1
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Eeso K, Gallan R, Goukeh MN, Tate K, Raja RKB, Popovic Z, Abichou T, Chen H, Locke BR, Tang Y. Degradation of per- and polyfluoroalkyl substances in landfill leachate by a thin-water-film nonthermal plasma reactor. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 161:104-115. [PMID: 36878039 DOI: 10.1016/j.wasman.2023.02.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are present in landfill leachate, posing potential challenges to leachate disposal and treatment. This work represents the first study of a thin-water-film nonthermal plasma reactor for PFAS degradation in landfill leachate. Of the 30 PFAS measured in three raw leachates, 21 were above the detection limits. The removal percentage depended on the category of PFAS. For example, perfluorooctanoic acid PFOA (C8) had the highest removal percentage (77% as an average of the three leachates) of the perfluoroalkyl carboxylic acids (PFCAs) category. The removal percentage decreased when the carbon number increased from 8 to 11 and decreased from 8 to 4. The effects of various landfill leachate components, including sodium chloride, acetate, humic acids, pH, and surfactants, had no or minor impacts (<30%) on PFOA mineralization in synthetic samples. This might be explained by the plasma-generation and PFAS-degradation mainly occurring at the gas/liquid interface. Shorter-chain PFCAs were produced as intermediates of PFOA degradation, and shorter-chain PFCAs and perfluorosulfonic acids (PFSAs) were produced as intermediates of perfluorooctanesulfonic acid (PFOS). The concentrations of the intermediates decreased with decreasing carbon number, suggesting a stepwise removal of difluoromethylene (CF2) in the degradation pathway. Potential PFAS species in the raw and treated leachates were identified at the molecular level through non-targeted Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The intermediates did not show accurate toxicity per Microtox bioassay.
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Affiliation(s)
- Karam Eeso
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL 32310, United States
| | - Rachel Gallan
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL 32310, United States
| | - Mojtaba Nouri Goukeh
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL 32310, United States
| | - Kerry Tate
- Chemistry Program, Florida Department of Environmental Protection, 2600 N Blair Stone Road, Tallahassee, FL 32399, United States
| | - Radha Krishna Bulusu Raja
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL 32310, United States
| | - Zeljka Popovic
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Tarek Abichou
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL 32310, United States
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Bruce R Locke
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL 32310, United States
| | - Youneng Tang
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL 32310, United States.
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2
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Popovic Z, Anderson LC, Zhang X, Butcher DS, Blakney GT, Zubarev RA, Marshall AG. Analysis of Isotopically Depleted Proteins Derived from Escherichia coli and Caenorhabditis elegans Cell Lines by Liquid Chromatography 21 T Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:137-144. [PMID: 36656140 DOI: 10.1021/jasms.2c00242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Protein mass measurement by mass spectrometry is complicated by wide isotopic distributions that result from incorporation of heavy isotopes of C, H, N, O, and S, thereby limiting signal-to-noise ratio (SNR) and accurate intact mass determination, particularly for larger proteins [Fenselau et al. Anal. Chem. 1983, 55 (2), 353-356]. Observation of the monoisotopic mass-to-charge ratio (m/z) is the simplest and most accurate way to determine intact protein mass, but as mass increases, the relative abundance of the monoisotopic peak becomes so low that it is often undetectable. Here, we used an isotopically depleted growth medium to culture bacterial cells (Escherichia coli), resulting in isotopically depleted proteins. Isotopically depleted proteins show increased sequence coverage, mass measurement accuracy, and increased S/N of the monoisotopic peak by Fourier transform ion cyclotron resonance mass spectrometry analysis. We then grew Caenorhabditis elegans cells in a medium containing living isotopically depleted E. coli cells, thereby producing the first isotopically depleted eukaryotic proteins. This is the first time isotopic depletion has been implemented for four isotopes (1H, 12C, 14N, and 16O), resulting in the highest degree of depletion ever used for protein analysis and further improving MS analysis.
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Affiliation(s)
- Zeljka Popovic
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Xuepei Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavagen 1, Solna, 171 77 Stockholm, Sweden
| | - David S Butcher
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Greg T Blakney
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Roman A Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavagen 1, Solna, 171 77 Stockholm, Sweden
| | - Alan G Marshall
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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3
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Kellie JF, Schneck NA, Causon JC, Baba T, Mehl JT, Pohl KI. Top-Down Characterization and Intact Mass Quantitation of a Monoclonal Antibody Drug from Serum by Use of a Quadrupole TOF MS System Equipped with Electron-Activated Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:17-26. [PMID: 36459688 DOI: 10.1021/jasms.2c00206] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Time-of-flight MS systems for biopharmaceutical and protein characterization applications may play an even more pivotal role in the future as biotherapeutics increase in drug pipelines and as top-down MS approaches increase in use. Here, a recently developed TOF MS system is examined for monoclonal antibody (mAb) characterization from serum samples. After immunocapture, purified drug material spiked into monkey serum or dosed for an in-life study is analyzed by top-down MS. While characterization aspects are a distinct advantage of the MS platform, MS system and software capabilities are also shown regarding intact protein quantitation. Such applications are demonstrated to help enable comprehensive protein molecule quantitation and characterization by use of TOF MS instrumentation.
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Affiliation(s)
- John F Kellie
- GSK, Collegeville, Pennsylvania 19426, United States
| | | | | | | | - John T Mehl
- GSK, Collegeville, Pennsylvania 19426, United States
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4
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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5
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Following de novo triglyceride dynamics in ovaries of Aedes aegypti during the previtellogenic stage. Sci Rep 2021; 11:9636. [PMID: 33953286 PMCID: PMC8099868 DOI: 10.1038/s41598-021-89025-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/14/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding the molecular and biochemical basis of egg development is a central topic in mosquito reproductive biology. Lipids are a major source of energy and building blocks for the developing ovarian follicles. Ultra-High Resolution Mass Spectrometry (UHRMS) combined with in vivo metabolic labeling of follicle lipids with deuterated water (2H2O) can provide unequivocal identification of de novo lipid species during ovarian development. In the present study, we followed de novo triglyceride (TG) dynamics during the ovarian previtellogenic (PVG) stage (2-7 days post-eclosion) of female adult Aedes aegypti. The incorporation of stable isotopes from the diet was evaluated using liquid chromatography (LC) in tandem with the high accuracy (< 0.3 ppm) and high mass resolution (over 1 M) of a 14.5 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (14.5 T FT-ICR MS) equipped with hexapolar detection. LC-UHRMS provides effective lipid class separation and chemical formula identification based on the isotopic fine structure. The monitoring of stable isotope incorporation into de novo incorporated TGs suggests that ovarian lipids are consumed or recycled during the PVG stage, with variable time dynamics. These results provide further evidence of the complexity of the molecular mechanism of follicular lipid dynamics during oogenesis in mosquitoes.
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Nagornov KO, Kozhinov AN, Nicol E, Tsybin OY, Touboul D, Brunelle A, Tsybin YO. Narrow Aperture Detection Electrodes ICR Cell with Quadrupolar Ion Detection for FT-ICR MS at the Cyclotron Frequency. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2258-2269. [PMID: 32966078 DOI: 10.1021/jasms.0c00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion signal detection at the true (unperturbed) cyclotron frequency instead of the conventional reduced cyclotron frequency has remained a formidable challenge since the inception of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Recently, routine FT-ICR MS at the true cyclotron frequency has become a reality with the implementation of ICR cells with narrow aperture detection electrodes (NADEL). Here, we describe the development and implementation of the next generation of these cells, namely, a 2xNADEL ICR cell, which comprises four flat detect and four ∼45° cylindrical excite electrodes, enabling independent ion excitation and quadrupolar ion detection. The performance of the 2xNADEL ICR cell was evaluated on two commercial FT-ICR MS platforms, 10 T LTQ FT from Thermo Scientific and 9.4 T SolariX XR from Bruker Daltonics. The cells provided accurate mass measurements in the analyses of singly and multiply charged peptides (root-mean-square, RMS, mass error Δm/m of 90 ppb), proteins (Δm/m = 200 ppb), and petroleum fractions (Δm/m < 200 ppb). Due to the reduced influence of measured frequency on the space charge and external (trapping) electric fields, the 2xNADEL ICR cells exhibited stable performance in a wide range of trapping potentials (1-20 V). Similarly, in a 13 h rat brain MALDI imaging experiment, the RMS mass error did not exceed 600 ppb even for low signal-to-noise ratio analyte peaks. Notably, the same set of calibration constants was applicable to Fourier spectra in all pixels, reducing the need for recalibration at the individual pixel level. Overall, these results support further experimental development and fundamentals investigation of this promising technology.
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Affiliation(s)
| | | | - Edith Nicol
- Laboratoire de Chimie Moléculaire, CNRS UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Oleg Yu Tsybin
- Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Alain Brunelle
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
- Laboratoire d'Archéologie Moléculaire et Structurale, LAMS UMR8220, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, 1015 Lausanne, Switzerland
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7
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Weisbrod CR, Anderson LC, Greer JB, DeHart CJ, Hendrickson CL. Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading. Anal Chem 2020; 92:12193-12200. [PMID: 32812743 DOI: 10.1021/acs.analchem.0c01064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fourier transform mass spectrometers routinely provide high mass resolution, mass measurement accuracy, and mass spectral dynamic range. In this work, we utilize 21 T Fourier transform ion cyclotron resonance (FT-ICR) to analyze product ions derived from the application of multiple dissociation techniques and/or multiple precursor ions within a single transient acquisition. This ion loading technique, which we call, "chimeric ion loading", saves valuable acquisition time, decreases sample consumption, and improves top-down protein sequence coverage. In the analysis of MCF7 cell lysate, we show collision-induced dissociation (CID) and electron-transfer dissociation (ETD) on each precursor on a liquid chromatography-mass spectrometry (LC-MS) timescale and improve mean sequence coverage dramatically (CID-only 15% vs chimeric 33%), even during discovery-based acquisition. This approach can also be utilized to multiplex the acquisition of product ion spectra of multiple charge states from a single protein precursor or multiple ETD/proton-transfer reactions (PTR) reaction periods. The analytical utility of chimeric ion loading is demonstrated for top-down proteomics, but it is also likely to be impactful for tandem mass spectrometry applications in other areas.
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Affiliation(s)
- Chad R Weisbrod
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Caroline J DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
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8
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Gavard R, Palacio Lozano DC, Guzman A, Rossell D, Spencer SEF, Barrow MP. Rhapso: Automatic Stitching of Mass Segments from Fourier Transform Ion Cyclotron Resonance Mass Spectra. Anal Chem 2019; 91:15130-15137. [PMID: 31664818 DOI: 10.1021/acs.analchem.9b03846] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides the resolution and mass accuracy needed to analyze complex mixtures such as crude oil. When mixtures contain many different components, a competitive effect within the ICR cell takes place that hampers the detection of a potentially large fraction of the components. Recently, a new data collection technique, which consists of acquiring several spectra of small mass ranges and assembling a complete spectrum afterward, enabled the observation of a record number of peaks with greater accuracy compared to broadband methods. There is a need for statistical methods to combine and preprocess segmented acquisition data. A particular challenge of quadrupole isolation is that near the window edges there is a drop in intensity, hampering the stitching of consecutive windows. We developed an algorithm called Rhapso to stitch peak lists corresponding to multiple different m/z regions from crude oil samples. Rhapso corrects potential edge effects to enable the use of smaller windows and reduce the required overlap between windows, corrects mass shifts between windows, and generates a single peak list for the full spectrum. Relative to a stitching performed manually, Rhapso increased the data processing speed and avoided potential human errors, simplifying the subsequent chemical analysis of the sample. Relative to a broadband spectrum, the stitched output showed an over 2-fold increase in assigned peaks and reduced mass error by a factor of 2. Rhapso is expected to enable routine use of this spectral stitching method for ultracomplex samples, giving a more detailed characterization of existing samples and enabling the characterization of samples that were previously too complex to analyze.
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Affiliation(s)
- Remy Gavard
- MAS CDT , University of Warwick , Coventry , CV4 7AL , United Kingdom
| | | | - Alexander Guzman
- Instituto Colombiano del Petróleo , Piedecuesta , 681011 , Colombia
| | - David Rossell
- Department of Statistics , University of Warwick , Coventry , CV4 7AL , United Kingdom.,Department of Economics & Business , Universitat Pompeu Fabra , Barcelona , 08005 , Spain
| | - Simon E F Spencer
- Department of Statistics , University of Warwick , Coventry , CV4 7AL , United Kingdom
| | - Mark P Barrow
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , United Kingdom
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9
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Kafader JO, Melani RD, Senko MW, Makarov AA, Kelleher NL, Compton PD. Measurement of Individual Ions Sharply Increases the Resolution of Orbitrap Mass Spectra of Proteins. Anal Chem 2019; 91:2776-2783. [PMID: 30609364 DOI: 10.1021/acs.analchem.8b04519] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is well-known that with Orbitrap-based Fourier-transform-mass-spectrometry (FT-MS) analysis, longer-time-domain signals are needed to better resolve species of interest. Unfortunately, increasing the signal-acquisition period comes at the expense of increasing ion decay, which lowers signal-to-noise ratios and ultimately limits resolution. This is especially problematic for intact proteins, including antibodies, which demonstrate rapid decay because of their larger collisional cross-sections, and result in more frequent collisions with background gas molecules. Provided here is a method that utilizes numerous low-ion-count spectra and single-ion processing to reconstruct a conventional m/ z spectrum. This technique has been applied to proteins varying in molecular weight from 8 to 150 kDa, with a resolving power of 677 000 achieved for transients of carbonic anhydrase (29 kDa) with a duration of only ∼250 ms. A resolution improvement ranging from 10- to 20-fold was observed for all proteins, providing isotopic resolution where none was previously present.
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Affiliation(s)
- Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
| | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
| | - Michael W Senko
- Thermo Fisher Scientific , San Jose , California 95134 , United States
| | | | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute , The Proteomics Center of Excellence at Northwestern University , Evanston , Illinois 60208 , United States
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10
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Wang Y, Olesik SV. Enhanced-Fluidity Liquid Chromatography-Mass Spectrometry for Intact Protein Separation and Characterization. Anal Chem 2018; 91:935-942. [PMID: 30523683 DOI: 10.1021/acs.analchem.8b03970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent advances in the analysis of proteins have increased the demand for more efficient techniques to separate intact proteins. Enhanced-fluidity liquid chromatography (EFLC) involves the addition of liquefied CO2 to conventional liquid mobile phases. The addition of liquefied CO2 increases diffusivity and decreases viscosity, which inherently leads to a more efficient separation. Herein, EFLC is applied to hydrophobic interaction chromatography (HIC) stationary phases for the first time to study the impact of liquefied CO2 to the chromatographic behavior of proteins. The effects of liquefied CO2 on chromatographic properties, charge state distributions (CSDs), and ionization efficiencies were evaluated. EFLC offered improved chromatographic performance compared to conventional liquid chromatography (LC) methods including a shorter analysis time, better peak shapes, and higher plate numbers. The addition of liquefied CO2 to the mobile phase provided an electrospray ionization (ESI)-friendly and "supercharging" reagent without sacrificing chromatographic performance, which can be used to improve peptide and protein identification in large-scale application.
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Affiliation(s)
- Yanhui Wang
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States of America
| | - Susan V Olesik
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States of America
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11
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Davila S, Liu P, Smith A, Marshall AG, Pedigo S. Spontaneous Calcium-Independent Dimerization of the Isolated First Domain of Neural Cadherin. Biochemistry 2018; 57:6404-6415. [PMID: 30387993 DOI: 10.1021/acs.biochem.8b00733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cadherins are calcium-dependent, transmembrane adhesion molecules that assemble through direct noncovalent association of their N-terminal extracellular modular domains. As the transmembrane component of adherens junctions, they indirectly link adherent cells' actin cytoskeletons. Here, we investigate the most distal extracellular domain of neural cadherin (N-cadherin), a protein required at excitatory synapses, the site of long-term potentiation. This domain is the site of the adhesive interface, and it forms a dimer spontaneously without binding calcium, a surprising finding given that calcium binding is required for proper physiological function. A critical tryptophan at position 2, W2, provides a spectroscopic probe for the "closed" monomer and strand-swapped dimer. Spectroscopic studies show that W2 remains docked in the two forms but has a different apparent interaction with the hydrophobic pocket. Size-exclusion chromatography was used to measure the levels of the monomer and dimer over time to study the kinetics and equilibria of the unexpected spontaneous dimer formation ( Kd = 130 μM; τ = 2 days at 4 °C). Our results support the idea that NCAD1 is missing critical contacts that facilitate the rapid exchange of the βA-strand. Furthermore, the monomer and dimer have equivalent and exceptionally high intrinsic stability for a 99-residue Ig-like domain with no internal disulfides ( Tm = 77 °C; Δ H = 85 kcal/mol). Ultimately, a complete analysis of synapse dynamics requires characterization of the kinetics and equilibria of N-cadherin. The studies reported here take a reductionist approach to understanding the essential biophysics of an atypical Ig-like domain that is the site of the adhesive interface of N-cadherin.
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Affiliation(s)
- Samantha Davila
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
| | - Peilu Liu
- Department of Chemistry & Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Alexis Smith
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
| | - Alan G Marshall
- Department of Chemistry & Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Susan Pedigo
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
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12
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Jiang T, Hoover ME, Holt MV, Freitas MA, Marshall AG, Young NL. Middle-Down Characterization of the Cell Cycle Dependence of Histone H4 Posttranslational Modifications and Proteoforms. Proteomics 2018; 18:e1700442. [PMID: 29667342 PMCID: PMC8087174 DOI: 10.1002/pmic.201700442] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/28/2018] [Indexed: 12/12/2022]
Abstract
Post-translational modifications (PTMs) of histones are important epigenetic regulatory mechanisms that are often dysregulated in cancer. We employ middle-down proteomics to investigate the PTMs and proteoforms of histone H4 during cell cycle progression. We use pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) for on-line liquid chromatography-mass spectrometry analysis to separate and analyze the proteoforms of histone H4. This procedure provides enhanced separation of proteoforms, including positional isomers, and simplifies downstream data analysis. We use ultrahigh mass accuracy and resolution Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer to unambiguously distinguish between acetylation and tri-methylation (∆m = 0.036 Da). In total, we identify and quantify 233 proteoforms of histone H4 in two breast cancer cell lines. We observe significant increases in S1 phosphorylation during mitosis, implicating an important role in mitotic chromatin condensation. A decrease of K20 unmodified proteoforms is observed as the cell cycle progresses, corresponding to an increase of K20 mono- and di-methylation. Acetylation at K5, K8, K12, and K16 declines as cells traverse from S phase to mitosis, suggesting cell cycle-dependence and an important role during chromatin replication and condensation. These new insights into the epigenetics of the cell cycle may provide new diagnostic and prognostic biomarkers.
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Affiliation(s)
- Tingting Jiang
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Michael E Hoover
- Department of Cancer Biology and Genetics, Ohio State University, 460 West 12th Avenue, Columbus, OH, 43210, USA
| | - Matthew V Holt
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, Ohio State University, 460 West 12th Avenue, Columbus, OH, 43210, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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13
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Shaw JB, Gorshkov MV, Wu Q, Paša-Tolić L. High Speed Intact Protein Characterization Using 4X Frequency Multiplication, Ion Trap Harmonization, and 21 Tesla FTICR-MS. Anal Chem 2018; 90:5557-5562. [PMID: 29613776 DOI: 10.1021/acs.analchem.7b04606] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mass spectrometric characterization of large biomolecules, such as intact proteins, requires the specificity afforded by ultrahigh resolution mass measurements performed at both the intact mass and product ion levels. Although the performance of time-of-flight mass analyzers is steadily increasing, the choice of mass analyzer for large biomolecules (e.g., proteins >50 kDa) is generally limited to the Fourier transform family of mass analyzers such as Orbitrap and ion cyclotron resonance (FTICR-MS), with the latter providing unmatched mass resolving power and measurement accuracy. Yet, protein analyses using FTMS are largely hindered by the low acquisition rates of spectra with ultrahigh resolving power. Frequency multiple detection schemes enable FTICR-MS to overcome this fundamental barrier and achieve resolving powers and acquisition speeds 4× greater than the limits imposed by magnetic field strength. Here we expand upon earlier work on the implementation of this technique for biomolecular characterization. We report the coupling of 21T FTICR-MS, 4X frequency multiplication, ion trapping field harmonization technology, and spectral data processing methods to achieve unprecedented acquisition rates and resolving power in mass spectrometry of large intact proteins. Isotopically resolved spectra of multiply charged ubiquitin ions were acquired using detection periods as short as 12 ms. Large proteins such as apo-transferrin (MW = 78 kDa) and monoclonal antibody (MW = 150 kDa) were isotopically resolved with detection periods of 384 and 768 ms, respectively. These results illustrate the future capability of accurate characterization of large proteins on time scales compatible with online separations.
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Affiliation(s)
- Jared B Shaw
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard . Richland , Washington 99352 , United States
| | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia.,Moscow Institute of Physics and Technology (State University) , Dolgoprudny , Moscow Region 141700 , Russia
| | - Qinghao Wu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard . Richland , Washington 99352 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Boulevard . Richland , Washington 99352 , United States
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14
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Schmidt EM, Pudenzi MA, Santos JM, Angolini CFF, Pereira RCL, Rocha YS, Denisov E, Damoc E, Makarov A, Eberlin MN. Petroleomics via Orbitrap mass spectrometry with resolving power above 1 000 000 at m/z 200. RSC Adv 2018; 8:6183-6191. [PMID: 35539593 PMCID: PMC9078259 DOI: 10.1039/c7ra12509g] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/27/2018] [Indexed: 12/18/2022] Open
Abstract
The performance of the high-field MegaOrbitrap Fourier transform mass spectrometer (FT-MS) with electrospray ionization (ESI) was evaluated to perform petroleum sample characterization via classical petroleomics approaches. Pertinent parameters that underpin the main figures of merit, that is, signal to noise ratios, dynamic range, spectral error, scan speed, mass accuracy and mass resolving power = Rp, and provide subsidies to develop these analyzers were tested. Comparisons are made with data obtained using the most common petroleomics instrument, which is a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), that has been used in the last decade in our laboratory for crude oil analysis providing Rp of 340 000 at m/z 400 with transients of 3 s duration, and has been extensively demonstrated to fulfill all major requirements for precise petroleomics investigations. The high-field compact MegaOrbitrap mass analyzer, when operated at an Rp = 840 000 at m/z 400 (Rp > 1 000 000 at m/z 200) with a detection time of 3 s, was found to be well suited for adequate characterization of crude oil. Accurate class classification and mass accuracy below 1 ppm was obtained leading to proper, comprehensive petroleomics characterization. The performance of the high-field MegaOrbitrap Fourier transform mass spectrometer (FT-MS) with electrospray ionization (ESI) was evaluated to perform petroleum sample characterization via classical petroleomics approaches.![]()
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Affiliation(s)
- Eduardo M. Schmidt
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Marcos A. Pudenzi
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Jandyson M. Santos
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Celio F. F. Angolini
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | | | | | | | | | | | - Marcos N. Eberlin
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
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15
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Li X, Tao Y, Murphy JW, Scherer AN, Lam TT, Marshall AG, Koleske AJ, Boggon TJ. The repeat region of cortactin is intrinsically disordered in solution. Sci Rep 2017; 7:16696. [PMID: 29196701 PMCID: PMC5711941 DOI: 10.1038/s41598-017-16959-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/19/2017] [Indexed: 01/14/2023] Open
Abstract
The multi-domain protein, cortactin, contains a 37-residue repeating motif that binds to actin filaments. This cortactin repeat region comprises 6½ similar copies of the motif and binds actin filaments. To better understand this region of cortactin, and its fold, we conducted extensive biophysical analysis. Size exclusion chromatography with multi-angle light scattering (SEC-MALS) reveals that neither constructs of the cortactin repeats alone or together with the adjacent helical region homo-oligomerize. Using circular dichroism (CD) we find that in solution the cortactin repeats resemble a coil-like intrinsically disordered protein. Small-angle X-ray scattering (SAXS) also indicates that the cortactin repeats are intrinsically unfolded, and the experimentally observed radius of gyration (Rg) is coincidental to that calculated by the program Flexible-Meccano for an unfolded peptide of this length. Finally, hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicates that the domain contains limited hydrophobic core regions. These experiments therefore provide evidence that in solution the cortactin repeat region of cortactin is intrinsically disordered.
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Affiliation(s)
- Xiaofeng Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yeqing Tao
- Department of Chemistry, Florida State University, 600 W., College Avenue, Tallahassee, FL, 32306, USA.,Biopharmaceutical Analytical Sciences, Biopharm R&D, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA, 19406, USA
| | - James W Murphy
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alexander N Scherer
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Yale MS & Proteomics Resource, Yale University, New Haven, CT, 06520, USA
| | - Alan G Marshall
- Department of Chemistry, Florida State University, 600 W., College Avenue, Tallahassee, FL, 32306, USA.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Anthony J Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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16
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Gavard R, Rossell D, Spencer SEF, Barrow MP. Themis: Batch Preprocessing for Ultrahigh-Resolution Mass Spectra of Complex Mixtures. Anal Chem 2017; 89:11383-11390. [PMID: 28985049 DOI: 10.1021/acs.analchem.7b02345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry affords the resolving power to determine an unprecedented number of components in complex mixtures, such as petroleum. The software tools required to also analyze these data struggle to keep pace with advancing instrument capabilities and increasing quantities of data, particularly in terms of combining information efficiently across multiple replicates. Improved confidence in data and the use of replicates is particularly important where strategic decisions will be based upon the analysis. We present a new algorithm named Themis, developed using R, to jointly preprocess replicate measurements of a sample with the aim of improving consistency as a preliminary step to assigning peaks to chemical compositions. The main features of the algorithm are quality control criteria to detect failed runs, ensuring comparable magnitudes across replicates, peak alignment, and the use of an adaptive mixture model-based strategy to help distinguish true peaks from noise. The algorithm outputs a list of peaks reliably observed across replicates and facilitates data handling by preprocessing all replicates in a single step. The processed data produced by our algorithm can subsequently be analyzed by use of relevant specialized software. While Themis has been demonstrated with petroleum as an example of a complex mixture, its basic framework will be useful for complex samples arising from a variety of other applications.
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Affiliation(s)
| | - David Rossell
- Department of Economics & Business, Universitat Pompeu Fabra , Barcelona 08005, Spain
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17
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Anderson LC, Håkansson M, Walse B, Nilsson CL. Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1796-1804. [PMID: 28681360 PMCID: PMC5556139 DOI: 10.1007/s13361-017-1705-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/16/2023]
Abstract
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a ~45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. Graphical Abstract ᅟ.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Carol L Nilsson
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX, 77555-1074, USA.
- Institute of Clinical Sciences-Lund, Lund University, SE-221 85, Lund, Sweden.
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18
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Weisbrod CR, Kaiser NK, Syka JEP, Early L, Mullen C, Dunyach JJ, English AM, Anderson LC, Blakney GT, Shabanowitz J, Hendrickson CL, Marshall AG, Hunt DF. Front-End Electron Transfer Dissociation Coupled to a 21 Tesla FT-ICR Mass Spectrometer for Intact Protein Sequence Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1787-1795. [PMID: 28721671 PMCID: PMC5711562 DOI: 10.1007/s13361-017-1702-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/13/2023]
Abstract
High resolution mass spectrometry is a key technology for in-depth protein characterization. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enables high-level interrogation of intact proteins in the most detail to date. However, an appropriate complement of fragmentation technologies must be paired with FTMS to provide comprehensive sequence coverage, as well as characterization of sequence variants, and post-translational modifications. Here we describe the integration of front-end electron transfer dissociation (FETD) with a custom-built 21 tesla FT-ICR mass spectrometer, which yields unprecedented sequence coverage for proteins ranging from 2.8 to 29 kDa, without the need for extensive spectral averaging (e.g., ~60% sequence coverage for apo-myoglobin with four averaged acquisitions). The system is equipped with a multipole storage device separate from the ETD reaction device, which allows accumulation of multiple ETD fragment ion fills. Consequently, an optimally large product ion population is accumulated prior to transfer to the ICR cell for mass analysis, which improves mass spectral signal-to-noise ratio, dynamic range, and scan rate. We find a linear relationship between protein molecular weight and minimum number of ETD reaction fills to achieve optimum sequence coverage, thereby enabling more efficient use of instrument data acquisition time. Finally, real-time scaling of the number of ETD reactions fills during method-based acquisition is shown, and the implications for LC-MS/MS top-down analysis are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Chad R Weisbrod
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA.
| | - Nathan K Kaiser
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | | | - Lee Early
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | | | - A Michelle English
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Lissa C Anderson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Greg T Blakney
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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19
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Tao Y, Fang P, Kim S, Guo M, Young NL, Marshall AG. Mapping the contact surfaces in the Lamin A:AIMP3 complex by hydrogen/deuterium exchange FT-ICR mass spectrometry. PLoS One 2017; 12:e0181869. [PMID: 28797100 PMCID: PMC5552228 DOI: 10.1371/journal.pone.0181869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear. Here we report solution-phase hydrogen/deuterium exchange (HDX) for AIMP3, LmnA, and AIMP3 in association with the LmnA C-terminus. Reversed-phase LC coupled with LTQ 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) results in high mass accuracy and resolving power for comparing the D-uptake profiles for AIMP3, LmnA, and their complex. The results show that the AIMP3-LmnA interaction involves one of the two putative binding sites and an adjacent novel interface on AIMP3. LmnA binds AIMP3 via its extreme C-terminus. Together these findings provide a structural insight for understanding the interaction between AIMP3 and LmnA in AIMP3 degradation.
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Affiliation(s)
- Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Pengfei Fang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, United States of America
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, United States of America
| | - Nicolas L. Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, United States of America
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20
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Dandamudi KPR, Muppaneni T, Sudasinghe N, Schaub T, Holguin FO, Lammers PJ, Deng S. Co-liquefaction of mixed culture microalgal strains under sub-critical water conditions. BIORESOURCE TECHNOLOGY 2017; 236:129-137. [PMID: 28399416 DOI: 10.1016/j.biortech.2017.03.165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/22/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
We report the co-liquefaction performance of unicellular, red alga Cyanidioschyzon merolae and Galdieria sulphuraria under sub-critical water conditions within a stainless-steel batch reactor under different temperatures (150-300°C), residence time (15-60min), and Cyanidioschyzon merolae to Galdieria sulphuraria mass loading (0-100%). Individual liquefaction of C. merolae and G. sulphuraria at 300°C achieved maximum biocrude oil yield of 18.9 and 14.0%, respectively. The yield of biocrude oil increased to 25.5%, suggesting a positive synergistic effect during the co-liquefaction of 80-20mass loading of C. merolae to G. sulphuraria. The biocrude oils were analyzed by FT-ICR MS which showed that co-liquefaction did not significantly affect the distribution of product compounds compared to individual oils. The co-liquefied biocrude and biochar have a higher-heating-value of 35.28 and 7.96MJ/kg. Ultimate and proximate analysis were performed on algae biomass, biocrude and biochar.
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Affiliation(s)
- Kodanda Phani Raj Dandamudi
- Chemical Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Tapaswy Muppaneni
- Chemical Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Nilusha Sudasinghe
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM 88003, USA; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanner Schaub
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM 88003, USA
| | - F Omar Holguin
- Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Peter J Lammers
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA
| | - Shuguang Deng
- Chemical Engineering Department, New Mexico State University, Las Cruces, NM 88003, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA.
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21
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Chen J, Zhang Q, Ren W, Li W. Piecing Together the Allosteric Patterns of Chaperonin GroEL. J Phys Chem B 2017; 121:4987-4996. [PMID: 28430446 DOI: 10.1021/acs.jpcb.7b01992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite considerable efforts, elucidating the allostery of large macromolecular assemblies at a molecular level in solution remains technically challenging due to its structural complexity. Here we have employed an approach combining amide backbone hydrogen/deuterium exchange coupled with mass spectrometry, fluorescence spectroscopy, and molecular simulations to characterize allosteric patterns of chaperonin GroEL, an ∼800 kDa tetradecamer from E. coli. Using available crystal structures of GroEL, we quantitatively map out GroEL allosteric changes in solution by resolving exchange behaviors of 133 overlapping proteolytic peptides with more than 95% sequence coverage. This comprehensive analysis gives a refined resolution down to five residues to pilot the GroEL allosteric determinants, of which the localized dynamics is monitored by tryptophan-mutated GroEL. Furthermore, the GroEL conformational transition is evaluated by molecular dynamics simulations with an atomic-interaction-based coarse-grained model. Collectively, we provide a practical methodology to analyze GroEL allostery in solution.
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Affiliation(s)
- Jin Chen
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences , Okazaki 444-8787, Japan
| | - Qian Zhang
- Department of Chemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Weitong Ren
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University , Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University , Nanjing 210093, China
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22
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Guan X, Brownstein NC, Young NL, Marshall AG. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo amino acid sequencing for a seven-protein mixture by paired single-residue transposed Lys-N and Lys-C digestion. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:207-217. [PMID: 27813191 DOI: 10.1002/rcm.7783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/29/2016] [Accepted: 10/30/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics to identify proteins from a sequence database. De novo sequencing is also available for sequencing peptides with relatively short sequence lengths. We recently showed that paired Lys-C and Lys-N proteases produce peptides of identical mass and similar retention time, but different tandem mass spectra. Such parallel experiments provide complementary information, and allow for up to 100% MS/MS sequence coverage. METHODS Here, we report digestion by paired Lys-C and Lys-N proteases of a seven-protein mixture: human hemoglobin alpha, bovine carbonic anhydrase 2, horse skeletal muscle myoglobin, hen egg white lysozyme, bovine pancreatic ribonuclease, bovine rhodanese, and bovine serum albumin, followed by reversed-phase nanoflow liquid chromatography, collision-induced dissociation, and 14.5 T Fourier transform ion cyclotron resonance mass spectrometry. RESULTS Matched pairs of product peptide ions of equal precursor mass and similar retention times from each digestion are compared, leveraging single-residue transposed information with independent interferences to confidently identify fragment ion types, residues, and peptides. Selected pairs of product ion mass spectra for de novo sequenced protein segments from each member of the mixture are presented. CONCLUSIONS Pairs of the transposed product ions as well as complementary information from the parallel experiments allow for both high MS/MS coverage for long peptide sequences and high confidence in the amino acid identification. Moreover, the parallel experiments in the de novo sequencing reduce false-positive matches of product ions from the single-residue transposed peptides from the same segment, and thereby further improve the confidence in protein identification. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xiaoyan Guan
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Naomi C Brownstein
- Department of Behavioral Sciences and Social Medicine, College of Medicine, Florida State University, 1115 W. Call St., Tallahassee, FL, 32306, USA
- Department of Statistics, Florida State University, 117 N. Woodward Ave., Tallahassee, FL, 32306, USA
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, MS-125, Houston, TX, 77030-3411, USA
| | - Alan G Marshall
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32303, USA
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24
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Structural characterization of human aminoacyl-tRNA synthetases for translational and nontranslational functions. Methods 2017; 113:83-90. [DOI: 10.1016/j.ymeth.2016.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
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25
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Anderson LC, DeHart CJ, Kaiser NK, Fellers RT, Smith DF, Greer JB, LeDuc RD, Blakney GT, Thomas PM, Kelleher NL, Hendrickson CL. Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry. J Proteome Res 2016; 16:1087-1096. [PMID: 27936753 DOI: 10.1021/acs.jproteome.6b00696] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Successful high-throughput characterization of intact proteins from complex biological samples by mass spectrometry requires instrumentation capable of high mass resolving power, mass accuracy, sensitivity, and spectral acquisition rate. These limitations often necessitate the performance of hundreds of LC-MS/MS experiments to obtain reasonable coverage of the targeted proteome, which is still typically limited to molecular weights below 30 kDa. The National High Magnetic Field Laboratory (NHMFL) recently installed a 21 T FT-ICR mass spectrometer, which is part of the NHMFL FT-ICR User Facility and available to all qualified users. Here we demonstrate top-down LC-21 T FT-ICR MS/MS of intact proteins derived from human colorectal cancer cell lysate. We identified a combined total of 684 unique protein entries observed as 3238 unique proteoforms at a 1% false discovery rate, based on rapid, data-dependent acquisition of collision-induced and electron-transfer dissociation tandem mass spectra from just 40 LC-MS/MS experiments. Our identifications included 372 proteoforms with molecular weights over 30 kDa detected at isotopic resolution, which substantially extends the accessible mass range for high-throughput top-down LC-MS/MS.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Caroline J DeHart
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Nathan K Kaiser
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Donald F Smith
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Greg T Blakney
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry and Molecular Biosciences and the Division of Hematology-Oncology, Northwestern University , Evanston, Illinois 60208, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32304, United States
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26
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Andersen AJC, Hansen PJ, Jørgensen K, Nielsen KF. Dynamic Cluster Analysis: An Unbiased Method for Identifying A + 2 Element Containing Compounds in Liquid Chromatographic High-Resolution Time-of-Flight Mass Spectrometric Data. Anal Chem 2016; 88:12461-12469. [PMID: 28193030 DOI: 10.1021/acs.analchem.6b03902] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Dynamic cluster analysis (DCA) is an automated, unbiased technique which can identify Cl, Br, S, and other A + 2 element containing metabolites in liquid chromatographic high-resolution mass spectrometric data. DCA is based on three features, primarily the previously unutilized A + 1 to A + 2 isotope cluster spacing which is a strong classifier in itself but improved with the addition of the monoisotopic mass, and the well-known A:A+2 intensity ratio. Utilizing only the A + 1 to A + 2 isotope cluster spacing and the monoisotopic mass it was possible to filter a chromatogram for metabolites which contain Cl, Br, and S. Screening simulated isotope patterns of the Antibase Natural Products Database it was determined that the A + 1 to A + 2 isotope cluster spacing can be used to correctly classify 97.4% of molecular formulas containing these elements, only misclassifying a few metabolites which were either over 2800 u or metabolites which contained other A + 2 elements, such as Cu, Ni, Mg, and Zn. It was determined that with an interisotopic mass accuracy of 1 ppm, in a fully automated process, using all three parameters, it is possible to specifically filter a chromatogram for S containing metabolites with monoisotopic masses less than 825 u. Furthermore, it was possible to specifically filter a chromatogram for Cl and Br containing metabolites with monoisotopic masses less than 1613 u. Here DCA is applied on (i) simulated isotope patterns of the Antibase natural products databases, (ii) LC-QTOF data of reference standards, and (iii) LC-QTOF data of crude extracts of 10 strains of laboratory grown cultures of the microalga Prymnesium parvum where it identified known metabolites of the prymnesin series as well as over 20 previously undescribed prymnesin-like molecular features.
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Affiliation(s)
- Aaron John Christian Andersen
- National Food Institute, Technical University of Denmark , Mørkhøj Bygade 19, 2800 Søborg, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark , Søltofts Plads 221, 2800 Kgs. Lyngby, Denmark
| | - Per Juel Hansen
- Marine Biological Section, Department of Biology, Copenhagen University , Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Kevin Jørgensen
- National Food Institute, Technical University of Denmark , Mørkhøj Bygade 19, 2800 Søborg, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark , Søltofts Plads 221, 2800 Kgs. Lyngby, Denmark
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Huba AK, Huba K, Gardinali PR. Understanding the atmospheric pressure ionization of petroleum components: The effects of size, structure, and presence of heteroatoms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 568:1018-1025. [PMID: 27363346 DOI: 10.1016/j.scitotenv.2016.06.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
Understanding the composition of crude oil and its changes with weathering is essential when assessing its provenience, fate, and toxicity. High-resolution mass spectrometry (HRMS) has provided the opportunity to address the complexity of crude oil by assigning molecular formulae, and sorting compounds into "classes" based on heteroatom content. However, factors such as suppression effects and discrimination towards certain components severely limit a truly comprehensive mass spectrometric characterization, and, despite the availability of increasingly better mass spectrometers, a complete characterization of oil still represents a major challenge. In order to fully comprehend the significance of class abundances, as well as the nature and identity of compounds detected, a good understanding of the ionization efficiency of the various compound classes is indispensable. The current study, therefore, analyzed model compounds typically found in crude oils by high-resolution mass spectrometry with atmospheric pressure photoionization (APPI), atmospheric pressure chemical ionization (APCI), and electrospray ionization (ESI), in order to provide a better understanding of benefits and drawbacks of each source. The findings indicate that, overall, APPI provides the best results, being able to ionize the broadest range of compounds, providing the best results with respect to ionization efficiencies, and exhibiting the least suppression effects. However, just like in the other two sources, in APPI several factors have shown to affect the ionization efficiency of petroleum model compounds. The main such factor is the presence or absence of functional groups that can be easily protonated/deprotonated, in addition to other factors such as size, methylation level, presence of heteroatoms, and ring structure. Overall, this study evidences the intrinsic limitations and benefits of each of the three sources, and should provide the fundamental knowledge required to expand the power of crude oil analysis by high-resolution mass spectrometry.
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Affiliation(s)
- Anna Katarina Huba
- Department of Chemistry & Biochemistry, Florida International University, 3000 NE 151 Street, Biscayne Bay Campus, North Miami, Florida 33181, USA
| | - Kristina Huba
- Department of Chemistry & Biochemistry, Florida International University, 3000 NE 151 Street, Biscayne Bay Campus, North Miami, Florida 33181, USA
| | - Piero R Gardinali
- Department of Chemistry & Biochemistry, Florida International University, 3000 NE 151 Street, Biscayne Bay Campus, North Miami, Florida 33181, USA; Southeast Environmental Research Center (SERC), Florida International University, 3000 NE 151 Street, Biscayne Bay Campus, North Miami, Florida 33181, USA
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28
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The excluded DNA strand is SEW important for hexameric helicase unwinding. Methods 2016; 108:79-91. [DOI: 10.1016/j.ymeth.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 02/04/2023] Open
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29
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Kostyukevich YI, Kharybin ON, Kononikhin AS, Popov IA, Nikolaev EN. Deuterium–hydrogen exchange reactions in peptides and polyatomic organic compounds, as studied on an ion cyclotron resonance mass spectrometer equipped with an ion trap with dynamic harmonization. HIGH ENERGY CHEMISTRY 2016. [DOI: 10.1134/s0018143916030097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Graham BW, Tao Y, Dodge KL, Thaxton CT, Olaso D, Young NL, Marshall AG, Trakselis MA. DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase. J Biol Chem 2016; 291:12467-12480. [PMID: 27044751 DOI: 10.1074/jbc.m116.719591] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 11/06/2022] Open
Abstract
The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect single-stranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding.
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Affiliation(s)
- Brian W Graham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Katie L Dodge
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Carly T Thaxton
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Danae Olaso
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306; National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798.
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31
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Nikolaev EN, Kostyukevich YI, Vladimirov GN. Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry: Theory and simulations. MASS SPECTROMETRY REVIEWS 2016; 35:219-58. [PMID: 24515872 DOI: 10.1002/mas.21422] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/16/2013] [Indexed: 05/22/2023]
Abstract
Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer offers highest resolving power and mass accuracy among all types of mass spectrometers. Its unique analytical characteristics made FT ICR important tool for proteomics, metabolomics, petroleomics, and investigation of complex mixtures. Signal acquisition in FT ICR MS takes long time (up to minutes). During this time ion-ion interaction considerably affects ion motion and result in decreasing of the resolving power. Understanding of those effects required complicated theory and supercomputer simulations but culminated in the invention of the ion trap with dynamic harmonization which demonstrated the highest resolving power ever achieved. In this review we summarize latest achievements in theory and simulation of FT ICR mass spectrometers.
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Affiliation(s)
- Eugene N Nikolaev
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k. 2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121, Moscow, Russia
| | - Yury I Kostyukevich
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k. 2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Gleb N Vladimirov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k. 2, 119334, Moscow, Russia
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32
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Park SG, Anderson GA, Navare AT, Bruce JE. Parallel Spectral Acquisition with an Ion Cyclotron Resonance Cell Array. Anal Chem 2016; 88:1162-8. [PMID: 26669509 PMCID: PMC4848028 DOI: 10.1021/acs.analchem.5b02987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass measurement accuracy is a critical analytical figure-of-merit in most areas of mass spectrometry application. However, the time required for acquisition of high-resolution, high mass accuracy data limits many applications and is an aspect under continual pressure for development. Current efforts target implementation of higher electrostatic and magnetic fields because ion oscillatory frequencies increase linearly with field strength. As such, the time required for spectral acquisition of a given resolving power and mass accuracy decreases linearly with increasing fields. Mass spectrometer developments to include multiple high-resolution detectors that can be operated in parallel could further decrease the acquisition time by a factor of n, the number of detectors. Efforts described here resulted in development of an instrument with a set of Fourier transform ion cyclotron resonance (ICR) cells as detectors that constitute the first MS array capable of parallel high-resolution spectral acquisition. ICR cell array systems consisting of three or five cells were constructed with printed circuit boards and installed within a single superconducting magnet and vacuum system. Independent ion populations were injected and trapped within each cell in the array. Upon filling the array, all ions in all cells were simultaneously excited and ICR signals from each cell were independently amplified and recorded in parallel. Presented here are the initial results of successful parallel spectral acquisition, parallel mass spectrometry (MS) and MS/MS measurements, and parallel high-resolution acquisition with the MS array system.
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Affiliation(s)
- Sung-Gun Park
- Department of Genome Sciences, University of Washington , Seattle, Washington 98109, United States
| | - Gordon A Anderson
- GAA Custom Engineering, LLC, Benton City, Washington 99320, United States
| | - Arti T Navare
- Department of Genome Sciences, University of Washington , Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington , Seattle, Washington 98109, United States
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33
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Han F, Liu T, Yin R, Zhang X, Ma L, Xu R, Wu Y. UHPLC-FT-ICR-MS combined with serum pharmacochemistry for bioactive compounds discovery of Zhi-Zi-Da-Huang-decoction against alcohol-induced hepatotoxicity in rats. RSC Adv 2016. [DOI: 10.1039/c6ra19422b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this study, a comprehensive strategy based on UHPLC-FT-ICR-MS and serum pharmacochemistry was developed to reveal the bioactive constituents of Zhi-Zi-Da-Huang decoction against alcohol-induced hepatotoxicity in rats after oral administration.
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Affiliation(s)
- Fei Han
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang
- China
| | - Tianfeng Liu
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang
- China
| | - Ran Yin
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang
- China
| | - Xiaoshu Zhang
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang
- China
| | - Li Ma
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang
- China
| | - Rui Xu
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang
- China
| | - Yawen Wu
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang
- China
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34
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Patrie SM. Top-Down Mass Spectrometry: Proteomics to Proteoforms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:171-200. [PMID: 27975217 DOI: 10.1007/978-3-319-41448-5_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter highlights many of the fundamental concepts and technologies in the field of top-down mass spectrometry (TDMS), and provides numerous examples of contributions that TD is making in biology, biophysics, and clinical investigations. TD workflows include variegated steps that may include non-specific or targeted preparative strategies, orthogonal liquid chromatography techniques, analyte ionization, mass analysis, tandem mass spectrometry (MS/MS) and informatics procedures. This diversity of experimental designs has evolved to manage the large dynamic range of protein expression and diverse physiochemical properties of proteins in proteome investigations, tackle proteoform microheterogeneity, as well as determine structure and composition of gas-phase proteins and protein assemblies.
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Affiliation(s)
- Steven M Patrie
- Computational and Systems Biology & Biomedical Engineering Graduate Programs, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA.
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35
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Hendrickson CL, Quinn JP, Kaiser NK, Smith DF, Blakney GT, Chen T, Marshall AG, Weisbrod CR, Beu SC. 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: A National Resource for Ultrahigh Resolution Mass Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1626-32. [PMID: 26091892 DOI: 10.1007/s13361-015-1182-2] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 05/16/2023]
Abstract
We describe the design and initial performance of the first 21 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The 21 tesla magnet is the highest field superconducting magnet ever used for FT-ICR and features high spatial homogeneity, high temporal stability, and negligible liquid helium consumption. The instrument includes a commercial dual linear quadrupole trap front end that features high sensitivity, precise control of trapped ion number, and collisional and electron transfer dissociation. A third linear quadrupole trap offers high ion capacity and ejection efficiency, and rf quadrupole ion injection optics deliver ions to a novel dynamically harmonized ICR cell. Mass resolving power of 150,000 (m/Δm(50%)) is achieved for bovine serum albumin (66 kDa) for a 0.38 s detection period, and greater than 2,000,000 resolving power is achieved for a 12 s detection period. Externally calibrated broadband mass measurement accuracy is typically less than 150 ppb rms, with resolving power greater than 300,000 at m/z 400 for a 0.76 s detection period. Combined analysis of electron transfer and collisional dissociation spectra results in 68% sequence coverage for carbonic anhydrase. The instrument is part of the NSF High-Field FT-ICR User Facility and is available free of charge to qualified users.
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Affiliation(s)
- Christopher L Hendrickson
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA,
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36
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Askenasy I, Pennington JM, Tao Y, Marshall AG, Young NL, Shang W, Stroupe ME. The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain That Mediates Holoenzyme Assembly. J Biol Chem 2015; 290:19319-33. [PMID: 26088143 PMCID: PMC4521050 DOI: 10.1074/jbc.m115.662379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/05/2015] [Indexed: 11/06/2022] Open
Abstract
Assimilatory NADPH-sulfite reductase (SiR) from Escherichia coli is a structurally complex oxidoreductase that catalyzes the six-electron reduction of sulfite to sulfide. Two subunits, one a flavin-binding flavoprotein (SiRFP, the α subunit) and the other an iron-containing hemoprotein (SiRHP, the β subunit), assemble to make a holoenzyme of about 800 kDa. How the two subunits assemble is not known. The iron-rich cofactors in SiRHP are unique because they are a covalent arrangement of a Fe4S4 cluster attached through a cysteine ligand to an iron-containing porphyrinoid called siroheme. The link between cofactor biogenesis and SiR stability is also ill-defined. By use of hydrogen/deuterium exchange and biochemical analysis, we show that the α8β4 SiR holoenzyme assembles through the N terminus of SiRHP and the NADPH binding domain of SiRFP. By use of small angle x-ray scattering, we explore the structure of the SiRHP N-terminal oligomerization domain. We also report a novel form of the hemoprotein that occurs in the absence of its cofactors. Apo-SiRHP forms a homotetramer, also dependent on its N terminus, that is unable to assemble with SiRFP. From these results, we propose that homotetramerization of apo-SiRHP serves as a quality control mechanism to prevent formation of inactive holoenzyme in the case of limiting cellular siroheme.
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Affiliation(s)
- Isabel Askenasy
- From the Department of Biological Science and Institute of Molecular Biophysics and
| | - Joseph M Pennington
- From the Department of Biological Science and Institute of Molecular Biophysics and
| | - Yeqing Tao
- the Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Alan G Marshall
- the Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, the National High Magnetic Field Laboratory, Tallahassee, Florida 32310, and
| | - Nicolas L Young
- the National High Magnetic Field Laboratory, Tallahassee, Florida 32310, and
| | - Weifeng Shang
- the Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - M Elizabeth Stroupe
- From the Department of Biological Science and Institute of Molecular Biophysics and
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37
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Guan X, Noble KA, Tao Y, Roux KH, Sathe SK, Young NL, Marshall AG. Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:812-819. [PMID: 26169135 DOI: 10.1002/jms.3589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution-phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX-MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope-contributing segments.
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Affiliation(s)
- Xiaoyan Guan
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Kyle A Noble
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Shridhar K Sathe
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
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38
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Nagornov KO, Kozhinov AN, Tsybin OY, Tsybin YO. Ion trap with narrow aperture detection electrodes for Fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:741-751. [PMID: 25773900 DOI: 10.1007/s13361-015-1089-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 06/04/2023]
Abstract
The current paradigm in ion trap (cell) design for Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the ion detection with wide aperture detection electrodes. Specifically, excitation and detection electrodes are typically 90° wide and positioned radially at a similar distance from the ICR cell axis. Here, we demonstrate that ion detection with narrow aperture detection electrodes (NADEL) positioned radially inward of the cell's axis is feasible and advantageous for FT-ICR MS. We describe design details and performance characteristics of a 10 T FT-ICR MS equipped with a NADEL ICR cell having a pair of narrow aperture (flat) detection electrodes and a pair of standard 90° excitation electrodes. Despite a smaller surface area of the detection electrodes, the sensitivity of the NADEL ICR cell is not reduced attributable to improved excite field distribution, reduced capacitance of the detection electrodes, and their closer positioning to the orbits of excited ions. The performance characteristics of the NADEL ICR cell are comparable with the state-of-the-art FT-ICR MS implementations for small molecule, peptide, protein, and petroleomics analyses. In addition, the NADEL ICR cell's design improves the flexibility of ICR cells and facilitates implementation of advanced capabilities (e.g., quadrupolar ion detection for improved mainstream applications). It also creates an intriguing opportunity for addressing the major bottleneck in FTMS-increasing its throughput via simultaneous acquisition of multiple transients or via generation of periodic non-sinusoidal transient signals.
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Affiliation(s)
- Konstantin O Nagornov
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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39
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Cho Y, Ahmed A, Islam A, Kim S. Developments in FT-ICR MS instrumentation, ionization techniques, and data interpretation methods for petroleomics. MASS SPECTROMETRY REVIEWS 2015; 34:248-263. [PMID: 24942384 DOI: 10.1002/mas.21438] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 11/25/2013] [Accepted: 03/26/2014] [Indexed: 06/03/2023]
Abstract
Because of the increasing importance of heavy and unconventional crude oil as an energy source, there is a growing need for petroleomics: the pursuit of more complete and detailed knowledge of the chemical compositions of crude oil. Crude oil has an extremely complex nature; hence, techniques with ultra-high resolving capabilities, such as Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), are necessary. FT-ICR MS has been successfully applied to the study of heavy and unconventional crude oils such as bitumen and shale oil. However, the analysis of crude oil with FT-ICR MS is not trivial, and it has pushed analysis to the limits of instrumental and methodological capabilities. For example, high-resolution mass spectra of crude oils may contain over 100,000 peaks that require interpretation. To visualize large data sets more effectively, data processing methods such as Kendrick mass defect analysis and statistical analyses have been developed. The successful application of FT-ICR MS to the study of crude oil has been critically dependent on key developments in FT-ICR MS instrumentation and data processing methods. This review offers an introduction to the basic principles, FT-ICR MS instrumentation development, ionization techniques, and data interpretation methods for petroleomics and is intended for readers having no prior experience in this field of study.
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Affiliation(s)
- Yunju Cho
- Department of Chemistry, Kyungpook National University, Daegu, 702-701, Korea
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40
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Minogue CE, Hebert AS, Rensvold JW, Westphall MS, Pagliarini DJ, Coon JJ. Multiplexed quantification for data-independent acquisition. Anal Chem 2015; 87:2570-5. [PMID: 25621425 DOI: 10.1021/ac503593d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Data-independent acquisition (DIA) strategies provide a sensitive and reproducible alternative to data-dependent acquisition (DDA) methods for large-scale quantitative proteomic analyses. Unfortunately, DIA methods suffer from incompatibility with common multiplexed quantification methods, specifically stable isotope labeling approaches such as isobaric tags and stable isotope labeling of amino acids in cell culture (SILAC). Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications (NeuCoDIA), producing a strategy that enables multiplexing within DIA scans without further convoluting the already complex MS(2) spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio (1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis of the mixed-ratio yeast samples revealed the strong accuracy and precision of our NeuCoDIA method, both of which were comparable to our established MS(1)-based quantification approach. NeuCoDIA also uncovered the dynamic protein changes that occur during myogenic differentiation, demonstrating the feasibility of this methodology for biological applications. We consequently establish DIA quantification of NeuCode SILAC as a useful and practical alternative to DDA-based approaches.
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Affiliation(s)
- Catherine E Minogue
- Department of Chemistry, ‡Genome Center of Wisconsin, §Department of Biomolecular Chemistry, and ∥Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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41
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Tsybin YO, Vvorobyev A, Zhurov KO, Laskay ÜA. On the use of electron capture rate constants to describe electron capture dissociation mass spectrometry of peptides. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:451-458. [PMID: 26307726 DOI: 10.1255/ejms.1370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Electron capture dissociation (ECD) tandem mass spectrometry (MS/MS) is a powerful analytical tool for peptide and protein structure analysis. The product ion abundance (PIA) distribution in ECD MS/MS is known to vary as a function of electron irradiation period. This variation complicates the development of a method of peptide identification by correlation of ECD MS/MS data with experimental and theoretical mass spectra. Here, we first develop a kinetic model to describe primary electron capture by peptide dications leading to product ion formation and secondary electron capture resulting in product ion neutralization. We apply the developed kinetic model to calculate product ion formation rate constants and electron capture rate constants of product ions from ECD mass spectra acquired using various electron irradiation periods. Contrary to ECD PIA distributions, the product ion formation rate constants are shown to be independent of electron irradiation period and, thus, may be employed to characterize ECD product ion formation more universally. The electron capture rate constants of product ions in ECD Fourier transform ion cyclotron resonance MS were found to correlate (with a correlation factor, R(2), of ca 0.9) with ion mobility cross sections of product ions in electron transfer dissociation. Finally, we demonstrate that the electron irradiation period influences the ratio of radical and even-electron c and z product ions.
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Affiliation(s)
- Yury O Tsybin
- Bi omolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Aleksey Vvorobyev
- 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
| | - Ünige A Laskay
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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42
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Park KH, Bang G, Min KC, Kim HS, Choi MC. Absolute internal mass calibration with carbon soot ions using high-resolution matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2147-2150. [PMID: 25156605 DOI: 10.1002/rcm.7002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 07/22/2014] [Accepted: 07/27/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Kyu Hwan Park
- Korea Basic Science Institute, Ochang, 363-883, Republic of Korea
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43
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Nagornov KO, Gorshkov MV, Kozhinov AN, Tsybin YO. High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Increased Throughput for Biomolecular Analysis. Anal Chem 2014; 86:9020-8. [DOI: 10.1021/ac501579h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Konstantin O. Nagornov
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Mikhail V. Gorshkov
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141707 Dolgoprudny,
Moscow Region, Russia
| | - Anton N. Kozhinov
- 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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44
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Qi Y, O'Connor PB. Data processing in Fourier transform ion cyclotron resonance mass spectrometry. MASS SPECTROMETRY REVIEWS 2014; 33:333-352. [PMID: 24403247 DOI: 10.1002/mas.21414] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 09/12/2013] [Accepted: 09/25/2013] [Indexed: 06/03/2023]
Abstract
The Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer intricately couples advanced physics, instrumentation, and electronics with chemical and particularly biochemical research. However, general understanding of the data processing methodologies used lags instrumentation, and most data processing algorithms we are familiar with in FT-ICR are not well studied; thus, professional skill and training in FT-ICR operation and data analysis is still the key to achieve high performance in FT-ICR. This review article is focused on FT-ICR data processing, and explains the procedures step-by-step for users with the goal of maximizing spectral features, such as mass accuracy, resolving power, dynamic range, and detection limits.
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Affiliation(s)
- Yulin Qi
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
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45
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Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, Wood WW, El Masri M, Westphall MS, Gasch AP, Coon JJ. NeuCode labels for relative protein quantification. Mol Cell Proteomics 2014; 13:2503-12. [PMID: 24938287 DOI: 10.1074/mcp.m114.040287] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We describe a synthesis strategy for the preparation of lysine isotopologues that differ in mass by as little as 6 mDa. We demonstrate that incorporation of these molecules into the proteomes of actively growing cells does not affect cellular proliferation, and we discuss how to use the embedded mass signatures (neutron encoding (NeuCode)) for multiplexed proteome quantification by means of high-resolution mass spectrometry. NeuCode SILAC amalgamates the quantitative accuracy of SILAC with the multiplexing of isobaric tags and, in doing so, offers up new opportunities for biological investigation. We applied NeuCode SILAC to examine the relationship between transcript and protein levels in yeast cells responding to environmental stress. Finally, we monitored the time-resolved responses of five signaling mutants in a single 18-plex experiment.
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Affiliation(s)
- Anna E Merrill
- From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; §Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Alexander S Hebert
- From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | | | - Christopher M Rose
- From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; §Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Derek J Bailey
- From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Joel C Bradley
- ‖Cambridge Isotope Laboratories, Andover, Massachusetts 01810
| | - William W Wood
- ‖Cambridge Isotope Laboratories, Andover, Massachusetts 01810
| | - Marwan El Masri
- ‖Cambridge Isotope Laboratories, Andover, Massachusetts 01810
| | - Michael S Westphall
- From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Audrey P Gasch
- From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; ¶Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Joshua J Coon
- From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; §Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; **Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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46
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Popov IA, Nagornov K, Vladimirov GN, Kostyukevich YI, Nikolaev EN. Twelve million resolving power on 4.7 T Fourier transform ion cyclotron resonance instrument with dynamically harmonized cell--observation of fine structure in peptide mass spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:790-799. [PMID: 24604470 DOI: 10.1007/s13361-014-0846-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/28/2014] [Accepted: 01/28/2014] [Indexed: 06/03/2023]
Abstract
Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T magnet using a dynamically harmonized Fourier transform ion cyclotron resonance (FT ICR) cell. Mass spectra of the fine structure of the isotopic distribution of a peptide were obtained and strong discrimination of small intensity peaks was observed in case of resonance excitation of the ions of the whole isotopic cluster to the same cyclotron radius. The absence of some peaks from the mass spectra of the fine structure was explained basing on results of computer simulations showing strong ion cloud interactions, which cause the coalescence of peaks with m/z close to that of the highest magnitude peak. The way to prevent peak discrimination is to excite ion clouds of different m/z to different cyclotron radii, which was demonstrated and investigated both experimentally and by computer simulations.
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Affiliation(s)
- Igor A Popov
- Talrose Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences, Moscow, Russia
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47
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Hernandez DR, DeBord JD, Ridgeway ME, Kaplan DA, Park MA, Fernandez-Lima F. Ion dynamics in a trapped ion mobility spectrometer. Analyst 2014; 139:1913-21. [PMID: 24571000 PMCID: PMC4144823 DOI: 10.1039/c3an02174b] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the present paper, theoretical simulations and experimental observations are used to describe the ion dynamics in a trapped ion mobility spectrometer. In particular, the ion motion, ion transmission and mobility separation are discussed as a function of the bath gas velocity, radial confinement, analysis time and speed. Mobility analysis and calibration procedure are reported for the case of sphere-like molecules for positive and negative ion modes. Results showed that a maximal mobility resolution can be achieved by optimizing the gas velocity, radial confinement (RF amplitude) and ramp speed (voltage range and ramp time). The mobility resolution scales with the electric field and gas velocity and R = 100-250 can be routinely obtained at room temperature.
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Affiliation(s)
- Diana Rosa Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. ; Fax: +1 305 348 3772; Tel: +1 305 348 2037
| | - John Daniel DeBord
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. ; Fax: +1 305 348 3772; Tel: +1 305 348 2037
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. ; Fax: +1 305 348 3772; Tel: +1 305 348 2037
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48
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Novotny NR, Capley EN, Stenson AC. Fact or artifact: the representativeness of ESI-MS for complex natural organic mixtures. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:316-26. [PMID: 24719347 DOI: 10.1002/jms.3345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/31/2014] [Accepted: 02/06/2014] [Indexed: 05/06/2023]
Abstract
Because mass spectrometers provide their own dispersion and resolution of analytes, electrospray ionization mass spectrometry (ESI-MS) has become a workhorse for the characterization of complex mixtures from aerosols to crude oil. Unfortunately, ESI mass spectra commonly contain multimers, adducts and fragments. For the characterization of complex mixtures of unknown initial composition, this presents a significant concern. Mixed-multimer formation could potentially lead to results that bare no resemblance to the original mixture. Conversely, ESI-MS has continually reflected subtle differences between natural organic matter mixtures that are in agreement with prediction or theory. Knowing the real limitations of the technique is therefore critical to avoiding both over-interpretation and unwarranted skepticism. Here, data were collected on four mass spectrometers under a battery of conditions. Results indicate that formation of unrepresentative ions cannot entirely be ruled out, but non-covalent multimers do not appear to make a major contribution to typical natural organic matter spectra based on collision-induced dissociation results. Multimers also appear notably reduced when a cooling gas is present in the accumulation region of the mass spectrometer. For less complex mixtures, the choice of spray solvent can make a difference, but generally spectrum cleanliness (i.e. representativeness) comes at the price of increased selectivity.
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Affiliation(s)
- Nicole R Novotny
- Chemistry Department, University of South Alabama, Mobile, AL, 36688, USA
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49
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Ficarro SB, Biagi JM, Wang J, Scotcher J, Koleva RI, Card JD, Adelmant G, He H, Askenazi M, Marshall AG, Young NL, Gray NS, Marto JA. Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:636-650. [PMID: 24496597 PMCID: PMC3971929 DOI: 10.1007/s13361-013-0811-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (1) robust targeting of peptide N-termini and lysyl side chains, (2) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (3) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (4) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da, are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition, we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally, we provide exemplar data that extend the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers.
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Affiliation(s)
- Scott B. Ficarro
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jessica M. Biagi
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Jinhua Wang
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jenna Scotcher
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
| | - Rositsa I. Koleva
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Joseph D. Card
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Guillaume Adelmant
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Huan He
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL
| | - Manor Askenazi
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Israel
| | - Alan G. Marshall
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL
| | - Nicolas L. Young
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
| | - Nathanael S. Gray
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jarrod A. Marto
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
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50
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Catherman AD, Skinner OS, Kelleher NL. Top Down proteomics: facts and perspectives. Biochem Biophys Res Commun 2014; 445:683-93. [PMID: 24556311 PMCID: PMC4103433 DOI: 10.1016/j.bbrc.2014.02.041] [Citation(s) in RCA: 319] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/10/2014] [Indexed: 12/29/2022]
Abstract
The rise of the "Top Down" method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious "inference" problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.
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Affiliation(s)
- Adam D Catherman
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Owen S Skinner
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States.
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