmSE-106 91, Sweden
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| | - P. Lynne Howell
- Molecular Medicine program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ONM5S 1A8, Canada
| | - John L. Rubinstein
- Molecular Medicine program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ONM5G 1L7, Canada
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5
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Rivera-Lugo R, Huang S, Lee F, Méheust R, Iavarone AT, Sidebottom AM, Oldfield E, Portnoy DA, Light SH. Distinct Energy-Coupling Factor Transporter Subunits Enable Flavin Acquisition and Extracytosolic Trafficking for Extracellular Electron Transfer in Listeria monocytogenes. mBio 2023; 14:e0308522. [PMID: 36744898 PMCID: PMC9973259 DOI: 10.1128/mbio.03085-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023] Open
Abstract
A variety of electron transfer mechanisms link bacterial cytosolic electron pools with functionally diverse redox activities in the cell envelope and extracellular space. In Listeria monocytogenes, the ApbE-like enzyme FmnB catalyzes extracytosolic protein flavinylation, covalently linking a flavin cofactor to proteins that transfer electrons to extracellular acceptors. L. monocytogenes uses an energy-coupling factor (ECF) transporter complex that contains distinct substrate-binding, transmembrane, ATPase A, and ATPase A' subunits (RibU, EcfT, EcfA, and EcfA') to import environmental flavins, but the basis of extracytosolic flavin trafficking for FmnB flavinylation remains poorly defined. In this study, we show that the EetB and FmnA proteins are related to ECF transporter substrate-binding and transmembrane subunits, respectively, and are essential for exporting flavins from the cytosol for flavinylation. Comparisons of the flavin import versus export capabilities of L. monocytogenes strains lacking different ECF transporter subunits demonstrate a strict directionality of substrate-binding subunit transport but partial functional redundancy of transmembrane and ATPase subunits. Based on these results, we propose that ECF transporter complexes with different subunit compositions execute directional flavin import/export through a broadly conserved mechanism. Finally, we present genomic context analyses that show that related ECF exporter genes are distributed across members of the phylum Firmicutes and frequently colocalize with genes encoding flavinylated extracytosolic proteins. These findings clarify the basis of ECF transporter export and extracytosolic flavin cofactor trafficking in Firmicutes. IMPORTANCE Bacteria import vitamins and other essential compounds from their surroundings but also traffic related compounds from the cytosol to the cell envelope where they serve various functions. Studying the foodborne pathogen Listeria monocytogenes, we find that the modular use of subunits from a prominent class of bacterial transporters enables the import of environmental vitamin B2 cofactors and the extracytosolic trafficking of a vitamin B2-derived cofactor that facilitates redox reactions in the cell envelope. These studies clarify the basis of bidirectional small-molecule transport across the cytoplasmic membrane and the assembly of redox-active proteins within the cell envelope and extracellular space.
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Affiliation(s)
- Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Shuo Huang
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Frank Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, California, USA
| | | | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Samuel H. Light
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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6
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May JC, McLean JA. Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations. Metabolomics 2022; 18:104. [PMID: 36472678 DOI: 10.1007/s11306-022-01961-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Ion mobility (IM) separation capabilities are now widely available to researchers through several commercial vendors and are now being adopted into many metabolomics workflows. The added peak capacity that ion mobility offers with minimal compromise to other analytical figures-of-merit has provided real benefits to sensitivity and structural selectivity and have allowed more specific metabolite annotations to be assigned in untargeted workflows. One of the greatest promises of contemporary IM-enabled instrumentation is the capability of operating multiple analytical dimensions inline with minimal sample volumes, which has the potential to address many grand challenges currently faced in the omics fields. However, comprehensive operation of multidimensional mass spectrometry comes with its own inherent challenges that, beyond operational complexity, may not be immediately obvious to practitioners of these techniques. AIM OF REVIEW In this review, we outline the strengths and considerations for incorporating IM analysis in metabolomics workflows and provide a critical but forward-looking perspective on the contemporary challenges and prospects associated with interpreting IM data into chemical knowledge. KEY SCIENTIFIC CONCEPTS OF REVIEW We outline a strategy for unifying IM-derived collision cross section (CCS) measurements obtained from different IM techniques and discuss the emerging field of high resolution ion mobility (HRIM) that is poised to address many of the contemporary challenges associated with ion mobility metabolomics. Whereas the LC step limits the throughput of comprehensive LC-IM-MS, the higher peak capacity of HRIM can allow fast LC gradients or rapid sample cleanup via solid-phase extraction (SPE) to be utilized, significantly improving the sample throughput.
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Affiliation(s)
- Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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7
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Chang D, Zaia J. Methods to improve quantitative glycoprotein coverage from bottom-up LC-MS data. MASS SPECTROMETRY REVIEWS 2022; 41:922-937. [PMID: 33764573 DOI: 10.1002/mas.21692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/24/2020] [Accepted: 03/11/2021] [Indexed: 05/18/2023]
Abstract
Advances in mass spectrometry instrumentation, methods development, and bioinformatics have greatly improved the ease and accuracy of site-specific, quantitative glycoproteomics analysis. Data-dependent acquisition is the most popular method for identification and quantification of glycopeptides; however, complete coverage of glycosylation site glycoforms remains elusive with this method. Targeted acquisition methods improve the precision and accuracy of quantification, but at the cost of throughput and discoverability. Data-independent acquisition (DIA) holds great promise for more complete and highly quantitative site-specific glycoproteomics analysis, while maintaining the ability to discover novel glycopeptides without prior knowledge. We review additional features that can be used to increase selectivity and coverage to the DIA workflow: retention time modeling, which would simplify the interpretation of complex tandem mass spectra, and ion mobility separation, which would maximize the sampling of all precursors at a giving chromatographic retention time. The instrumentation and bioinformatics to incorporate these features into glycoproteomics analysis exist. These improvements in quantitative, site-specific analysis will enable researchers to assess glycosylation similarity in related biological systems, answering new questions about the interplay between glycosylation state and biological function.
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Affiliation(s)
- Deborah Chang
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
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8
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Rojas Echeverri JC, Volke D, Milkovska-Stamenova S, Hoffmann R. Evaluating Peptide Fragment Ion Detection Using Traveling Wave Ion Mobility Spectrometry with Signal-Enhanced MS E (SEMS E). Anal Chem 2022; 94:10930-10941. [PMID: 35904512 DOI: 10.1021/acs.analchem.2c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The inherent poor sampling of fragment ions in time-of-flight mass analyzers was recently improved for data-dependent acquisition (DDA) by considering their drift times in traveling wave ion mobility spectrometry (TWIMS). Here, we extend this TWIMS-DDA approach to the data-independent acquisition (DIA) mode MSE to improve the signal intensities of fragment ions by providing improved ion beam sampling efficiency, which we termed therefore signal-enhanced MSE (SEMSE). The theoretical expectation that SEMSE improves the number of identified peptides, the number of quantifiable peptides, and the lower limit of quantitation in wideband DIA was evaluated on an electrospray ionisation-ion mobility spectrometry-quadrupole-time-of-flight-MS (ESI-IMS-Q-TOF-MS) (Synapt G2-Si) in comparison to five established TWIMS-DDA and TWIMS-MSE methods with respect to the number of peptide identifications, the spectral quality of supporting peptide spectra matches, and (most importantly) fragment ion signal sensitivity. A comparison of the fragment signals clearly indicated that SEMSE provides 6.8- to 11.5-fold larger peak areas than established MSE techniques. While this clearly shows the advantages of SEMSE, the inherent limitations of the current software tools do not allow using all benefits in routine analyses. As the simultaneous fragmentation of co-eluting peptides limited peptide identification, DDA and MSE data sets were integrated using Skyline.
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Affiliation(s)
- Juan Camilo Rojas Echeverri
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Daniela Volke
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Sanja Milkovska-Stamenova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
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9
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Grant CR, Amor M, Trujillo HA, Krishnapura S, Iavarone AT, Komeili A. Distinct gene clusters drive formation of ferrosome organelles in bacteria. Nature 2022; 606:160-164. [PMID: 35585231 PMCID: PMC10906721 DOI: 10.1038/s41586-022-04741-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/07/2022] [Indexed: 12/20/2022]
Abstract
Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification1-3. The most common modes of iron storage use proteinaceous compartments, such as ferritins and related proteins4,5. Although lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown6,7. Here we focus on one such compartment, herein named the 'ferrosome', that was previously observed in the anaerobic bacterium Desulfovibrio magneticus6. Using a proteomic approach, we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes in D. magneticus. Fez proteins are encoded in a putative operon and include FezB, a P1B-6-ATPase found in phylogenetically and metabolically diverse species of bacteria and archaea. We show that two other bacterial species, Rhodopseudomonas palustris and Shewanella putrefaciens, make ferrosomes through the action of their six-gene fez operon. Additionally, we find that fez operons are sufficient for ferrosome formation in foreign hosts. Using S. putrefaciens as a model, we show that ferrosomes probably have a role in the anaerobic adaptation to iron starvation. Overall, this work establishes ferrosomes as a new class of iron storage organelles and sets the stage for studying their formation and structure in diverse microorganisms.
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Affiliation(s)
- Carly R Grant
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Matthieu Amor
- Aix-Marseille Université, CEA, CNRS, BIAM, Saint-Paul-lez-Durance, France
| | - Hector A Trujillo
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sunaya Krishnapura
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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10
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A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics. Sci Data 2022; 9:126. [PMID: 35354825 PMCID: PMC8967878 DOI: 10.1038/s41597-022-01216-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/23/2022] [Indexed: 12/23/2022] Open
Abstract
In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design. Therefore, we acquired a hybrid proteome mixture on different instrument platforms and in all currently available families of data acquisition. Here, we present a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset acquired using several of the most commonly used current day instrumental platforms. The dataset consists of over 700 LC-MS runs, including adequate replicates allowing robust statistics and covering over nearly 10 different data formats, including scanning quadrupole and ion mobility enabled acquisitions. Datasets are available via ProteomeXchange (PXD028735). Measurement(s) | Digital Data Repository | Technology Type(s) | Digital Data Repository |
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11
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Furlani IL, da Cruz Nunes E, Canuto GAB, Macedo AN, Oliveira RV. Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:179-213. [PMID: 34628633 DOI: 10.1007/978-3-030-77252-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Metabolomics is a discipline that offers a comprehensive analysis of metabolites in biological samples. In the last decades, the notable evolution in liquid chromatography and mass spectrometry technologies has driven an exponential progress in LC-MS-based metabolomics. Targeted and untargeted metabolomics strategies are important tools in health and medical science, especially in the study of disease-related biomarkers, drug discovery and development, toxicology, diet, physical exercise, and precision medicine. Clinical and biological problems can now be understood in terms of metabolic phenotyping. This overview highlights the current approaches to LC-MS-based metabolomics analysis and its applications in the clinical research.
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Affiliation(s)
- Izadora L Furlani
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Estéfane da Cruz Nunes
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Gisele A B Canuto
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Adriana N Macedo
- Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Regina V Oliveira
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil.
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12
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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13
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Gomez-Zepeda D, Frausto M, Nájera-González HR, Herrera-Estrella L, Ordaz-Ortiz JJ. Mass spectrometry-based quantification and spatial localization of small organic acid exudates in plant roots under phosphorus deficiency and aluminum toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1791-1806. [PMID: 33797826 DOI: 10.1111/tpj.15261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Low-molecular-weight organic acid (OA) extrusion by plant roots is critical for plant nutrition, tolerance to cations toxicity, and plant-microbe interactions. Therefore, methodologies for the rapid and precise quantification of OAs are necessary to be incorporated in the analysis of roots and their exudates. The spatial location of root exudates is also important to understand the molecular mechanisms directing OA production and release into the rhizosphere. Here, we report the development of two complementary methodologies for OA determination, which were employed to evaluate the effect of inorganic ortho-phosphate (Pi) deficiency and aluminum toxicity on OA excretion by Arabidopsis roots. OA exudation by roots is considered a core response to different types of abiotic stress and for the interaction of roots with soil microbes, and for decades has been a target trait to produce plant varieties with increased capacities of Pi uptake and Al tolerance. Using targeted ultra-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UPLC-HRMS/MS), we achieved the quantification of six OAs in root exudates at sub-micromolar detection limits with an analysis time of less than 5 min per sample. We also employed targeted (MS/MS) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to detect the spatial location of citric and malic acid with high specificity in roots and exudates. Using these methods, we studied OA exudation in response to Al toxicity and Pi deficiency in Arabidopsis seedlings overexpressing genes involved in OA excretion. Finally, we show the transferability of the MALDI-MSI method by analyzing OA excretion in Marchantia polymorpha gemmalings subjected to Pi deficiency.
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Affiliation(s)
- David Gomez-Zepeda
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
| | - Moises Frausto
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Héctor-Rogelio Nájera-González
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
| | - Luis Herrera-Estrella
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - José-Juan Ordaz-Ortiz
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
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14
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Engström P, Burke TP, Tran CJ, Iavarone AT, Welch MD. Lysine methylation shields an intracellular pathogen from ubiquitylation and autophagy. SCIENCE ADVANCES 2021; 7:eabg2517. [PMID: 34172444 PMCID: PMC8232902 DOI: 10.1126/sciadv.abg2517] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
Many intracellular pathogens avoid detection by their host cells. However, it remains unknown how they avoid being tagged by ubiquitin, an initial step leading to antimicrobial autophagy. Here, we show that the intracellular bacterial pathogen Rickettsia parkeri uses two protein-lysine methyltransferases (PKMTs) to modify outer membrane proteins (OMPs) and prevent their ubiquitylation. Mutants deficient in the PKMTs were avirulent in mice and failed to grow in macrophages because of ubiquitylation and autophagic targeting. Lysine methylation protected the abundant surface protein OmpB from ubiquitin-dependent depletion from the bacterial surface. Analysis of the lysine-methylome revealed that PKMTs modify a subset of OMPs, including OmpB, by methylation at the same sites that are modified by host ubiquitin. These findings show that lysine methylation is an essential determinant of rickettsial pathogenesis that shields bacterial proteins from ubiquitylation to evade autophagic targeting.
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Affiliation(s)
- Patrik Engström
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Thomas P Burke
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cuong J Tran
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthew D Welch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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15
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Majuta SN, DeBastiani A, Li P, Valentine SJ. Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:473-485. [PMID: 33417454 PMCID: PMC8132193 DOI: 10.1021/jasms.0c00376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL·min-1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over state-of-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20-50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.
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Affiliation(s)
- Sandra N. Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
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16
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Memory-Enhancing Effects of Origanum majorana Essential Oil in an Alzheimer's Amyloid beta1-42 Rat Model: A Molecular and Behavioral Study. Antioxidants (Basel) 2020; 9:antiox9100919. [PMID: 32993114 PMCID: PMC7600529 DOI: 10.3390/antiox9100919] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/18/2022] Open
Abstract
Origanum L. (Lamiaceae) is an important genus of medicinal and aromatic plants used in traditional medicine since ancient times as culinary herbs and remedies. The aim of the present study was to evaluate the chemical composition, as well as the biochemical and cellular activities of freshly prepared Origanum majorana L. essential oil (OmEO) in an Alzheimer’s disease (AD) amyloid beta1-42 (Aβ1-42) rat model. OmEO (1% and 3%) was inhaled for 21 consecutive days, while Aβ1-42 was administered intracerebroventricularly to induce AD-like symptoms. Our data demonstrate that OmEO increased antioxidant activity and enhanced brain-derived neurotrophic factor (BDNF) expression, which in concert contributed to the improvement of cognitive function of animals. Moreover, OmEO presented beneficial effects on memory performance in Y-maze and radial arm-maze tests in the Aβ1-42 rat AD model.
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17
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Achour B, Al-Majdoub ZM, Rostami-Hodjegan A, Barber J. Mass Spectrometry of Human Transporters. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:223-247. [PMID: 32084322 DOI: 10.1146/annurev-anchem-091719-024553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transporters are key to understanding how an individual will respond to a particular dose of a drug. Two patients with similar systemic concentrations may have quite different local concentrations of a drug at the required site. The transporter profile of any individual depends upon a variety of genetic and environmental factors, including genotype, age, and diet status. Robust models (virtual patients) are therefore required and these models are data hungry. Necessary data include quantitative transporter profiles at the relevant organ. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is currently the most powerful method available for obtaining this information. Challenges include sourcing the tissue, isolating the hydrophobic membrane-embedded transporter proteins, preparing the samples for MS (including proteolytic digestion), choosing appropriate quantification methodology, and optimizing the LC-MS/MS conditions. Great progress has been made with all of these, especially within the last few years, and is discussed here.
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Affiliation(s)
- Brahim Achour
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Zubida M Al-Majdoub
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
- Certara, Princeton, New Jersey 08540, USA
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
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18
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Nys G, Nix C, Cobraiville G, Servais AC, Fillet M. Enhancing protein discoverability by data independent acquisition assisted by ion mobility mass spectrometry. Talanta 2020; 213:120812. [DOI: 10.1016/j.talanta.2020.120812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 11/28/2022]
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19
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Mikkat S, Dominik A, Stange J, Eggert M. Comparison of accompanying proteins in different therapeutic human serum albumin preparations. Biologicals 2020; 64:41-48. [DOI: 10.1016/j.biologicals.2020.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
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20
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Morris CB, Poland JC, May JC, McLean JA. Fundamentals of Ion Mobility-Mass Spectrometry for the Analysis of Biomolecules. Methods Mol Biol 2020; 2084:1-31. [PMID: 31729651 DOI: 10.1007/978-1-0716-0030-6_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for both the instrumental arrangements and key application areas that are commonly encountered in bioanalytical settings. New advances in these high-throughput strategies are described with description of complementary informatics tools to effectively utilize these data-intensive measurements. Rapid separations such as these are especially important in systems, synthetic, and chemical biology in which many small molecules are transient and correspond to various biological classes for integrated omics measurements. This chapter highlights the fundamentals of IM-MS and its applications toward biomolecular separations and discusses methods currently being used in the fields of proteomics, lipidomics, and metabolomics.
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Affiliation(s)
- Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - James C Poland
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - Jody C May
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA. .,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA.
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21
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Evasion of autophagy mediated by Rickettsia surface protein OmpB is critical for virulence. Nat Microbiol 2019; 4:2538-2551. [PMID: 31611642 PMCID: PMC6988571 DOI: 10.1038/s41564-019-0583-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/10/2019] [Indexed: 01/05/2023]
Abstract
Rickettsia are obligate intracellular bacteria that evade antimicrobial autophagy in the host cell cytosol by unknown mechanisms. Other cytosolic pathogens block different steps of autophagy targeting, including the initial step of polyubiquitin-coat formation. One mechanism of evasion is to mobilize actin to the bacterial surface. Here, we show that actin mobilization is insufficient to block autophagy recognition of the pathogen Rickettsia parkeri. Instead, R. parkeri employs outer membrane protein B (OmpB) to block ubiquitylation of the bacterial surface proteins, including OmpA, and subsequent recognition by autophagy receptors. OmpB is also required for the formation of a capsule-like layer. Although OmpB is dispensable for bacterial growth in endothelial cells, it is essential for R. parkeri to block autophagy in macrophages and to colonize mice because of its ability to promote autophagy evasion in immune cells. Our results indicate that OmpB acts as a protective shield to obstruct autophagy recognition, thereby revealing a distinctive bacterial mechanism to evade antimicrobial autophagy.
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22
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Kerr RA, Keire DA, Ye H. The impact of standard accelerated stability conditions on antibody higher order structure as assessed by mass spectrometry. MAbs 2019; 11:930-941. [PMID: 30913973 PMCID: PMC6601562 DOI: 10.1080/19420862.2019.1599632] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/23/2019] [Accepted: 03/21/2019] [Indexed: 01/12/2023] Open
Abstract
Protein therapeutic higher order structure (HOS) is a quality attribute that can be assessed to help predict shelf life. To model product shelf-life values, possible sample-dependent pathways of degradation that may affect drug efficacy or safety need to be evaluated. As changes in drug thermal stability over time can be correlated with an increased risk of HOS perturbations, the effect of long-term storage on the product should be measured as a function of temperature. Here, complementary high-resolution mass spectrometry methods for HOS analysis were used to identify storage-dependent changes of biotherapeutics (bevacizumab (Avastin), trastuzumab (Herceptin), rituximab (Rituxan), and the NIST reference material 8671 (NISTmAb)) under accelerated or manufacturer-recommended storage conditions. Collision-induced unfolding ion mobility-mass spectrometry data showed changes in monoclonal antibody folded stability profiles that were consistent with the appearance of a characteristic unfolded population. Orthogonal hydrogen-deuterium exchange-mass spectrometry data revealed that the observed changes in unfolding occurred in parallel to changes in HOS localized to the periphery of the hinge region. Using intact reverse-phase liquid chromatography-mass spectrometry, we identified several mass species indicative of peptide backbone hydrolysis, located between the variable and constant domains of the heavy chain of bevacizumab. Taken together, our data highlighted the capability of these approaches to identify age- or temperature-dependent changes in biotherapeutic HOS.
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Affiliation(s)
- Richard A. Kerr
- Division of Pharmaceutical Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, USA
| | - David A. Keire
- Division of Pharmaceutical Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, USA
| | - Hongping Ye
- Division of Pharmaceutical Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, USA
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23
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Jin Y, Wen M, Yuan Q, Zhang J, Tan W. Beneficial effects of Coomassie staining on proteomic analysis employing PAGE separation followed with whole-gel slicing, in-gel digestion and quantitative LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1110-1111:25-35. [DOI: 10.1016/j.jchromb.2019.01.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 01/12/2023]
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24
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Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. mSystems 2019; 4:mSystems00297-18. [PMID: 30746495 PMCID: PMC6365646 DOI: 10.1128/msystems.00297-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/12/2019] [Indexed: 12/13/2022] Open
Abstract
Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways. Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl coenzyme A (acetyl-CoA) and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis. Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either nonspecific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase from Pseudomonas putida that we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism. IMPORTANCE Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.
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25
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Smith BJ, Martins-de-Souza D, Fioramonte M. A Guide to Mass Spectrometry-Based Quantitative Proteomics. Methods Mol Biol 2019; 1916:3-39. [PMID: 30535679 DOI: 10.1007/978-1-4939-8994-2_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
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Affiliation(s)
- Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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26
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MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES. Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2182-2188. [PMID: 30047074 PMCID: PMC6191345 DOI: 10.1007/s13361-018-2028-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 05/04/2023]
Abstract
Recent advances in ion mobility spectrometry (IMS) have illustrated its power in determining the structural characteristics of a molecule, especially when coupled with other separations dimensions such as liquid chromatography (LC) and mass spectrometry (MS). However, these three separation techniques together greatly complicate data analyses, making better informatics tools essential for assessing the resulting data. In this manuscript, Skyline was adapted to analyze LC-IMS-CID-MS data from numerous instrument vendor datasets and determine the effect of adding the IMS dimension into the normal LC-MS molecular pipeline. For the initial evaluation, a tryptic digest of bovine serum albumin (BSA) was spiked into a yeast protein digest at seven different concentrations, and Skyline was able to rapidly analyze the MS and CID-MS data for 38 of the BSA peptides. Calibration curves for the precursor and fragment ions were assessed with and without the IMS dimension. In all cases, addition of the IMS dimension removed noise from co-eluting peptides with close m/z values, resulting in calibration curves with greater linearity and lower detection limits. This study presents an important informatics development since to date LC-IMS-CID-MS data from the different instrument vendors is often assessed manually and cannot be analyzed quickly. Because these evaluations require days for the analysis of only a few target molecules in a limited number of samples, it is unfeasible to evaluate hundreds of targets in numerous samples. Thus, this study showcases Skyline's ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly. Graphical Abstract ᅟ.
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Affiliation(s)
- Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brian S Pratt
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jarrett D Egertson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd. MSIN K8-98, P.O. Box 999, Richland, WA, 99352, USA
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd. MSIN K8-98, P.O. Box 999, Richland, WA, 99352, USA.
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Pettit ME, Donnarumma F, Murray KK, Solouki T. Infrared laser ablation sampling coupled with data independent high resolution UPLC-IM-MS/MS for tissue analysis. Anal Chim Acta 2018; 1034:102-109. [DOI: 10.1016/j.aca.2018.06.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 12/30/2022]
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Light SH, Su L, Rivera-Lugo R, Cornejo JA, Louie A, Iavarone AT, Ajo-Franklin CM, Portnoy DA. A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria. Nature 2018; 562:140-144. [PMID: 30209391 PMCID: PMC6221200 DOI: 10.1038/s41586-018-0498-z] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/03/2018] [Indexed: 11/10/2022]
Abstract
Extracellular electron transfer (EET) describes microbial bioelectrochemical processes in which electrons are transferred from the cytosol to the exterior of the cell1. Mineral-respiring bacteria use elaborate haem-based electron transfer mechanisms2-4 but the existence and mechanistic basis of other EETs remain largely unknown. Here we show that the food-borne pathogen Listeria monocytogenes uses a distinctive flavin-based EET mechanism to deliver electrons to iron or an electrode. By performing a forward genetic screen to identify L. monocytogenes mutants with diminished extracellular ferric iron reductase activity, we identified an eight-gene locus that is responsible for EET. This locus encodes a specialized NADH dehydrogenase that segregates EET from aerobic respiration by channelling electrons to a discrete membrane-localized quinone pool. Other proteins facilitate the assembly of an abundant extracellular flavoprotein that, in conjunction with free-molecule flavin shuttles, mediates electron transfer to extracellular acceptors. This system thus establishes a simple electron conduit that is compatible with the single-membrane structure of the Gram-positive cell. Activation of EET supports growth on non-fermentable carbon sources, and an EET mutant exhibited a competitive defect within the mouse gastrointestinal tract. Orthologues of the genes responsible for EET are present in hundreds of species across the Firmicutes phylum, including multiple pathogens and commensal members of the intestinal microbiota, and correlate with EET activity in assayed strains. These findings suggest a greater prevalence of EET-based growth capabilities and establish a previously underappreciated relevance for electrogenic bacteria across diverse environments, including host-associated microbial communities and infectious disease.
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Affiliation(s)
- Samuel H Light
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lin Su
- Molecular Foundry, Molecular Biophysics and Integrated Bioimaging, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210018, China
| | - Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jose A Cornejo
- Molecular Foundry, Molecular Biophysics and Integrated Bioimaging, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexander Louie
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | - Caroline M Ajo-Franklin
- Molecular Foundry, Molecular Biophysics and Integrated Bioimaging, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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Garabedian A, Benigni P, Ramirez CE, Baker ES, Liu T, Smith RD, Fernandez-Lima F. Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:817-826. [PMID: 28889248 PMCID: PMC5844780 DOI: 10.1007/s13361-017-1787-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/29/2017] [Accepted: 08/10/2017] [Indexed: 05/12/2023]
Abstract
In the present work, the potential of trapped ion mobility spectrometry coupled to TOF mass spectrometry (TIMS-TOF MS) for discovery and targeted monitoring of peptide biomarkers from human-in-mouse xenograft tumor tissue was evaluated. In particular, a TIMS-MS workflow was developed for the detection and quantification of peptide biomarkers using internal heavy analogs, taking advantage of the high mobility resolution (R = 150-250) prior to mass analysis. Five peptide biomarkers were separated, identified, and quantified using offline nanoESI-TIMS-CID-TOF MS; the results were in good agreement with measurements using a traditional LC-ESI-MS/MS proteomics workflow. The TIMS-TOF MS analysis permitted peptide biomarker detection based on accurate mobility, mass measurements, and high sequence coverage for concentrations in the 10-200 nM range, while simultaneously achieving discovery measurements of not initially targeted peptides as markers from the same proteins and, eventually, other proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Cesar E Ramirez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Erin S Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA.
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA.
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Brown CJ, Kaufman T, Trinidad JC, Clemmer DE. Proteome changes in the aging Drosophila melanogaster head. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 425:36-46. [PMID: 30906200 PMCID: PMC6426325 DOI: 10.1016/j.ijms.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A combination of liquid chromatography, ion mobility spectrometry, mass spectrometry, and database searching techniques were used to characterize the proteomes of four biological replicates of adult Drosophila melanogaster heads at seven time points across their lifespans. Based on the detection of tryptic peptides, the identities of 1281 proteins were determined. An estimate of the abundance of each protein, based on the three most intense peptide ions, shows that the quantified species vary in concentration over a factor of ~103. Compared to initial studies in the field of Drosophila proteomics, our current results show an eight-fold higher temporal protein coverage with increased quantitative accuracy. Across the lifespan, we observe a range of trends in the abundance of different proteins, including: an increase in abundance of proteins involved in oxidative phosphorylation, and the tricarboxylic acid cycle; a decrease in proteasomal proteins, as well as ribosomal proteins; and, many types of proteins, which remain relatively unchanged. For younger flies, proteomes are relatively similar within their age group. For older flies, proteome similarity decreases within their age group. These combined results illustrate a correlation between increasing age and decreasing proteostasis.
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Affiliation(s)
- Christopher J. Brown
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, United States
| | - Thomas Kaufman
- Department of Biology, Indiana University, Bloomington, IN, 47405, United States
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, United States
- Corresponding authors. (J.C. Trinidad), (D.E. Clemmer)
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, United States
- Corresponding authors. (J.C. Trinidad), (D.E. Clemmer)
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Kaufmann A, Walker S. Comparison of linear intrascan and interscan dynamic ranges of Orbitrap and ion-mobility time-of-flight mass spectrometers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1915-1926. [PMID: 28875592 DOI: 10.1002/rcm.7981] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE The linear intrascan and interscan dynamic ranges of mass spectrometers are important in metabolome and residue analysis. A large linear dynamic range is mandatory if both low- and high-abundance ions have to be detected and quantitated in heavy matrix samples. These performance criteria, as provided by modern high-resolution mass spectrometry (HRMS), were systematically investigated. METHODS The comparison included two generations of Orbitraps, and an ion mobility quadrupole time-of-flight (QTOF) system In addition, different scan modes, as provided by the utilized instruments, were investigated. Calibration curves of different compounds covering a concentration range of five orders of magnitude were measured to evaluate the linear interscan dynamic range. The linear intrascan dynamic range and the resulting mass accuracy were evaluated by repeating these measurements in the presence of a very intense background. RESULTS Modern HRMS instruments can show linear dynamic ranges of five orders of magnitude. Often, however, the linear dynamic range is limited by the detection capability (sensitivity and selectivity) and by the electrospray ionization. Orbitraps, as opposed to TOF instruments, show a reduced intrascan dynamic range. This is due to the limited C-trap and Orbitrap capacity. The tested TOF instrument shows poorer mass accuracies than the Orbitraps. In contrast, hyphenation with an ion-mobility device seems not to affect the linear dynamic range. CONCLUSIONS The linear dynamic range of modern HRMS instrumentation has been significantly improved. This also refers to the virtual absence of systematic mass shifts at high ion abundances. The intrascan dynamic range of the current Orbitrap technology may still be a limitation when analyzing complex matrix extracts. On the other hand, the linear dynamic range is not only limited by the detector technology, but can also be shortened by peripheral devices, where the ionization and transfer of ions take place.
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Affiliation(s)
- Anton Kaufmann
- Official Food Control Authority, Fehrenstrasse 15, 8032, Zürich, Switzerland
| | - Stephan Walker
- Official Food Control Authority, Fehrenstrasse 15, 8032, Zürich, Switzerland
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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Oehmcke-Hecht S, Nass LE, Wichura JB, Mikkat S, Kreikemeyer B, Fiedler T. Deletion of the L-Lactate Dehydrogenase Gene ldh in Streptococcus pyogenes Leads to a Loss of SpeB Activity and a Hypovirulent Phenotype. Front Microbiol 2017; 8:1841. [PMID: 28983299 PMCID: PMC5613712 DOI: 10.3389/fmicb.2017.01841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/08/2017] [Indexed: 01/19/2023] Open
Abstract
Streptococcus pyogenes uses lactic acid fermentation for the generation of ATP. Here, we analyzed the impact of a deletion of the L-lactate dehydrogenase gene ldh on the virulence of S. pyogenes M49. While the ldh deletion does not cause a general growth deficiency in laboratory media, the growth in human blood and plasma is significantly hampered. The ldh deletion strain is furthermore less virulent in a Galleria mellonella infection model. We show that the ldh deletion leads to a decrease in the activity of the cysteine protease SpeB, an important secreted virulence factor of S. pyogenes. The reduced SpeB activity is caused by a hampered autocatalytic activation of the SpeB zymogen into the mature SpeB. The missing SpeB activity furthermore leads to increased plasmin activation and a reduced activation of the contact system on the surface of S. pyogenes. All these effects can be reversed when ldh is reintroduced into the mutant via a plasmid. The results demonstrate a previously unappreciated role for LDH in modulation of SpeB maturation.
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Affiliation(s)
- Sonja Oehmcke-Hecht
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Leif E Nass
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Jan B Wichura
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical CentreRostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
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Impact of blood sample collection methods on blood protein profiling studies. Clin Chim Acta 2017; 471:128-134. [DOI: 10.1016/j.cca.2017.05.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/16/2017] [Accepted: 05/25/2017] [Indexed: 12/16/2022]
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Construction and characterization of the Korean whole saliva proteome to determine ethnic differences in human saliva proteome. PLoS One 2017; 12:e0181765. [PMID: 28742128 PMCID: PMC5524414 DOI: 10.1371/journal.pone.0181765] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/06/2017] [Indexed: 11/25/2022] Open
Abstract
As the first step to discover protein disease biomarkers from saliva, global analyses of the saliva proteome have been carried out since the early 2000s, and more than 3,000 proteins have been identified in human saliva. Recently, ethnic differences in the human plasma proteome have been reported, but such corresponding studies on human saliva in this aspect have not been previously reported. Thus, here, in order to determine ethnic differences in the human saliva proteome, a Korean whole saliva (WS) proteome catalogue indexing 480 proteins was built and characterized through nLC-Q-IMS-TOF analyses of WS samples collected from eleven healthy South Korean male adult volunteers for the first time. Identification of 226 distinct Korean WS proteins, not observed in the integrated human saliva protein dataset, and significant gene ontology distribution differences in the Korean WS proteome compared to the integrated human saliva proteome strongly support ethnic differences in the human saliva proteome. Additionally, the potential value of ethnicity-specific human saliva proteins as biomarkers for diseases highly prevalent in that ethnic group was confirmed by finding 35 distinct Korean WS proteins likely to be associated with the top 10 deadliest diseases in South Korea. Finally, the present Korean WS protein list can serve as the first level reference for future proteomic studies including disease biomarker studies on Korean saliva.
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Exogenous Auxin Elicits Changes in the Arabidopsis thaliana Root Proteome in a Time-Dependent Manner. Proteomes 2017; 5:proteomes5030016. [PMID: 28698516 PMCID: PMC5620533 DOI: 10.3390/proteomes5030016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/27/2017] [Accepted: 07/04/2017] [Indexed: 11/24/2022] Open
Abstract
Auxin is involved in many aspects of root development and physiology, including the formation of lateral roots. Improving our understanding of how the auxin response is mediated at the protein level over time can aid in developing a more complete molecular framework of the process. This study evaluates the effects of exogenous auxin treatment on the Arabidopsis root proteome after exposure of young seedlings to auxin for 8, 12, and 24 h, a timeframe permitting the initiation and full maturation of individual lateral roots. Root protein extracts were processed to peptides, fractionated using off-line strong-cation exchange, and analyzed using ultra-performance liquid chromatography and data independent acquisition-based mass spectrometry. Protein abundances were then tabulated using label-free techniques and evaluated for significant changes. Approximately 2000 proteins were identified during the time course experiment, with the number of differences between the treated and control roots increasing over the 24 h time period, with more proteins found at higher abundance with exposure to auxin than at reduced abundance. Although the proteins identified and changing in levels at each time point represented similar biological processes, each time point represented a distinct snapshot of the response. Auxin coordinately regulates many physiological events in roots and does so by influencing the accumulation and loss of distinct proteins in a time-dependent manner. Data are available via ProteomeXchange with the identifier PXD001400.
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Cryar A, Groves K, Quaglia M. Online Hydrogen-Deuterium Exchange Traveling Wave Ion Mobility Mass Spectrometry (HDX-IM-MS): a Systematic Evaluation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1192-1202. [PMID: 28374315 PMCID: PMC5438439 DOI: 10.1007/s13361-017-1633-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 05/11/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an important tool for measuring and monitoring protein structure. A bottom-up approach to HDX-MS provides peptide level deuterium uptake values and a more refined localization of deuterium incorporation compared with global HDX-MS measurements. The degree of localization provided by HDX-MS is proportional to the number of peptides that can be identified and monitored across an exchange experiment. Ion mobility spectrometry (IMS) has been shown to improve MS-based peptide analysis of biological samples through increased separation capacity. The integration of IMS within HDX-MS workflows has been commercialized but presently its adoption has not been widespread. The potential benefits of IMS, therefore, have not yet been fully explored. We herein describe a comprehensive evaluation of traveling wave ion mobility integrated within an online-HDX-MS system and present the first reported example of UDMSE acquisition for HDX analysis. Instrument settings required for optimal peptide identifications are described and the effects of detector saturation due to peak compression are discussed. A model system is utilized to confirm the comparability of HDX-IM-MS and HDX-MS uptake values prior to an evaluation of the benefits of IMS at increasing sample complexity. Interestingly, MS and IM-MS acquisitions were found to identify distinct populations of peptides that were unique to the respective methods, a property that can be utilized to increase the spatial resolution of HDX-MS experiments by >60%. Graphical Abstract ᅟ.
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Affiliation(s)
- Adam Cryar
- LGC, Queens Road, Teddington, London, TW11 0LY, UK.
| | - Kate Groves
- LGC, Queens Road, Teddington, London, TW11 0LY, UK
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Pade N, Mikkat S, Hagemann M. Ethanol, glycogen and glucosylglycerol represent competing carbon pools in ethanol-producing cells of Synechocystis sp. PCC 6803 under high-salt conditions. MICROBIOLOGY-SGM 2017; 163:300-307. [PMID: 28100303 DOI: 10.1099/mic.0.000433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cyanobacteria are photoautotrophic micro-organisms, which are increasingly being used as microbial cell factories to produce, for example, ethanol directly from solar energy and CO2. Here, we analysed the effects of different salt concentrations on an ethanol-producing strain of Synechocystis sp. PCC 6803 that overexpresses the pyruvate decarboxylase (pdc) from Zymomonas mobilis and the native alcohol dehydrogenase (adhA). Moderate salinities of 2 % NaCl had no negative impact on ethanol production, whereas the addition of 4 % NaCl resulted in significantly decreased ethanol yields compared to low-salt conditions. Proteomic analysis identified a defined set of proteins with increased abundances in ethanol-producing cells. Among them, we found strong up-regulation of α-1,4 glucan phosphorylase (GlgP, Slr1367) in the producer strain, which consistently resulted in a massive depletion of glycogen pools in these cells regardless of the salinity. The salt-induced accumulation of the compatible solute glucosylglycerol was not affected by the ethanol production. Glycogen and probably compatible solutes could present competing pools with respect to organic carbon, explaining the decreased ethanol production at the highest salinity.
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Affiliation(s)
- Nadin Pade
- Department Plant Physiology, University of Rostock, Institute for Biological Science, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, University Medicine Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Martin Hagemann
- Department Plant Physiology, University of Rostock, Institute for Biological Science, Albert-Einstein-Str. 3, 18059 Rostock, Germany
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Technological advances and proteomic applications in drug discovery and target deconvolution: identification of the pleiotropic effects of statins. Drug Discov Today 2017; 22:848-869. [PMID: 28284830 DOI: 10.1016/j.drudis.2017.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/09/2017] [Accepted: 03/01/2017] [Indexed: 01/05/2023]
Abstract
Proteomic-based techniques provide a powerful tool for identifying the full spectrum of protein targets of a drug, elucidating its mechanism(s) of action, and identifying biomarkers of its efficacy and safety. Herein, we outline the technological advancements in the field, and illustrate the contribution of proteomics to the definition of the pharmacological profile of statins, which represent the cornerstone of the prevention and treatment of cardiovascular diseases (CVDs). Statins act by inhibiting 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA) reductase, thus reducing cholesterol biosynthesis and consequently enhancing the clearance of low-density lipoproteins from the blood; however, HMG-CoA reductase inhibition can result in a multitude of additional effects beyond lipid lowering, known as 'pleiotropic effects'. The case of statins highlights the unique contribution of proteomics to the target profiling of a drug molecule.
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40
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Gombar R, Pitcher TE, Lewis JA, Auld J, Vacratsis PO. Proteomic characterization of seminal plasma from alternative reproductive tactics of Chinook salmon ( Oncorhynchus tswatchysha ). J Proteomics 2017; 157:1-9. [DOI: 10.1016/j.jprot.2017.01.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 01/24/2017] [Accepted: 01/28/2017] [Indexed: 12/11/2022]
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Abstract
In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
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Jin Y, Chen J, Wang A, Zhang J, Chen S, Manabe T, Tan W. Analysis of low-density lipoprotein-associated proteins using the method of digitized native protein mapping. Electrophoresis 2016; 37:2063-74. [DOI: 10.1002/elps.201600100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Ya Jin
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
- Pre-Incubator for Innovative Drugs & Medicine; School of Bioscience and Bioengineering, South China University of Technology; Guangzhou P. R. China
| | - Jin Chen
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
- Pre-Incubator for Innovative Drugs & Medicine; School of Bioscience and Bioengineering, South China University of Technology; Guangzhou P. R. China
| | - Ahui Wang
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
- Pre-Incubator for Innovative Drugs & Medicine; School of Bioscience and Bioengineering, South China University of Technology; Guangzhou P. R. China
| | - Jun Zhang
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
| | - Shumin Chen
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
- Pre-Incubator for Innovative Drugs & Medicine; School of Bioscience and Bioengineering, South China University of Technology; Guangzhou P. R. China
| | | | - Wen Tan
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
- Pre-Incubator for Innovative Drugs & Medicine; School of Bioscience and Bioengineering, South China University of Technology; Guangzhou P. R. China
- Key Laboratory of Industrial Biotechnology of Guangdong Higher Education Institutes; South China University of Technology; Guangzhou P. R. China
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Huang L, Wickramasekara SI, Akinyeke T, Stewart BS, Jiang Y, Raber J, Maier CS. Ion mobility-enhanced MS(E)-based label-free analysis reveals effects of low-dose radiation post contextual fear conditioning training on the mouse hippocampal proteome. J Proteomics 2016; 140:24-36. [PMID: 27020882 PMCID: PMC5029422 DOI: 10.1016/j.jprot.2016.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 11/15/2022]
Abstract
UNLABELLED Recent advances in the field of biodosimetry have shown that the response of biological systems to ionizing radiation is complex and depends on the type and dose of radiation, the tissue(s) exposed, and the time lapsed after exposure. The biological effects of low dose radiation on learning and memory are not well understood. An ion mobility-enhanced data-independent acquisition (MS(E)) approach in conjunction with the ISOQuant software tool was utilized for label-free quantification of hippocampal proteins with the goal of determining protein alteration associated with low-dose whole body ionizing radiation (X-rays, 1Gy) of 5.5-month-old male C57BL/6J mice post contextual fear conditioning training. Global proteome analysis revealed deregulation of 73 proteins (out of 399 proteins). Deregulated proteins indicated adverse effects of irradiation on myelination and perturbation of energy metabolism pathways involving a shift from the TCA cycle to glutamate oxidation. Our findings also indicate that proteins associated with synaptic activity, including vesicle recycling and neurotransmission, were altered in the irradiated mice. The elevated LTP and decreased LTD suggest improved synaptic transmission and enhanced efficiency of neurotransmitter release which would be consistent with the observed comparable contextual fear memory performance of the mice following post-training whole body or sham-irradiation. SIGNIFICANCE This study is significant because the biological consequences of low dose radiation on learning and memory are complex and not yet well understood. We conducted a IMS-enhanced MS(E)-based label-free quantitative proteomic analysis of hippocampal tissue with the goal of determining protein alteration associated with low-dose whole body ionizing radiation (X-ray, 1Gy) of 5.5-month-old male C57BL/6J mice post contextual fear conditioning training. The IMS-enhanced MS(E) approach in conjunction with ISOQuant software was robust and accurate with low median CV values of 0.99% for the technical replicates of samples from both the sham and irradiated group. The biological variance was as low as 1.61% for the sham group and 1.31% for the irradiated group. The applied data generation and processing workflow allowed the quantitative evaluation of 399 proteins. The current proteomic analysis indicates that myelination is sensitive to low dose radiation. The observed protein level changes imply modulation of energy metabolism pathways in the radiation exposed group, specifically changes in protein abundance levels suggest a shift from TCA cycle to glutamate oxidation to satisfy energy demands. Most significantly, our study reveals deregulation of proteins involved in processes that govern synaptic activity including enhanced synaptic vesicle cycling, and altered long-term potentiation (LTP) and depression (LTD). An elevated LTP and decreased LTD suggest improved synaptic transmission and enhanced efficiency of neurotransmitter release which is consistent with the observed comparable contextual fear memory performance of the mice following post-training whole body or sham-irradiation. Overall, our results underscore the importance of low dose radiation experiments for illuminating the sensitivity of biochemical pathways to radiation, and the modulation of potential repair and compensatory response mechanisms. This kind of studies and associated findings may ultimately lead to the design of strategies for ameliorating hippocampal and CNS injury following radiation exposure as part of medical therapies or as a consequence of occupational hazards.
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Affiliation(s)
- Lin Huang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | | | - Tunde Akinyeke
- Department of Behavioral Neuroscience, Division of Neuroscience, ONPRC, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Blair S Stewart
- Department of Behavioral Neuroscience, Division of Neuroscience, ONPRC, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jacob Raber
- Department of Behavioral Neuroscience, Division of Neuroscience, ONPRC, Oregon Health and Science University, Portland, Oregon 97239, United States; Departments of Neurology and Radiation Medicine, Division of Neuroscience, ONPRC, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States.
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Distler U, Kuharev J, Navarro P, Tenzer S. Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics. Nat Protoc 2016; 11:795-812. [DOI: 10.1038/nprot.2016.042] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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45
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Ewing MA, Glover MS, Clemmer DE. Hybrid ion mobility and mass spectrometry as a separation tool. J Chromatogr A 2016; 1439:3-25. [DOI: 10.1016/j.chroma.2015.10.080] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/05/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
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Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. The metabolic background is a global player in Saccharomyces gene expression epistasis. Nat Microbiol 2016; 1:15030. [PMID: 27572163 PMCID: PMC5131842 DOI: 10.1038/nmicrobiol.2015.30] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/17/2015] [Indexed: 01/20/2023]
Abstract
The regulation of gene expression in response to nutrient availability is fundamental to the genotype-phenotype relationship. The metabolic-genetic make-up of the cell, as reflected in auxotrophy, is hence likely to be a determinant of gene expression. Here, we address the importance of the metabolic-genetic background by monitoring transcriptome, proteome and metabolome in a repertoire of 16 Saccharomyces cerevisiae laboratory backgrounds, combinatorially perturbed in histidine, leucine, methionine and uracil biosynthesis. The metabolic background affected up to 85% of the coding genome. Suggesting widespread confounding, these transcriptional changes show, on average, 83% overlap between unrelated auxotrophs and 35% with previously published transcriptomes generated for non-metabolic gene knockouts. Background-dependent gene expression correlated with metabolic flux and acted, predominantly through masking or suppression, on 88% of transcriptional interactions epistatically. As a consequence, the deletion of the same metabolic gene in a different background could provoke an entirely different transcriptional response. Propagating to the proteome and scaling up at the metabolome, metabolic background dependencies reveal the prevalence of metabolism-dependent epistasis at all regulatory levels. Urging a fundamental change of the prevailing laboratory practice of using auxotrophs and nutrient supplemented media, these results reveal epistatic intertwining of metabolism with gene expression on the genomic scale.
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Affiliation(s)
- Mohammad Tauqeer Alam
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Aleksej Zelezniak
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Pavel Shliaha
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Roland Schwarz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Elahe Radmanesfahar
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Antje Krüger
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Enrica Calvani
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Stefan Christen
- Department of Molecular Systems Biology, Eidgenoessische Technische Hochschule, Zurich, Switzerland
| | | | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Kathryn S Lilley
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge, United Kingdom
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
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Strzelecka D, Holman SW, Eyers CE. Evaluation of dimethyl sulfoxide (DMSO) as a mobile phase additive during top 3 label-free quantitative proteomics. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 391:157-160. [PMID: 26869853 PMCID: PMC4708063 DOI: 10.1016/j.ijms.2015.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Dimethyl sulfoxide (DMSO) has been advocated as a beneficial additive to electrospray solvents for peptide analysis due to the improved ionisation efficiency conferred. Previous reports have shown that the resultant improvements in peptide ion signal intensities are non-uniform. As a result, it was hypothesised that inclusion of DMSO in electrospray solvents could be detrimental to the outcome of intensity-based label-free absolute quantification approaches, specifically the top 3 method. The effect of DMSO as a mobile phase additive in top 3 label-free quantification was therefore evaluated. We show that inclusion of DMSO enhances data quality, improving the precision and number of proteins quantified, with no significant change to the quantification values observed in its absence.
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Key Words
- DIA, data-independent acquisition
- DMSO
- DMSO, dimethyl sulfoxide
- ESI, electrospray ionisation
- HDMSE, ion mobility-assisted MSE
- LC, liquid chromatography
- LC–MS
- Label-free
- MS, mass spectrometry
- MS/MS, tandem mass spectrometry
- MSE, mass spectrometry with elevated energy (a form of data-independent tandem mass spectrometry)
- Peptide
- Proteomics
- Q-ToF, quadrupole-time-of-flight
- Quantification
- SWATH, sequential window acquisition of all theoretical fragment ion spectra
- cpc, copies per cell
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Affiliation(s)
- Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Stephen W. Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
- Corresponding author. Tel.: +44 151 795 4424.
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Sarbu M, Zhu F, Peter-Katalinić J, Clemmer DE, Zamfir AD. Application of ion mobility tandem mass spectrometry to compositional and structural analysis of glycopeptides extracted from the urine of a patient diagnosed with Schindler disease. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1929-1937. [PMID: 26443390 DOI: 10.1002/rcm.7288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/17/2015] [Accepted: 07/23/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Schindler disease is caused by the deficient activity of α-N-acetylgalactosaminidase, which leads to an abnormal accumulation of O-glycopeptides in tissues and body fluids. In this work the Schindler condition is for the first time approached by ion mobility (IMS) tandem mass spectrometry (MS/MS), for determining urine glycopeptide fingerprints and discriminate isomeric structures. METHODS IMS-MS experiments were conducted on a Synapt G2s mass spectrometer operating in negative ion mode. A glycopeptide mixture extracted from the urine of a patient suffering from Schindler disease was dissolved in methanol and infused into the mass spectrometer by electrospray ionization using a syringe-pump system. MS/MS was performed by collision-induced dissociation (CID) at low energies, after mobility separation in the transfer cell. Data acquisition and processing were performed using MassLynx and Waters Driftscope software. RESULTS IMS-MS data indicated that the attachment of one or two amino acids to the carbohydrate backbone has a minimal influence on the molecule conformation, which limits the discrimination of the free oligosaccharides from the glycosylated amino acids and dipeptides. The structural analysis by CID MS/MS in combination with IMS-MS of species exhibiting the same m/z but different configurations demonstrated for the first time the presence of positional isomers for some of the Schindler disease biomarker candidates. CONCLUSIONS The IMS-MS and CID MS/MS platform was for the first time optimized and applied to Schindler disease glycourinome. By this approach the separation and characterization of Neu5Ac positional isomers was possible. IMS CID MS/MS showed the ability to determine the type of the glycopeptide isomers from a series of possible candidates.
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Affiliation(s)
- Mirela Sarbu
- West University of Timisoara, Romania
- Aurel Vlaicu University of Arad, Romania
| | - Feifei Zhu
- Department of Chemistry, Indiana University, Bloomington, USA
| | - Jasna Peter-Katalinić
- Institute for Medical Physics and Biophysics, University of Muenster, Germany
- Department of Biotechnology, University of Rijeka, Croatia
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, USA
| | - Alina D Zamfir
- Aurel Vlaicu University of Arad, Romania
- National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Romania
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Meier F, Beck S, Grassl N, Lubeck M, Park MA, Raether O, Mann M. Parallel Accumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device. J Proteome Res 2015; 14:5378-87. [PMID: 26538118 DOI: 10.1021/acs.jproteome.5b00932] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In liquid chromatography-mass spectrometry (LC-MS)-based proteomics, many precursors elute from the column simultaneously. In data-dependent analyses, these precursors are fragmented one at a time, whereas the others are discarded entirely. Here we employ trapped ion mobility spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF) mass spectrometer to remove this limitation. In TIMS, all precursor ions are accumulated in parallel and released sequentially as a function of their ion mobility. Instead of selecting a single precursor mass with the quadrupole mass filter, we here implement synchronized scans in which the quadrupole is mass positioned with sub-millisecond switching times at the m/z values of appropriate precursors, such as those derived from a topN precursor list. We demonstrate serial selection and fragmentation of multiple precursors in single 50 ms TIMS scans. Parallel accumulation-serial fragmentation (PASEF) enables hundreds of MS/MS events per second at full sensitivity. Modeling the effect of such synchronized scans for shotgun proteomics, we estimate that about a 10-fold gain in sequencing speed should be achievable by PASEF without a decrease in sensitivity.
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Affiliation(s)
- Florian Meier
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Scarlet Beck
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Niklas Grassl
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Markus Lubeck
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Melvin A Park
- Bruker Daltonics Inc., 40 Manning Road, Billerica, Massachusetts 01821, United States
| | - Oliver Raether
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
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Sherrod SD, McLean JA. Systems-Wide High-Dimensional Data Acquisition and Informatics Using Structural Mass Spectrometry Strategies. Clin Chem 2015; 62:77-83. [PMID: 26453699 DOI: 10.1373/clinchem.2015.238261] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/12/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND Untargeted multiomics data sets are obtained for samples in systems, synthetic, and chemical biology by integrating chromatographic separations with ion mobility-mass spectrometry (IM-MS) analysis. The data sets are interrogated using bioinformatics strategies to organize the data for identification prioritization. CONTENT The use of big data approaches for data mining of massive data sets in systems-wide analyses is presented. Untargeted biological data across multiomics dimensions are obtained using a variety of chromatography strategies with structural MS. Separation timescales for different techniques and the resulting data deluge when combined with IM-MS are presented. Data mining self-organizing map strategies are used to rapidly filter the data, highlighting those features describing uniqueness to the query. Examples are provided in longitudinal analyses in synthetic biology and human liver exposure to acetaminophen, and in chemical biology for natural product discovery from bacterial biomes. CONCLUSIONS Matching the separation timescales of different forms of chromatography with IM-MS provides sufficient multiomics selectivity to perform untargeted systems-wide analyses. New data mining strategies provide a means for rapidly interrogating these data sets for feature prioritization and discovery in a range of applications in systems, synthetic, and chemical biology.
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Affiliation(s)
- Stacy D Sherrod
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN.
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