1
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Ni Z, Arevalo R. Collision cross-section measurements of small molecules via transient decay profiles observed in Orbitrap mass analyzers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9887. [PMID: 39185582 DOI: 10.1002/rcm.9887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/30/2024] [Accepted: 07/26/2024] [Indexed: 08/27/2024]
Abstract
Collision cross section (CCS) of organic compounds can be measured via Fourier transform-based mass spectrometry (MS) by modeling the decay rate of transient signals in the analyzer. Deriving CCS values of low-mass molecules (mass < 2000 Da and CCS < 500 Å2) with Orbitrap MS is challenging due to their high axial frequencies and small absolute variances in cross-sectional profiles. Here, we acquired mass spectra of progressively more complex low-mass analytes using commercial Orbitrap mass spectrometers. The transient signals were processed using Fast Fourier transform (FFT) and short-time Fourier transform (StFFT) to derive decay constants of multiple select ionic species from a single MS full-scan experiment. Decay constants were translated into CCS values using at least two internal standards in the same mass spectrum. Our results suggest target ionic species should have high S/N in order to derive CCS values with ≤0.5% uncertainty. Limitations in the precision of CCS measurements reflect local space charge effects that disturb ion motion in the analyzer. The derived CCS values of polymer like fragments of Ultramark 1621 and small molecules such as individual protonated amino acids can achieve average ±1% error with selection of internal standards across a wide mass range. Future studies need to optimize the strategy to select internal standards in order to improve the precision and accuracy of CCS measurements for small molecules via Orbitrap MS.
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Affiliation(s)
- Ziqin Ni
- Department of Geology, University of Maryland, College Park, Maryland, USA
| | - Ricardo Arevalo
- Department of Geology, University of Maryland, College Park, Maryland, USA
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2
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Xie H, Sdougkou K, Bonnefille B, Papazian S, Bergdahl IA, Rantakokko P, Martin JW. Chemical Exposomics in Human Plasma by Lipid Removal and Large-Volume Injection Gas Chromatography-High-Resolution Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:17592-17605. [PMID: 39376097 PMCID: PMC11465644 DOI: 10.1021/acs.est.4c05942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 10/09/2024]
Abstract
For comprehensive chemical exposomics in blood, analytical workflows are evolving through advances in sample preparation and instrumental methods. We hypothesized that gas chromatography-high-resolution mass spectrometry (GC-HRMS) workflows could be enhanced by minimizing lipid coextractives, thereby enabling larger injection volumes and lower matrix interference for improved target sensitivity and nontarget molecular discovery. A simple protocol was developed for small plasma volumes (100-200 μL) by using isohexane (H) to extract supernatants of acetonitrile-plasma (A-P). The HA-P method was quantitative for a wide range of hydrophobic multiclass target analytes (i.e., log Kow > 3.0), and the extracts were free of major lipids, thereby enabling robust large-volume injections (LVIs; 25 μL) in long sequences (60-70 h, 70-80 injections) to a GC-Orbitrap HRMS. Without lipid removal, LVI was counterproductive because method sensitivity suffered from the abundant matrix signal, resulting in low ion injection times to the Orbitrap. The median method quantification limit was 0.09 ng/mL (range 0.005-4.83 ng/mL), and good accuracy was shown for a certified reference serum. Applying the method to plasma from a Swedish cohort (n = 32; 100 μL), 51 of 103 target analytes were detected. Simultaneous nontarget analysis resulted in 112 structural annotations (12.8% annotation rate), and Level 1 identification was achieved for 7 of 8 substances in follow-up confirmations. The HA-P method is potentially scalable for application in cohort studies and is also compatible with many liquid-chromatography-based exposomics workflows.
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Affiliation(s)
- Hongyu Xie
- Department
of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Kalliroi Sdougkou
- Department
of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Bénilde Bonnefille
- Department
of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, 171 65 Solna, Sweden
| | - Stefano Papazian
- Department
of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, 171 65 Solna, Sweden
| | - Ingvar A. Bergdahl
- Department
of Public Health and Clinical Medicine, Section for Sustainable Health, Umeå University, 901 87 Umeå, Sweden
| | - Panu Rantakokko
- Department
of Public Health, Lifestyles and Living Environments Unit, National Institute for Health and Welfare, Neulaniementie 4, 702 10 Kuopio, Finland
| | - Jonathan W. Martin
- Department
of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, 171 65 Solna, Sweden
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3
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Hollenback AJ, Jaisi DP. Position-Specific Oxygen Isotope Analysis in Inositol Phosphates by Using Electrospray Ionization-Quadrupole-Orbitrap Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2176-2186. [PMID: 39082822 DOI: 10.1021/jasms.4c00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Conventional isotope-ratio mass spectrometry measurements obscure position-specific isotope distributions in molecular compounds because these measurements require an initial step that converts compounds into simple gases by combustion or pyrolysis. Here, we used electrospray ionization (ESI)-based Orbitrap mass spectrometry to measure oxygen isotope ratios in the phosphate and hydroxyl moieties of inositol phosphates. A thermal hydrolysis experiment was conducted using 18O-labeled water to examine the position-specific oxygen isotope exchange in inositol hexakisphosphate (IP6) as well as its hydrolysis products IP5, IP3, and PO3 fragments. Measurement precisions of the position-specific and molecular-average oxygen isotope values of inositol phosphates were better than ±1.1‰ and ±0.5‰, respectively. Under optimized ionization and Orbitrap parameters, this level of precision was obtained within 30 min of run time at 60 μM initial concentration of inositol phosphate. The ability to measure phosphate-specific oxygen isotopes in inositol phosphate enabled the quantification of isotope exchange, which did not occur in phosphate on IP6, IP5, IP3, and PO3 fragments, meaning that the change in isotopes should have resulted from hydroxyls in the ring. Isotope mass balance calculations corroborated that hydroxyl oxygens are derived from 18O-labeled water. With the observed sensitivity and precision achieved in this study, Orbitrap IRMS proved to be a promising tool for investigating the position-specific oxygen isotopes in organophosphorus compounds. These outcomes open up numerous potential applications that can expand our understanding of phosphorus cycling in the environment.
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Affiliation(s)
- Anthony J Hollenback
- Harker Interdisciplinary Science and Engineering Laboratory, Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716, United States
| | - Deb P Jaisi
- Harker Interdisciplinary Science and Engineering Laboratory, Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716, United States
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4
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Greguš M, Koller A, Ray S, Ivanov AR. Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples. J Proteome Res 2024; 23:2230-2240. [PMID: 38690845 PMCID: PMC11165581 DOI: 10.1021/acs.jproteome.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Deep proteomic profiling of complex biological and medical samples available at low nanogram and subnanogram levels is still challenging. Thorough optimization of settings, parameters, and conditions in nanoflow liquid chromatography-tandem mass spectrometry (MS)-based proteomic profiling is crucial for generating informative data using amount-limited samples. This study demonstrates that by adjusting selected instrument parameters, e.g., ion injection time, automated gain control, and minimally altering the conditions for resuspending or storing the sample in solvents of different compositions, up to 15-fold more thorough proteomic profiling can be achieved compared to conventionally used settings. More specifically, the analysis of 1 ng of the HeLa protein digest standard by Q Exactive HF-X Hybrid Quadrupole-Orbitrap and Orbitrap Fusion Lumos Tribrid mass spectrometers yielded an increase from 1758 to 5477 (3-fold) and 281 to 4276 (15-fold) peptides, respectively, demonstrating that higher protein identification results can be obtained using the optimized methods. While the instruments applied in this study do not belong to the latest generation of mass spectrometers, they are broadly used worldwide, which makes the guidelines for improving performance desirable to a wide range of proteomics practitioners.
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Affiliation(s)
- Michal Greguš
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Antonius Koller
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Somak Ray
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Alexander R. Ivanov
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
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5
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Ivanova B. Special Issue with Research Topics on "Recent Analysis and Applications of Mass Spectra on Biochemistry". Int J Mol Sci 2024; 25:1995. [PMID: 38396673 PMCID: PMC10888122 DOI: 10.3390/ijms25041995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Analytical mass spectrometry applies irreplaceable mass spectrometric (MS) methods to analytical chemistry and chemical analysis, among other areas of analytical science [...].
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
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6
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Chung HH, Huang P, Chen CL, Lee C, Hsu CC. Next-generation pathology practices with mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2023; 42:2446-2465. [PMID: 35815718 DOI: 10.1002/mas.21795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique that reveals the spatial distribution of various molecules in biological samples, and it is widely used in pathology-related research. In this review, we summarize common MSI techniques, including matrix-assisted laser desorption/ionization and desorption electrospray ionization MSI, and their applications in pathological research, including disease diagnosis, microbiology, and drug discovery. We also describe the improvements of MSI, focusing on the accumulation of imaging data sets, expansion of chemical coverage, and identification of biological significant molecules, that have prompted the evolution of MSI to meet the requirements of pathology practices. Overall, this review details the applications and improvements of MSI techniques, demonstrating the potential of integrating MSI techniques into next-generation pathology practices.
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Affiliation(s)
- Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Penghsuan Huang
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chuping Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
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7
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Harper CC, Avadhani VS, Hanozin E, Miller ZM, Williams ER. Dynamic Energy Measurements in Charge Detection Mass Spectrometry Eliminate Adverse Effects of Ion-Ion Interactions. Anal Chem 2023; 95:10077-10086. [PMID: 37343124 PMCID: PMC10389283 DOI: 10.1021/acs.analchem.3c01520] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Ion-ion interactions in charge detection mass spectrometers that use electrostatic traps to measure masses of individual ions have not been reported previously, although ion trajectory simulations have shown that these types of interactions affect ion energies and thereby degrade measurement performance. Here, examples of interactions between simultaneously trapped ions that have masses ranging from ca. 2 to 350 MDa and ca. 100 to 1000 charges are studied in detail using a dynamic measurement method that makes it possible to track the evolution of the mass, charge, and energy of individual ions over their trapping lifetimes. Signals from ions that have similar oscillation frequencies can have overlapping spectral leakage artifacts that result in slightly increased uncertainties in the mass determination, but these effects can be mitigated by the careful choice of parameters used in the short-time Fourier transform analysis. Energy transfers between physically interacting ions are also observed and quantified with individual ion energy measurement resolution as high as ∼950. The mass and charge of interacting ions do not change, and their corresponding measurement uncertainties are equivalent to ions that do not undergo physical interactions. Simultaneous trapping of multiple ions in CDMS can greatly decrease the acquisition time necessary to accumulate a statistically meaningful number of individual ion measurements. These results demonstrate that while ion-ion interactions can occur when multiple ions are trapped, they have negligible effects on mass accuracy when using the dynamic measurement method.
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Affiliation(s)
- Conner C. Harper
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Veena S. Avadhani
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Emeline Hanozin
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Zachary M. Miller
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, United States
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8
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Claesen J, Rockwood A, Gorshkov M, Valkenborg D. The isotope distribution: A rose with thorns. MASS SPECTROMETRY REVIEWS 2023. [PMID: 36744702 DOI: 10.1002/mas.21820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/03/2022] [Accepted: 10/21/2022] [Indexed: 06/18/2023]
Abstract
The isotope distribution, which reflects the number and probabilities of occurrence of different isotopologues of a molecule, can be theoretically calculated. With the current generation of (ultra)-high-resolution mass spectrometers, the isotope distribution of molecules can be measured with high sensitivity, resolution, and mass accuracy. However, the observed isotope distribution can differ substantially from the expected isotope distribution. Although differences between the observed and expected isotope distribution can complicate the analysis and interpretation of mass spectral data, they can be helpful in a number of specific applications. These applications include, yet are not limited to, the identification of peptides in proteomics, elucidation of the elemental composition of small organic molecules and metabolites, as well as wading through peaks in mass spectra of complex bioorganic mixtures such as petroleum and humus. In this review, we give a nonexhaustive overview of factors that have an impact on the observed isotope distribution, such as elemental isotope deviations, ion sampling, ion interactions, electronic noise and dephasing, centroiding, and apodization. These factors occur at different stages of obtaining the isotope distribution: during the collection of the sample, during the ionization and intake of a molecule in a mass spectrometer, during the mass separation and detection of ionized molecules, and during signal processing.
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Affiliation(s)
- Jürgen Claesen
- Department of Epidemiology and Data Science, Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, The Netherlands
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Alan Rockwood
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Mikhail Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Dirk Valkenborg
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
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9
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Baquer G, Sementé L, Mahamdi T, Correig X, Ràfols P, García-Altares M. What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022:e21794. [PMID: 35822576 DOI: 10.1002/mas.21794] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) has become a widespread analytical technique to perform nonlabeled spatial molecular identification. The Achilles' heel of MSI is the annotation and identification of molecular species due to intrinsic limitations of the technique (lack of chromatographic separation and the difficulty to apply tandem MS). Successful strategies to perform annotation and identification combine extra analytical steps, like using orthogonal analytical techniques to identify compounds; with algorithms that integrate the spectral and spatial information. In this review, we discuss different experimental strategies and bioinformatics tools to annotate and identify compounds in MSI experiments. We target strategies and tools for small molecule applications, such as lipidomics and metabolomics. First, we explain how sample preparation and the acquisition process influences annotation and identification, from sample preservation to the use of orthogonal techniques. Then, we review twelve software tools for annotation and identification in MSI. Finally, we offer perspectives on two current needs of the MSI community: the adaptation of guidelines for communicating confidence levels in identifications; and the creation of a standard format to store and exchange annotations and identifications in MSI.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Toufik Mahamdi
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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10
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Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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11
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Levitsky LI, Bubis JA, Gorshkov MV, Tarasova IA. AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results. J Proteomics 2021; 248:104350. [PMID: 34389500 DOI: 10.1016/j.jprot.2021.104350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/21/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022]
Abstract
Characterization of post-translational modifications is among the most challenging tasks in tandem mass spectrometry-based proteomics which has yet to find an efficient solution. The ultra-tolerant (open) database search attempts to meet this challenge. However, interpretation of the mass shifts observed in open search still requires an effective and automated solution. We have previously introduced the AA_stat tool for analysis of amino acid frequencies at different mass shifts and generation of hypotheses on unaccounted in vitro modifications. Here, we report on the new version of AA_stat, which now complements amino acid frequency statistics with a number of new features: (1) MS/MS-based localization of mass shifts and localization scoring, including shifts which are the sum of modifications; (2) inferring fixed modifications to increase method sensitivity; (3) inferring monoisotopic peak assignment errors and variable modifications based on abundant mass shift localizations to increase the yield of closed search; (4) new mass calibration algorithm to account for partial systematic shifts; (5) interactive integration of all results and a rated list of possible mass shift interpretations. With these options, we improve interpretation of open search results and demonstrate the utility of AA_stat for profiling of abundant and rare amino acid modifications. AA_stat is implemented in Python as an open-source command-line tool available at https://github.com/SimpleNumber/aa_stat. SIGNIFICANCE: Mass spectrometry-based PTM characterization has a long history, yet most of the methods rely on a priori knowledge of modifications of interest and do not provide a whole proteome modification landscape in a blind manner. The open database search is an efficient attempt to address this challenge by identifying peptides with mass shifts corresponding to possible modifications. Then, interpreting these mass shifts is required. Therefore, development of bioinformatics software for post-processing of the open search results, which is capable of detection and accurate annotation of new or unexpected modifications, from characterization of sample preparation efficiency and quality control to discovery of rare post-translational modifications, is of high importance.
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Affiliation(s)
- Lev I Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia.
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12
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Eriksson J, Sánchez Brotons A, Rezeli M, Suits F, Markó-Varga G, Horvatovich P. MSIWarp: A General Approach to Mass Alignment in Mass Spectrometry Imaging. Anal Chem 2020; 92:16138-16148. [PMID: 33317272 PMCID: PMC7745203 DOI: 10.1021/acs.analchem.0c03833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/16/2020] [Indexed: 02/02/2023]
Abstract
Mass spectrometry imaging (MSI) is a technique that provides comprehensive molecular information with high spatial resolution from tissue. Today, there is a strong push toward sharing data sets through public repositories in many research fields where MSI is commonly applied; yet, there is no standardized protocol for analyzing these data sets in a reproducible manner. Shifts in the mass-to-charge ratio (m/z) of molecular peaks present a major obstacle that can make it impossible to distinguish one compound from another. Here, we present a label-free m/z alignment approach that is compatible with multiple instrument types and makes no assumptions on the sample's molecular composition. Our approach, MSIWarp (https://github.com/horvatovichlab/MSIWarp), finds an m/z recalibration function by maximizing a similarity score that considers both the intensity and m/z position of peaks matched between two spectra. MSIWarp requires only centroid spectra to find the recalibration function and is thereby readily applicable to almost any MSI data set. To deal with particularly misaligned or peak-sparse spectra, we provide an option to detect and exclude spurious peak matches with a tailored random sample consensus (RANSAC) procedure. We evaluate our approach with four publicly available data sets from both time-of-flight (TOF) and Orbitrap instruments and demonstrate up to 88% improvement in m/z alignment.
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Affiliation(s)
| | - Alejandro Sánchez Brotons
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Melinda Rezeli
- Department
of Biomedical Engineering, Lund University, Lund 221 00, Sweden
| | - Frank Suits
- IBM
Research - Australia, 60 City Road, Southbank, VIC 3006, Australia
| | - György Markó-Varga
- Department
of Biomedical Engineering, Lund University, Lund 221 00, Sweden
| | - Peter Horvatovich
- Department
of Biomedical Engineering, Lund University, Lund 221 00, Sweden
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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13
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Ivanov MV, Bubis JA, Gorshkov V, Tarasova IA, Levitsky LI, Lobas AA, Solovyeva EM, Pridatchenko ML, Kjeldsen F, Gorshkov MV. DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes. Anal Chem 2020; 92:4326-4333. [DOI: 10.1021/acs.analchem.9b05095] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mark V. Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Julia A. Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Irina A. Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Lev I. Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna A. Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elizaveta M. Solovyeva
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina L. Pridatchenko
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Mikhail V. Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
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14
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Khodjaniyazova S, Nazari M, Garrard KP, Matos MPV, Jackson GP, Muddiman DC. Characterization of the Spectral Accuracy of an Orbitrap Mass Analyzer Using Isotope Ratio Mass Spectrometry. Anal Chem 2018; 90:1897-1906. [DOI: 10.1021/acs.analchem.7b03983] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Sitora Khodjaniyazova
- Department
of Chemistry and Molecular Education, Technology, and Research Innovation
Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Milad Nazari
- Department
of Chemistry and Molecular Education, Technology, and Research Innovation
Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Kenneth P. Garrard
- Department
of Chemistry and Molecular Education, Technology, and Research Innovation
Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
- Precision
Engineering Consortium, Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | | | | | - David C. Muddiman
- Department
of Chemistry and Molecular Education, Technology, and Research Innovation
Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
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15
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Kaufmann A, Walker S. Coalescence and self-bunching observed in commercial high-resolution mass spectrometry instrumentation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:503-515. [PMID: 29297948 DOI: 10.1002/rcm.8054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/30/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Self-bunching and coalescence are well-known effects in Fourier transform ion cyclotron resonance (FTICR) and multi-reflection time-of-flight (TOF) mass spectrometry. These detrimental effects can also be observed in currently more frequently used high-resolution mass spectrometry (HRMS) instruments, such as the Orbitrap and single-reflection TOF. METHODS A modern single-reflection TOF and a Q-Orbitrap were used to produce conditions in which self-bunching and coalescence were observed. This was done by infusion experiments of several isobaric compounds. The peak widths of some low mass isobaric ions as well as the mass resolution of such mixtures were investigated. Attention was paid to possible self-bunching and coalescence effects. RESULTS For the utilized TOF mass spectrometer, the measured peak widths of the ions become significantly narrower (self-bunching) when increasing the ion abundance. On the other hand, isobaric ion pairs (delta < 30 milli m/z units) became unresolvable above a certain ion abundance (coalescence). The tested Orbitrap shows similar behavior, although coalescence appeared only at delta <15 milli m/z units. Coalescence was shown to affect the quantitative data, while self-bunching can lead to biased relative isotopic ratios. CONCLUSIONS The conventional measurement of a peak width does not truly reflect the mass resolving power of modern HRMS instrumentation. The mass resolving power is better demonstrated by resolving a mixture of isobaric compounds. Measurements obtained at low and high ion abundances should be investigated. Coalescence and self-bunching can reduce the truly available mass resolving power and therefore negatively affect quantitative and qualitative measurements.
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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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16
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Nagornov KO, Kozhinov AN, Tsybin YO. Cyclotron Phase-Coherent Ion Spatial Dispersion in a Non-Quadratic Trapping Potential is Responsible for FT-ICR MS at the Cyclotron Frequency. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:63-77. [PMID: 29119518 DOI: 10.1007/s13361-017-1821-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) at the cyclotron frequency instead of the reduced cyclotron frequency has been experimentally demonstrated using narrow aperture detection electrode (NADEL) ICR cells. Here, based on the results of SIMION simulations, we provide the initial mechanistic insights into the cyclotron frequency regime generation in FT-ICR MS. The reason for cyclotron frequency regime is found to be a new type of a collective motion of ions with a certain dispersion in the initial characteristics, such as pre-excitation ion velocities, in a highly non-quadratic trapping potential as realized in NADEL ICR cells. During ion detection, ions of the same m/z move in phase for cyclotron ion motion but out of phase for magnetron (drift) ion motion destroying signals at the fundamental and high order harmonics that comprise reduced cyclotron frequency components. After an initial magnetron motion period, ion clouds distribute into a novel type of structures - ion slabs, elliptical cylinders, or star-like structures. These structures rotate at the Larmor (half-cyclotron) frequency on a plane orthogonal to the magnetic field, inducing signals at the true cyclotron frequency on each of the narrow aperture detection electrodes. To eliminate the reduced cyclotron frequency peak upon dipolar ion detection, a number of slabs or elliptical cylinders organizing a star-like configuration are formed. In a NADEL ICR cell with quadrupolar ion detection, a single slab or an elliptical cylinder is sufficient to minimize the intensity of the reduced cyclotron frequency components, particularly the second harmonic. Graphical Abstract ᅟ.
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Affiliation(s)
| | | | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, 1015, Lausanne, Switzerland.
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17
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Ivanov MV, Tarasova IA, Levitsky LI, Solovyeva EM, Pridatchenko ML, Lobas AA, Bubis JA, Gorshkov MV. MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity. J Proteome Res 2017; 16:3989-3999. [DOI: 10.1021/acs.jproteome.7b00365] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mark V. Ivanov
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Irina A. Tarasova
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Lev I. Levitsky
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Elizaveta M. Solovyeva
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Marina L. Pridatchenko
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Anna A. Lobas
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Julia A. Bubis
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Mikhail V. Gorshkov
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
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18
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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19
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Kaufmann A, Walker S. Extension of the Q Orbitrap intrascan dynamic range by using a dedicated customized scan. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1087-1095. [PMID: 27003046 DOI: 10.1002/rcm.7530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE The intrascan dynamic range of modern Orbitrap instrumentation is specified to reach 1:5000, while the interscan dynamic range is significantly larger due to the utilization of the automatic gain control feature. There are some applications (e.g. residue analysis in complex matrices, metabolomics or structural elucidation) where a wider intrascan dynamic range is desirable. METHODS The Application Programming Interface (API) of the Q Exactive Orbitrap mass spectrometer has been used to program a customized scan in order to cover a larger intrascan dynamic range. Different approaches were used, which were all based on the variation of the isolation time of low-abundance versus high-abundance mass range segments. The differently attenuated mass range segments isolated by the quadrupole were sequentially forwarded to the C-trap. Finally, the accumulated mass segments were measured within the Orbitrap analyzer. RESULTS The spectra obtained by the customized scans show an enlarged dynamic range. This has been demonstrated by monitoring the higher isotope mass peaks (first and second isotope) of a low intensity analyte. Furthermore, a practical application (veterinary drugs in bovine kidney) has been investigated with the proposed customized scan. Analytes eluting within the retention time region of very intense matrix peaks (e.g. peptides) showed improved detectability when utilizing the customized scan. CONCLUSIONS The extension of the intrascan dynamic range by a customized scan is helpful when analyzing residues which happen to elute together with a dominating matrix peak or within a high ion abundance region (e.g. dead volume). Furthermore, this feature helps in the process of determining the elemental composition of compounds by permitting the investigation of low-abundance ions (e.g. belonging to the isotopic fine structure of the investigated compound).
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Affiliation(s)
- A Kaufmann
- Official Food Control Authority, Kontales Labor Zürich, Fehrenstrasse 15, 8032, Zürich, Switzerland
| | - S Walker
- Official Food Control Authority, Kontales Labor Zürich, Fehrenstrasse 15, 8032, Zürich, Switzerland
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20
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Tarasova IA, Surin AK, Fornelli L, Pridatchenko ML, Suvorina MY, Gorshkov MV. Ion coalescence in Fourier transform mass spectrometry: should we worry about this in shotgun proteomics? EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:459-470. [PMID: 26307727 DOI: 10.1255/ejms.1356] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Coupling of motion of the ion clouds with close m/z values is a well-established phenomenon for ion- trapping mass analyzers. In Fourier transform ion cyclotron resonance mass spectrometry it is known as ion coalescence. Recently, ion coalescence was demonstrated and semiquantitatively characterized for the Orbitrap mass analyzer as well. When it occurs, the coalescence negatively affects the basic characteristics of a mass analyzer. Specifically, the dynamic range available for the high resolving power mass measurements reduces. In shotgun proteomics, another potentially adverse effect of ion coalescence is interference of the isotopic envelopes for the coeluting precursor ions of close m/z values, subjected to isolation before fragmentation. In this work we characterize coalescence events for synthetic peptide mixtures with fully and partially overlapping (13)C-isotope envelopes including pairs of peptides with glutamine deamidation. Furthermore, we demonstrate that fragmentation of the otherwise coalesced peptide ion clouds may remove the locking between them owing to the total charge redistribution between more ion species in the mass spectrum. Finally, we estimated the possible scale of the coalescence phenomenon for shotgun proteomics by considering the fraction of coeluted peptide pairs with the close masses using literature data for the yeast proteome. It was found that up to one tenth of all peptide identifications with the relative mass differences of 20 ppm or less in the corresponding pairs may potentially experience the coalescence of the (13)C-isotopic envelopes. However, sample complexity in a real proteomics experiment and precursor ion signal splitting between many channels in tandem mass spectrometry drastically increase the threshold for coalescence, thus leading to practically coalescence-free proteomics based on Fourier transform mass spectrometry.
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Affiliation(s)
- Irina A Tarasova
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia.
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Str., Pushchino 142292, Moscow region, Russia.
| | - Luca Fornelli
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.Departments of Chemistry and Molecular Biosciences, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208.
| | - Marina L Pridatchenko
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia.
| | - Mariya Yu Suvorina
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Str., Pushchino 142292, Moscow region, Russia.
| | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia. Moscow Institute of Physics and Technology (State University), 9 Institutskii Per., Dolgoprudny 141700, Moscow region, Russia.
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21
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Qu J, Young R, Page BJ, Shen X, Tata N, Li J, Duan X, Fallavollita JA, Canty JM. Reproducible ion-current-based approach for 24-plex comparison of the tissue proteomes of hibernating versus normal myocardium in swine models. J Proteome Res 2014; 13:2571-84. [PMID: 24697261 PMCID: PMC4015685 DOI: 10.1021/pr5000472] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Hibernating
myocardium is an adaptive response to repetitive myocardial
ischemia that is clinically common, but the mechanism of adaptation
is poorly understood. Here we compared the proteomes of hibernating
versus normal myocardium in a porcine model with 24 biological replicates.
Using the ion-current-based proteomic strategy optimized in this study
to expand upon previous proteomic work, we identified differentially
expressed proteins in new molecular pathways of cardiovascular interest.
The methodological strategy includes efficient extraction with detergent
cocktail; precipitation/digestion procedure with high, quantitative
peptide recovery; reproducible nano-LC/MS analysis on a long, heated
column packed with small particles; and quantification based on ion-current
peak areas. Under the optimized conditions, high efficiency and reproducibility
were achieved for each step, which enabled a reliable comparison of
24 the myocardial samples. To achieve confident discovery of differentially
regulated proteins in hibernating myocardium, we used highly stringent
criteria to define “quantifiable proteins”. These included
the filtering criteria of low peptide FDR and S/N > 10 for peptide
ion currents, and each protein was quantified independently from ≥2
distinct peptides. For a broad methodological validation, the quantitative
results were compared with a parallel, well-validated 2D-DIGE analysis
of the same model. Excellent agreement between the two orthogonal
methods was observed (R = 0.74), and the ion-current-based
method quantified almost one order of magnitude more proteins. In
hibernating myocardium, 225 significantly altered proteins were discovered
with a low false-discovery rate (∼3%). These proteins are involved
in biological processes including metabolism, apoptosis, stress response,
contraction, cytoskeleton, transcription, and translation. This provides
compelling evidence that hibernating myocardium adapts to chronic
ischemia. The major metabolic mechanisms include a down-regulation
of mitochondrial respiration and an increase in glycolysis. Meanwhile,
cardioprotective and cytoskeletal proteins are increased, while cardiomyocyte
contractile proteins are reduced. These intrinsic adaptations to regional
ischemia maintain long-term cardiomyocyte viability at the expense
of contractile function.
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Affiliation(s)
- Jun Qu
- Department of Pharmaceutical Sciences, ‡Department of Biochemistry, §Department of Medicine, ∥Department of Physiology and Biophysics, ⊥The Center for Research in Cardiovascular Medicine, and #Center for Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo , Buffalo, New York 14214, United States
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22
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Ghavidel FZ, Mertens I, Baggerman G, Laukens K, Burzykowski T, Valkenborg D. The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results. J Proteomics 2014; 98:150-8. [DOI: 10.1016/j.jprot.2013.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 12/11/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
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23
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Bodzon-Kulakowska A, Drabik A, Ner J, Kotlinska JH, Suder P. Desorption electrospray ionisation (DESI) for beginners--how to adjust settings for tissue imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1-9. [PMID: 24285384 DOI: 10.1002/rcm.6755] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Desorption electrospray ionisation (DESI) is the ambient technique used for surface imaging. Despite its simplicity, the proper use of this technique is not easy, and usually leads to discouragement, especially in the case of biological sample measurements. Here, we present some tips and tricks which may be helpful during a complex process of ion source optimisation to achieve the desired results. METHODS Rat liver tissue as an example of a biological sample and a surface covered with rhodamine-containing marker were measured using a DESI ion source (OMNIspray source, Prosolia, Indianapolis, IN, USA) connected to a AmaZon ETD ion trap mass spectrometer (Bruker Daltonics, Bremen, Germany). RESULTS The geometry of the ion source (nebulisation capillary angle, its distance to the surface, and to the MS inlet), and other settings like nebulising gas pressure, solvent flow and capillary voltage, were changed during the optimisation process. The results obtained for different parameters are presented. CONCLUSIONS Differences between the results and the method of optimisation for biological and non-biological samples were shown. The influence of different parameters on the quality of mass spectra was indicated. Optimal parameters for the tissue and non-biological sample analysis were suggested.
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Affiliation(s)
- Anna Bodzon-Kulakowska
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and Ceramics, AGH University of Science and Technology, Mickiewicza 30 ave, 30-059, Krakow, Poland
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24
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Zhang J, Ma J, Zhang W, Xu C, Zhu Y, Xie H. FTDR 2.0: A Tool To Achieve Sub-ppm Level Recalibrated Accuracy in Routine LC–MS Analysis. J Proteome Res 2013; 12:3857-64. [DOI: 10.1021/pr400003a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jiyang Zhang
- College of Mechatronic Engineering
and Automatic Control, National University of Defense Technology, Changsha, 410073, China
| | - Jie Ma
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Wei Zhang
- College of Mechatronic Engineering
and Automatic Control, National University of Defense Technology, Changsha, 410073, China
| | - Changming Xu
- College of Mechatronic Engineering
and Automatic Control, National University of Defense Technology, Changsha, 410073, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Hongwei Xie
- College of Mechatronic Engineering
and Automatic Control, National University of Defense Technology, Changsha, 410073, China
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25
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Barry JA, Robichaud G, Muddiman DC. Mass recalibration of FT-ICR mass spectrometry imaging data using the average frequency shift of ambient ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1137-45. [PMID: 23715870 PMCID: PMC3739293 DOI: 10.1007/s13361-013-0659-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 04/29/2013] [Accepted: 04/29/2013] [Indexed: 05/04/2023]
Abstract
Achieving and maintaining high mass measurement accuracy (MMA) throughout a mass spectrometry imaging (MSI) experiment is vital to the identification of the observed ions. However, when using FTMS instruments, fluctuations in the total ion abundance at each pixel due to inherent biological variation in the tissue section can introduce space charge effects that systematically shift the observed mass. Herein we apply a recalibration based on the observed cyclotron frequency shift of ions found in the ambient laboratory environment, polydimethylcyclosiloxanes (PDMS). This calibration method is capable of achieving part per billion (ppb) mass accuracy with relatively high precision for an infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI dataset. Comparisons with previously published mass calibration approaches are also presented.
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Affiliation(s)
| | | | - David C. Muddiman
- Author for Correspondence W.M. Keck FT-ICR Mass Spectrometry Laboratory Department of Chemistry North Carolina State University Raleigh, North Carolina 27695 Phone: 919-513-0084 Fax: 919-513-7993
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26
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Kozhinov AN, Zhurov KO, Tsybin YO. Iterative Method for Mass Spectra Recalibration via Empirical Estimation of the Mass Calibration Function for Fourier Transform Mass Spectrometry-Based Petroleomics. Anal Chem 2013; 85:6437-45. [DOI: 10.1021/ac400972y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anton N. Kozhinov
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Konstantin O. Zhurov
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yury O. Tsybin
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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27
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Smith DF, Kharchenko A, Konijnenburg M, Klinkert I, Paša-Tolić L, Heeren RMA. Advanced mass calibration and visualization for FT-ICR mass spectrometry imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1865-1872. [PMID: 22926971 DOI: 10.1007/s13361-012-0464-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/28/2012] [Accepted: 07/31/2012] [Indexed: 06/01/2023]
Abstract
Mass spectrometry imaging by Fourier transform ion cyclotron resonance (FT-ICR) yields hundreds of unique peaks, many of which cannot be resolved by lower performance mass spectrometers. The high mass accuracy and high mass resolving power allow confident identification of small molecules and lipids directly from biological tissue sections. Here, calibration strategies for FT-ICR MS imaging were investigated. Sub-parts-per-million mass accuracy is demonstrated over an entire tissue section. Ion abundance fluctuations are corrected by addition of total and relative ion abundances for a root-mean-square error of 0.158 ppm on 16,764 peaks. A new approach for visualization of FT-ICR MS imaging data at high resolution is presented. The "Mosaic Datacube" provides a flexible means to visualize the entire mass range at a mass spectral bin width of 0.001 Da. The high resolution Mosaic Datacube resolves spectral features not visible at lower bin widths, while retaining the high mass accuracy from the calibration methods discussed.
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Affiliation(s)
- Donald F Smith
- FOM Institute AMOLF, Science Park 104, Amsterdam, The Netherlands
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28
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Croley TR, White KD, Callahan JH, Musser SM. The chromatographic role in high resolution mass spectrometry for non-targeted analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1569-78. [PMID: 22711514 DOI: 10.1007/s13361-012-0392-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 04/05/2012] [Accepted: 04/09/2012] [Indexed: 05/22/2023]
Abstract
Resolution improvements in time-of-flight instrumentation and the emergence of the Orbitrap mass spectrometer have researchers using high resolution mass spectrometry to determine elemental compositions and performing screening methods based on the full-scan data from these instruments. This work is focused on examining instrument performance of both a QTOF and a bench-top Orbitrap. In this study, the impact of chromatographic resolution on mass measurement accuracy, mass measurement precision, and ion suppression is examined at a fundamental level. This work was extended to a mixture of over 200 pesticides to determine how well two different software algorithms componentized and correctly identified these compounds under different sets of chromatographic conditions, where co-elution was expected to vary markedly.
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Affiliation(s)
- Timothy R Croley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20770, USA.
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Gorshkov MV, Fornelli L, Tsybin YO. Observation of ion coalescence in Orbitrap Fourier transform mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1711-1717. [PMID: 22730091 DOI: 10.1002/rcm.6289] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Similar to other mass spectrometric technologies based on ion trapping in a spatially restricted area, the performance of Orbitrap Fourier transform mass spectrometry (FTMS) is affected by the interaction between the trapped ion clouds. One of the effects associated with Coulombic interaction inside the ion trap is the ion cloud coupling, known in ion cyclotron resonance (ICR) FTMS as coalescence, or a phase-locking phenomenon. Nevertheless, the direct observation of ion coalescence has not been reported for Orbitrap FTMS yet. METHODS We have performed experiments on ion coalescence with a pair of isobaric peptides in the state-of-the-art hybrid linear ion trap high-field compact Orbitrap Elite FT mass spectrometer using both standard and advanced signal processing modes. RESULTS For the instrument configuration employed in this work we found that ion coalescence occurs when two singly charged peptides with the mass difference of 22 mDa and molecular weight of about 1060 Da have the total abundance of at least 7.5*10(4) charges. CONCLUSIONS We experimentally demonstrate the existence of the ion coalescence phenomenon in Orbitrap FTMS for peptides for a wide range of total trapped ion population. Using the applicable modeling of the phase-locking threshold we estimate the effect of ion coalescence on the performance of Orbitrap FTMS.
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Affiliation(s)
- Mikhail V Gorshkov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia.
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Kharchenko A, Vladimirov G, Heeren RMA, Nikolaev EN. Performance of Orbitrap mass analyzer at various space charge and non-ideal field conditions: simulation approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:977-987. [PMID: 22354683 DOI: 10.1007/s13361-011-0325-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 05/31/2023]
Abstract
The orbital trap mass analyzer provides a number of unique analytical features along with inevitable limitations as an electrostatic instrument operating in high space charge regimes resulting in systematic measured frequency errors as an effect of stored ion clouds on the trap field and each other effect of non-ideal machining the trap electrodes, effect of injection slot, effect of real versus theoretical trap dimensions, etc. This paper deals with determining the influence of the space charge effect and imperfection of the electrostatic field on the motion of ion ensembles in the orbital trap. We examine effects of theoretically modeled non-harmonicity of the electrostatic potential and the number of confined ions on stability of coherent ion motion in the trap that determines the frequency shifts of axial ion oscillation. Three different Orbitrap geometries were considered: geometry close to preproduction Orbitrap, close to standard Orbitrap, close to high field Orbitrap. Frequency shifts for m/z = 500 and for charge state +23 of cytochrome c isotopic cluster particles with 10(4)-6*10(6) elemental charges in the trap were considered. Refined spectra were calculated using the filter diagonalization method proposed by Mandelshtam et al. and applied to mass spectrometry by O'Connor and Aizikov.
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Affiliation(s)
- Andriy Kharchenko
- FOM Institute for Atomic and Molecular Physics, Amsterdam, The Netherlands
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Affiliation(s)
- Feng Xian
- Department
of Chemistry and
Biochemistry, Florida State University,
95 Chieftain Way, Tallahassee, Florida 32310-4390, United States
| | - Christopher L. Hendrickson
- Department
of Chemistry and
Biochemistry, Florida State University,
95 Chieftain Way, Tallahassee, Florida 32310-4390, United States
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800
East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Alan G. Marshall
- Department
of Chemistry and
Biochemistry, Florida State University,
95 Chieftain Way, Tallahassee, Florida 32310-4390, United States
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800
East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
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Optimization of Exactive Orbitrap™ acquisition parameters for quantitative bioanalysis. Bioanalysis 2011; 3:863-71. [PMID: 21510760 DOI: 10.4155/bio.11.37] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Orbitrap™ mass spectrometry has made significant impacts in the qualitative field of mass spectrometry, and it can be a potentially powerful quantitative technique. Because the Orbitrap is a relatively new platform, our understanding of this technology is not as well-versed as other mass spectrometric techniques. RESULTS An investigation of the optimal acquisition parameters for quantitation was conducted for propranolol, reserpine, leucine enkephalin and neurotensin from mouse plasma samples. The lower limits of quantitation were demonstrated to be 1-3 nM while the quantitation linear dynamic range extends to four orders of magnitude. This level of performance is sufficient for most bioanalytical applications in drug discovery. CONCLUSION Increasing the ion population in the Orbitrap improves detection and lowers the limit of quantitation, but the upper limit of quantitation can suffer. A better understanding of the operating parameters will help guide us toward better experimental designs and the best conditions for quantitation.
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