251
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Garimella SVB, Hamid AM, Deng L, Ibrahim YM, Webb IK, Baker ES, Prost SA, Norheim RV, Anderson GA, Smith RD. Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming. Anal Chem 2016; 88:11877-11885. [PMID: 27934097 PMCID: PMC5470847 DOI: 10.1021/acs.analchem.6b03660] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this work we report an approach for spatial and temporal gas-phase ion population manipulation, wherein we collapse ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS). We do this for ions moving from a conventional traveling wave (TW)-driven region to a region where the TW is intermittently halted or "stuttered". This approach causes the ion packets spanning a number of TW-created traveling traps (TT) to be redistributed into fewer TT, resulting in spatial compression. The degree of spatial compression is controllable and determined by the ratio of stationary time of the TW in the second region to its moving time. This compression ratio ion mobility programming (CRIMP) approach has been implemented using "structures for lossless ion manipulations" (SLIM) in conjunction with MS. CRIMP with the SLIM-MS platform is shown to provide increased peak intensities, reduced peak widths, and improved signal-to-noise (S/N) ratios with MS detection. CRIMP also provides a foundation for extremely long path length and multipass IM separations in SLIM providing greatly enhanced IM resolution by reducing the detrimental effects of diffusional peak broadening and increasing peak widths.
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Affiliation(s)
| | | | | | - Yehia M. Ibrahim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ian K. Webb
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin S. Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Spencer A. Prost
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Randolph V. Norheim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | - Richard D. Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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252
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McMahon WP, Subramanian A, Minardi CS, Dalvi R, Jorabchi K. Pulsed Nano-ESI Atmospheric-Pressure Ion Mobility Mass Spectrometry with Enhanced Ion Sampling. Anal Chem 2016; 88:11767-11773. [PMID: 27782389 DOI: 10.1021/acs.analchem.6b03395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) has gained considerable attention for detection of clusters and weakly bound species created by electrospray ionization (ESI). Atmospheric-pressure (AP) IM-MS offers an advantage in these studies compared to its low-pressure counterpart, owing to soft introduction of ions into the mobility cell with minimal ion activation. Here, we report new approaches to improve the sensitivity and soft ion introduction in AP-IM-MS. For the former, we demonstrate enhanced aerodynamic sampling of ions from the mobility cell into the MS using pulsed-field sampling. In this approach, ions are driven toward the MS, and the field is shut down once the ions reach the vicinity of the MS inlet orifice. The pulsed-field operation provides arrival times without the need for an exit ion gate in the mobility cell and leads to improvements in sensitivity of up to 1 order of magnitude. For soft ion generation, we report a pulsed nano-ESI source to introduce a packet of ions into the room-temperature mobility cell without induced desolvation. Further, we demonstrate the application of the pulsed nano-ESI AP-IM-MS with enhanced ion sampling for detection of solvent clusters of amines and peptide aggregates.
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Affiliation(s)
- William P McMahon
- Department of Chemistry, Georgetown University , Washington DC 20057, United States
| | - Arjuna Subramanian
- Department of Chemistry, Georgetown University , Washington DC 20057, United States
| | - Carina S Minardi
- Department of Chemistry, Georgetown University , Washington DC 20057, United States
| | - Rohan Dalvi
- Department of Chemistry, Georgetown University , Washington DC 20057, United States
| | - Kaveh Jorabchi
- Department of Chemistry, Georgetown University , Washington DC 20057, United States
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253
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Allen SJ, Bush MF. Radio-Frequency (rf) Confinement in Ion Mobility Spectrometry: Apparent Mobilities and Effective Temperatures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2054-2063. [PMID: 27582119 DOI: 10.1007/s13361-016-1479-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Ion mobility is a powerful tool for separating and characterizing the structures of ions. Here, a radio-frequency (rf) confining drift cell is used to evaluate the drift times of ions over a broad range of drift field strengths (E/P, V cm-1 Torr-1). The presence of rf potentials radially confines ions and results in excellent ion transmission at low E/P (less than 1 V cm-1 Torr-1), thereby reducing the dependence of ion transmission on the applied drift voltage. Non-linear responses between drift time and reciprocal drift voltages are observed for extremely low E/P and high rf amplitudes. Under these conditions, pseudopotential wells generated by the rf potentials dampen the mobility of ions. The effective potential approximation is used to characterize this mobility dampening behavior, which can be mitigated by adjusting rf amplitudes and electrode dimensions. Using SIMION trajectories and statistical arguments, the effective temperatures of ions in an rf-confining drift cell are evaluated. Results for the doubly charged peptide GRGDS suggest that applied rf potentials can result in a subtle increase (2 K) in effective temperature compared to an electrostatic drift tube. Additionally, simulations of native-like ions of the protein complex avidin suggest that rf potentials have a negligible effect on the effective temperature of these ions. In general, the results of this study suggest that applied rf potentials enable the measurement of drift times at extremely low E/P and that these potentials have negligible effects on ion effective temperature. Graphical Abstract ᅟ.
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Affiliation(s)
- Samuel J Allen
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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254
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Ion mobility spectrometry: Current status and application for chemical warfare agents detection. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.06.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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255
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Regueiro J, Negreira N, Berntssen MHG. Ion-Mobility-Derived Collision Cross Section as an Additional Identification Point for Multiresidue Screening of Pesticides in Fish Feed. Anal Chem 2016; 88:11169-11177. [PMID: 27779869 DOI: 10.1021/acs.analchem.6b03381] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ion mobility spectrometry allows for the measurement of the collision cross section (CCS), which provides information about the shape of an ionic molecule in the gas phase. Although the hyphenation of traveling-wave ion mobility spectrometry (TWIMS) with high-resolution quadrupole time-of-flight mass spectrometry (QTOFMS) has been mainly used for structural elucidation purposes, its potential for fast screening of small molecules in complex samples has not yet been thoroughly evaluated. The current work explores the capabilities of ultrahigh-performance liquid chromatography (UHPLC) coupled to a new design TWIMS-QTOFMS for the screening and identification of a large set of pesticides in complex salmon feed matrices. A database containing TWIMS-derived CCS values for more than 200 pesticides is hereby presented. CCS measurements showed high intra- and interday repeatability (RSD < 1%), and they were not affected by the complexity of the investigated matrices (ΔCCS ≤ 1.8%). The use of TWIMS in combination with QTOFMS was demonstrated to provide an extra-dimension, which resulted in increased peak capacity and selectivity in real samples. Thus, many false-positive detections could be straightforwardly discarded just by applying a maximum ΔCCS tolerance of ±2%. CCS was proposed as a valuable additional identification point in the pesticides screening workflow. Several commercial fish feed samples were finally analyzed to demonstrate the applicability of the proposed approach. Ethoxyquin and pirimiphos-methyl were identified in most of the analyzed samples, whereas tebuconazole and piperonil butoxide were identified for the first time in fish feed samples.
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Affiliation(s)
- Jorge Regueiro
- National Institute of Nutrition and Seafood Research (NIFES), P.O. Box 2029 Nordnes, N-5817 Bergen, Norway
| | - Noelia Negreira
- National Institute of Nutrition and Seafood Research (NIFES), P.O. Box 2029 Nordnes, N-5817 Bergen, Norway
| | - Marc H G Berntssen
- National Institute of Nutrition and Seafood Research (NIFES), P.O. Box 2029 Nordnes, N-5817 Bergen, Norway
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256
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Zhou Z, Shen X, Tu J, Zhu ZJ. Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry. Anal Chem 2016; 88:11084-11091. [DOI: 10.1021/acs.analchem.6b03091] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhiwei Zhou
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
| | - Xiaotao Shen
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
| | - Jia Tu
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
| | - Zheng-Jiang Zhu
- Interdisciplinary
Research
Center on Biology and Chemistry and Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 P. R. China
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257
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Harper B, Neumann EK, Stow SM, May JC, McLean JA, Solouki T. Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution. Anal Chim Acta 2016; 939:64-72. [PMID: 27639144 PMCID: PMC5744691 DOI: 10.1016/j.aca.2016.07.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 01/23/2023]
Abstract
Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810-1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) "shift factors" to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.8 Å(2), 295.1 Å(2), 296.8 Å(2), and 300.1 Å(2); all four of these CCS values were within 1.5% of independently measured DTIM-MS values.
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Affiliation(s)
- Brett Harper
- Institute of Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - Elizabeth K Neumann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Sarah M Stow
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - Jody C May
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA.
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258
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Brantley MR, Pettit ME, Harper B, Brown B, Solouki T. Automated peak width measurements for targeted analysis of ion mobility unresolved species. Anal Chim Acta 2016; 941:49-60. [DOI: 10.1016/j.aca.2016.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/09/2016] [Indexed: 12/11/2022]
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259
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Ortmayr K, Causon TJ, Hann S, Koellensperger G. Increasing selectivity and coverage in LC-MS based metabolome analysis. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.06.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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260
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Stephan S, Hippler J, Köhler T, Deeb AA, Schmidt TC, Schmitz OJ. Contaminant screening of wastewater with HPLC-IM-qTOF-MS and LC+LC-IM-qTOF-MS using a CCS database. Anal Bioanal Chem 2016; 408:6545-55. [PMID: 27497965 DOI: 10.1007/s00216-016-9820-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/11/2016] [Accepted: 07/20/2016] [Indexed: 12/30/2022]
Abstract
Non-target analysis has become an important tool in the field of water analysis since a broad variety of pollutants from different sources are released to the water cycle. For identification of compounds in such complex samples, liquid chromatography coupled to high resolution mass spectrometry are often used. The introduction of ion mobility spectrometry provides an additional separation dimension and allows determining collision cross sections (CCS) of the analytes as a further physicochemical constant supporting the identification. A CCS database with more than 500 standard substances including drug-like compounds and pesticides was used for CCS data base search in this work. A non-target analysis of a wastewater sample was initially performed with high performance liquid chromatography (HPLC) coupled to an ion mobility-quadrupole-time of flight mass spectrometer (IM-qTOF-MS). A database search including exact mass (±5 ppm) and CCS (±1 %) delivered 22 different compounds. Furthermore, the same sample was analyzed with a two-dimensional LC method, called LC+LC, developed in our group for the coupling to IM-qTOF-MS. This four dimensional separation platform revealed 53 different compounds, identified over exact mass and CCS, in the examined wastewater sample. It is demonstrated that the CCS database can also help to distinguish between isobaric structures exemplified for cyclophosphamide and ifosfamide. Graphical Abstract Scheme of sample analysis and database screening.
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Affiliation(s)
- Susanne Stephan
- Applied Analytical Chemistry, University of Duisburg-Essen, Universitaetsstr. 5, 45141, Essen, Germany
| | - Joerg Hippler
- Applied Analytical Chemistry, University of Duisburg-Essen, Universitaetsstr. 5, 45141, Essen, Germany
| | - Timo Köhler
- Applied Analytical Chemistry, University of Duisburg-Essen, Universitaetsstr. 5, 45141, Essen, Germany
| | - Ahmad A Deeb
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitaetsstr. 5, 45141, Essen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitaetsstr. 5, 45141, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitaetsstr. 2, 45141, Essen, Germany
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Universitaetsstr. 5, 45141, Essen, Germany.
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261
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Bliss E, Heywood WE, Benatti M, Sebire NJ, Mills K. An optimised method for the proteomic profiling of full thickness human skin. Biol Proced Online 2016; 18:15. [PMID: 27445641 PMCID: PMC4955162 DOI: 10.1186/s12575-016-0045-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/24/2016] [Indexed: 12/23/2022] Open
Abstract
Background The skin is the largest organ of the human body and is the first line barrier defence against trauma, microbial infiltration and radiation. Skin diseases can be a result of multi-systemic disease or an isolated condition. Due to its proteolysis resistant properties there are relatively few human skin proteomic datasets published compared with other human organs or body fluids. Skin is a challenging tissue to analyse using traditional proteomic techniques due to its high lipid content, insolubility and extensive cross-linking of proteins. This can complicate the isolation and digestion of proteins for analysis using mass spectrometry techniques. Results We have optimised a sample preparation procedure to improve solubilisation and mass spectral compatibility of full thickness skin samples. Using this technique, we were able to obtain data for the proteome profile of full thickness human skin using on-line two-dimensional liquid chromatography, followed by ultra-high definition label-free mass spectrometry analysis (UDMSE). We were able to identify in excess of 2000 proteins from a full thickness skin sample. Conclusions The adoption of on-line fractionation and optimised acquisition protocols utilising ion mobility separation (IMS) technology has significantly increased the scope for protein identifications ten-fold. Electronic supplementary material The online version of this article (doi:10.1186/s12575-016-0045-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emily Bliss
- Centre for Translational Omics, UCL Institute of Child Health, 30 Guilford Street, London, WC1N 1EH UK
| | - Wendy E Heywood
- Centre for Translational Omics, UCL Institute of Child Health, 30 Guilford Street, London, WC1N 1EH UK
| | - Malika Benatti
- Histopathology Department, Great Ormond Street Hospital, London, WC1N 3JH UK
| | - Neil J Sebire
- Histopathology Department, Great Ormond Street Hospital, London, WC1N 3JH UK
| | - Kevin Mills
- Centre for Translational Omics, UCL Institute of Child Health, 30 Guilford Street, London, WC1N 1EH UK
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262
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Hines K, May JC, McLean JA, Xu L. Evaluation of Collision Cross Section Calibrants for Structural Analysis of Lipids by Traveling Wave Ion Mobility-Mass Spectrometry. Anal Chem 2016; 88:7329-36. [PMID: 27321977 PMCID: PMC4955523 DOI: 10.1021/acs.analchem.6b01728] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/18/2016] [Indexed: 02/07/2023]
Abstract
Collision cross section (CCS) measurement of lipids using traveling wave ion mobility-mass spectrometry (TWIM-MS) is of high interest to the lipidomics field. However, currently available calibrants for CCS measurement using TWIM are predominantly peptides that display quite different physical properties and gas-phase conformations from lipids, which could lead to large CCS calibration errors for lipids. Here we report the direct CCS measurement of a series of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) in nitrogen using a drift tube ion mobility (DTIM) instrument and an evaluation of the accuracy and reproducibility of PCs and PEs as CCS calibrants for phospholipids against different classes of calibrants, including polyalanine (PolyAla), tetraalkylammonium salts (TAA), and hexakis(fluoroalkoxy)phosphazines (HFAP), in both positive and negative modes in TWIM-MS analysis. We demonstrate that structurally mismatched calibrants lead to larger errors in calibrated CCS values while the structurally matched calibrants, PCs and PEs, gave highly accurate and reproducible CCS values at different traveling wave parameters. Using the lipid calibrants, the majority of the CCS values of several classes of phospholipids measured by TWIM are within 2% error of the CCS values measured by DTIM. The development of phospholipid CCS calibrants will enable high-accuracy structural studies of lipids and add an additional level of validation in the assignment of identifications in untargeted lipidomics experiments.
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Affiliation(s)
- Kelly
M. Hines
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jody C. May
- Department
of Chemistry, Center for Innovative Technology, Vanderbilt Institute
of Chemical Biology, Vanderbilt Institute for Integrative Biosystems
Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department
of Chemistry, Center for Innovative Technology, Vanderbilt Institute
of Chemical Biology, Vanderbilt Institute for Integrative Biosystems
Research and Education, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Libin Xu
- Department
of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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263
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Deng L, Ibrahim YM, Baker ES, Aly NA, Hamid AM, Zhang X, Zheng X, Garimella SVB, Webb IK, Prost SA, Sandoval JA, Norheim RV, Anderson GA, Tolmachev AV, Smith RD. Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry. ChemistrySelect 2016; 1:2396-2399. [PMID: 28936476 DOI: 10.1002/slct.201600460] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mass spectrometry (MS)-based multi-omic measurements, including proteomics, metabolomics, lipidomics, and glycomics, are increasingly transforming our ability to characterize and understand biological systems. Multi-omic analyses and the desire for comprehensive measurement coverage presently have limitations due to the chemical diversity and range of abundances of biomolecules in complex samples. Advances addressing these challenges increasingly are based upon the ability to quickly separate, react and otherwise manipulate sample components for analysis by MS. Here we report on a new approach using Structures for Lossless Ion Manipulations (SLIM) to enable long serpentine path ion mobility spectrometry (IMS) separations followed by MS analyses. This approach provides previously unachieved resolution for biomolecular species, in conjunction with more effective ion utilization, and a basis for greatly improved characterization of very small sample sizes.
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Affiliation(s)
- Liulin Deng
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Yehia M Ibrahim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Erin S Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Noor A Aly
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Ahmed M Hamid
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Xing Zhang
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Xueyun Zheng
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Sandilya V B Garimella
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Ian K Webb
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Spencer A Prost
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Jeremy A Sandoval
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Randolph V Norheim
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Gordon A Anderson
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Aleksey V Tolmachev
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352 (USA)
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264
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May JC, McLean JA. Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:387-409. [PMID: 27306312 PMCID: PMC5763907 DOI: 10.1146/annurev-anchem-071015-041734] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Hybrid analytical instrumentation constructed around mass spectrometry (MS) is becoming the preferred technique for addressing many grand challenges in science and medicine. From the omics sciences to drug discovery and synthetic biology, multidimensional separations based on MS provide the high peak capacity and high measurement throughput necessary to obtain large-scale measurements used to infer systems-level information. In this article, we describe multidimensional MS configurations as technologies that are big data drivers and review some new and emerging strategies for mining information from large-scale datasets. We discuss the information content that can be obtained from individual dimensions, as well as the unique information that can be derived by comparing different levels of data. Finally, we summarize some emerging data visualization strategies that seek to make highly dimensional datasets both accessible and comprehensible.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235;
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee 37235;
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265
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Hutson MS, Alexander PG, Allwardt V, Aronoff DM, Bruner-Tran KL, Cliffel DE, Davidson JM, Gough A, Markov DA, McCawley LJ, McKenzie JR, McLean JA, Osteen KG, Pensabene V, Samson PC, Senutovitch NK, Sherrod SD, Shotwell MS, Taylor DL, Tetz LM, Tuan RS, Vernetti LA, Wikswo JP. Organs-on-Chips as Bridges for Predictive Toxicology. ACTA ACUST UNITED AC 2016. [DOI: 10.1089/aivt.2016.0003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M. Shane Hutson
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Physics & Astronomy, Vanderbilt University, Nashville, Tennessee
| | - Peter G. Alexander
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Vanessa Allwardt
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
| | - David M. Aronoff
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kaylon L. Bruner-Tran
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Obstetrics & Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David E. Cliffel
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Jeffrey M. Davidson
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
- Research Service, Department of Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Albert Gough
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Dmitry A. Markov
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lisa J. McCawley
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jennifer R. McKenzie
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - John A. McLean
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Kevin G. Osteen
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Obstetrics & Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
- Research Service, Department of Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Virginia Pensabene
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Philip C. Samson
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Physics & Astronomy, Vanderbilt University, Nashville, Tennessee
| | - Nina K. Senutovitch
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Stacy D. Sherrod
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Matthew S. Shotwell
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee
| | - D. Lansing Taylor
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lauren M. Tetz
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rocky S. Tuan
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Orthopaedic Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Department of Bioengineering, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Center for Cellular and Molecular Engineering, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Center for Military Medicine Research, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Lawrence A. Vernetti
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - John P. Wikswo
- Vanderbilt-Pittsburgh Resource for Organotypic Models for Predictive Toxicology, Vanderbilt University, Nashville, Tennessee, and University of Pittsburgh, Pittsburgh, Pennsylvania
- Vanderbilt Institute for Integrative Biosystems Research & Education, Vanderbilt University, Nashville, Tennessee
- Department of Physics & Astronomy, Vanderbilt University, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Molecular Physiology & Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee
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266
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Garimella SVB, Ibrahim YM, Tang K, Webb IK, Baker ES, Tolmachev AV, Chen TC, Anderson GA, Smith RD. Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1128-35. [PMID: 27052738 PMCID: PMC4955798 DOI: 10.1007/s13361-016-1371-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 05/13/2023]
Abstract
A novel concept for ion spatial peak compression is described, and discussed primarily in the context of ion mobility spectrometry (IMS). Using theoretical and numerical methods, the effects of using non-constant (e.g., linearly varying) electric fields on ion distributions (e.g., an ion mobility peak) is evaluated both in the physical and temporal domains. The application of a linearly decreasing electric field in conjunction with conventional drift field arrangements is shown to lead to a reduction in IMS physical peak width. When multiple ion packets (i.e., peaks) in a selected mobility window are simultaneously subjected to such fields, there is ion packet compression (i.e., a reduction in peak widths for all species). This peak compression occurs with only a modest reduction of resolution, which can be quickly recovered as ions drift in a constant field after the compression event. Compression also yields a significant increase in peak intensities. Ion mobility peak compression can be particularly useful for mitigating diffusion-driven peak broadening over very long path length separations (e.g., in cyclic multi-pass arrangements), and for achieving higher S/N and IMS resolution over a selected mobility range. Graphical Abstract ᅟ.
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Affiliation(s)
- Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ian K Webb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Aleksey V Tolmachev
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tsung-Chi Chen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Gordon A Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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267
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May JC, Gant-Branum RL, McLean JA. Targeting the untargeted in molecular phenomics with structurally-selective ion mobility-mass spectrometry. Curr Opin Biotechnol 2016; 39:192-197. [PMID: 27132126 DOI: 10.1016/j.copbio.2016.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/06/2016] [Accepted: 04/13/2016] [Indexed: 12/25/2022]
Abstract
Systems-wide molecular phenomics is rapidly expanding through technological advances in instrumentation and bioinformatics. Strategies such as structural mass spectrometry, which utilizes size and shape measurements with molecular weight, serve to characterize the sum of molecular expression in biological contexts, where broad-scale measurements are made that are interpreted through big data statistical techniques to reveal underlying patterns corresponding to phenotype. The data density, data dimensionality, data projection, and data interrogation are all critical aspects of these approaches to turn data into salient information. Untargeted molecular phenomics is already having a dramatic impact in discovery science from drug discovery to synthetic biology. It is evident that these emerging techniques will integrate closely in broad efforts aimed at precision medicine.
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Affiliation(s)
- Jody Christopher May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Randi Lee Gant-Branum
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - John Allen McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA.
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268
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A novel four-dimensional analytical approach for analysis of complex samples. Anal Bioanal Chem 2016; 408:3751-9. [DOI: 10.1007/s00216-016-9460-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 12/28/2022]
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269
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Xiao X, Miller LL, Bernstein R, Hochrein JM. Thermal degradation of β-carotene studied by ion mobility atmospheric solid analysis probe mass spectrometry: full product pattern and selective ionization enhancement. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:309-314. [PMID: 27041662 DOI: 10.1002/jms.3755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
Atmospheric solid analysis probe mass spectrometry has the capability of capturing full product patterns simultaneously including both volatile and semi-volatile compounds produced at elevated temperatures. Real-time low-energy collision-induced fragmentation combined with ion mobility separations enables rapid identification of the chemical structures of products. We present here for the first time the recognition of full product patterns resulting from the thermal degradation of β-carotene at temperatures up to 600 °C. Solvent vapor-induced ionization enhancement is observed, which reveals parallel thermal dissociation processes that lead to even- and odd-numbered mass products. The drift-time distributions of high mass products, along with β-carotene, were monitored with temperature, showing multiple conformations that are associated with the presence of two β-rings. Products of masses 346/347, however, show a single conformation distribution, which indicates the separation of two β-rings resulting from the direct bond scission at the polyene hydrocarbon chain. The thermal degradation pathways are evaluated and discussed.
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Affiliation(s)
- Xiaoyin Xiao
- Sandia National Laboratories, Albuquerque, NM, USA
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270
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Silveira JA, Michelmann K, Ridgeway ME, Park MA. Fundamentals of Trapped Ion Mobility Spectrometry Part II: Fluid Dynamics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:585-595. [PMID: 26864793 DOI: 10.1007/s13361-015-1310-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 06/05/2023]
Abstract
Trapped ion mobility spectrometry (TIMS) is a new high resolution (R up to ~300) separation technique that utilizes an electric field to hold ions stationary against a moving gas. Recently, an analytical model for TIMS was derived and, in part, experimentally verified. A central, but not yet fully explored, component of the model involves the fluid dynamics at work. The present study characterizes the fluid dynamics in TIMS using simulations and ion mobility experiments. Results indicate that subsonic laminar flow develops in the analyzer, with pressure-dependent gas velocities between ~120 and 170 m/s measured at the position of ion elution. One of the key philosophical questions addressed is: how can mobility be measured in a dynamic system wherein the gas is expanding and its velocity is changing? We noted previously that the analytically useful work is primarily done on ions as they traverse the electric field gradient plateau in the analyzer. In the present work, we show that the position-dependent change in gas velocity on the plateau is balanced by a change in pressure and temperature, ultimately resulting in near position-independent drag force. That the drag force, and related variables, are nearly constant allows for the use of relatively simple equations to describe TIMS behavior. Nonetheless, we derive a more comprehensive model, which accounts for the spatial dependence of the flow variables. Experimental resolving power trends were found to be in close agreement with the theoretical dependence of the drag force, thus validating another principal component of TIMS theory.
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Affiliation(s)
| | | | - Mark E Ridgeway
- Bruker Daltonics, 40 Manning Road, Billerica, MA, 01821, USA
| | - Melvin A Park
- Bruker Daltonics, 40 Manning Road, Billerica, MA, 01821, USA.
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271
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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272
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Khakinejad M, Kondalaji SG, Donohoe GC, Valentine SJ. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:451-61. [PMID: 26802030 PMCID: PMC4814291 DOI: 10.1007/s13361-015-1304-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 05/17/2023]
Abstract
Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H](2-) ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H](3-) ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H](2-) ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H](3-) ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.
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Affiliation(s)
- Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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273
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Khakinejad M, Kondalaji SG, Donohoe GC, Valentine SJ. Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 3. Estimating Surface Area Exposure by Deuterium Uptake. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:462-73. [PMID: 26620531 PMCID: PMC4872623 DOI: 10.1007/s13361-015-1305-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 05/17/2023]
Abstract
Gas-phase hydrogen deuterium exchange (HDX), collision cross section (CCS) measurement, and molecular dynamics simulation (MDS) techniques were utilized to develop and compare three methods for estimating the relative surface area exposure of separate peptide chains within bovine insulin ions. Electrosprayed [M - 3H](3-) and [M - 5H](5-) insulin ions produced a single conformer type with respective collision cross sections of 528 ± 5 Å(2) and 808 ± 2 Å(2). [M - 4H](4-) ions were comprised of more compact (Ω = 676 ± 3 Å(2)) and diffuse (i.e., more elongated, Ω = 779 ± 3 Å(2)) ion conformer types. Ions were subjected to HDX in the drift tube using D2O as the reagent gas. Collision-induced dissociation was used to fragment mobility-selected, isotopically labeled [M - 4H](4-) and [M - 5H](5-) ions into the protein subchains. Deuterium uptake levels of each chain can be explained by limited inter-chain isotopic scrambling upon collisional activation. Using nominal ion structures from MDS and a hydrogen accessibility model, the deuterium uptake for each chain was correlated to its exposed surface area. In separate experiments, the per-residue deuterium content for the protonated and deprotonated ions of the synthetic peptide KKDDDDDIIKIIK were compared. The differences in deuterium content indicated the regional HDX accessibility for cations versus anions. Using ions of similar conformational type, this comparison highlights the complementary nature of HDX data obtained from positive- and negative-ion analysis.
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Affiliation(s)
- Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | - Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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274
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Nassar AF, Williams BJ, Yaworksy DC, Patel V, Rusling JF. Rapid label-free profiling of oral cancer biomarker proteins using nano-UPLC-Q-TOF ion mobility mass spectrometry. Proteomics Clin Appl 2016; 10:280-9. [DOI: 10.1002/prca.201500025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/19/2015] [Accepted: 12/09/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Ala. F. Nassar
- Department of Internal Medicine, School of Medicine; Yale University; New Haven CT USA
- Department of Chemistry; University of Connecticut; Storrs CT USA
| | | | | | - Vyomesh Patel
- Cancer Research Initiatives Foundation (CARF); Sime Darby Medical Centre; Subang Jaya Malaysia
| | - James F. Rusling
- Department of Chemistry; University of Connecticut; Storrs CT USA
- Neag Comprehensive Cancer Center; University of Connecticut Health Center; Farmington CT USA
- Department of Cell Biology; University of Connecticut Health Center; Farmington CT USA
- Institute of Material Science; University of Connecticut; Storrs CT USA
- School of Chemistry; National University of Ireland; Galway Ireland
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275
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Sun Y, Vahidi S, Sowole MA, Konermann L. Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:31-40. [PMID: 26369778 DOI: 10.1007/s13361-015-1244-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
The question whether electrosprayed protein ions retain solution-like conformations continues to be a matter of debate. One way to address this issue involves comparisons of collision cross sections (Ω) measured by ion mobility spectrometry (IMS) with Ω values calculated for candidate structures. Many investigations in this area employ traveling wave IMS (TWIMS). It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on ubiquitin, cytochrome c, myoglobin, and hemoglobin, we demonstrate that Ω values and collisional unfolding profiles are virtually indistinguishable under both conditions. These findings suggest that gas-phase structures and ion internal energies are independent of the type of electrospray source. We also note that TWIMS calibration can be challenging because differences in the extent of collisional activation relative to drift tube reference data may lead to ambiguous peak assignments. It is demonstrated that this problem can be circumvented by employing collisionally heated calibrant ions. Overall, our data are consistent with the view that exposure of native proteins to electrospray conditions can generate kinetically trapped ions that retain solution-like structures on the millisecond time scale of TWIMS experiments. ᅟ
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Affiliation(s)
- Yu Sun
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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276
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Szymańska E, Davies AN, Buydens LMC. Chemometrics for ion mobility spectrometry data: recent advances and future prospects. Analyst 2016; 141:5689-5708. [DOI: 10.1039/c6an01008c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This is the first comprehensive review on chemometric techniques used in ion mobility spectrometry data analysis.
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Affiliation(s)
- Ewa Szymańska
- Radboud University
- Institute for Molecules and Materials
- 6500 GL Nijmegen
- The Netherlands
- TI-COAST
| | - Antony N. Davies
- School of Applied Sciences
- Faculty of Computing
- Engineering and Science
- University of South Wales
- UK
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277
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Rijs NJ, Weiske T, Schlangen M, Schwarz H. Effect of adduct formation with molecular nitrogen on the measured collisional cross sections of transition metal-1,10-phenanthroline complexes in traveling wave ion-mobility spectrometry: N2 is not always an "inert" buffer gas. Anal Chem 2015; 87:9769-76. [PMID: 26378338 DOI: 10.1021/acs.analchem.5b01985] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The number of separations and analyses of molecular species using traveling wave ion-mobility spectrometry-mass spectrometry (TWIMS-MS) is increasing, including those extending the technique to analytes containing metal atoms. A critical aspect of such applications of TWIMS-MS is the validity of the collisional cross sections (CCSs) measured and whether they can be accurately calibrated against other ion-mobility spectrometry (IMS) techniques. Many metal containing species have potential reactivity toward molecular nitrogen, which is present in high concentration in the typical Synapt-G2 TWIMS cell. Here, we analyze the effect of nitrogen on the drift time of a series of cationic 1,10-phenanthroline complexes of the late transition metals, [(phen)M](+), (M = Ni, Pd, Pt, Cu, Ag, Au, Zn, Cd, and Hg) in order to understand potential deviations from expected drift time behaviors. These metal complexes were chosen for their metal open-coordination site and lack of rotameric species. The target species were generated via electrospray ionization (ESI), analyzed using TWIMS in N2 drift gas, and the observed drift time trends compared. Theoretically derived CCSs for all species (via both the projection approximation and trajectory method) were also compared. The results show that, indeed, for metal containing species in this size regime, reaction with molecular nitrogen has a dramatic effect on measured drift times and must not be ignored when comparing and interpreting TWIMS arrival time distributions. Density-functional theory (DFT) calculations are employed to analyze the periodic differences due to the metal's interaction with nitrogen (and background water) in detail.
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Affiliation(s)
- Nicole J Rijs
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Thomas Weiske
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
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278
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Song Y, Nelp M, Bandarian V, Wysocki VH. Refining the Structural Model of a Heterohexameric Protein Complex: Surface Induced Dissociation and Ion Mobility Provide Key Connectivity and Topology Information. ACS CENTRAL SCIENCE 2015; 1:477-487. [PMID: 26744735 PMCID: PMC4690985 DOI: 10.1021/acscentsci.5b00251] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 05/21/2023]
Abstract
Toyocamycin nitrile hydratase (TNH) is a protein hexamer that catalyzes the hydration of toyocamycin to produce sangivamycin. The structure of hexameric TNH and the arrangement of subunits within the complex, however, have not been solved by NMR or X-ray crystallography. Native mass spectrometry (MS) clearly shows that TNH is composed of two copies each of the α, β, and γ subunits. Previous surface induced dissociation (SID) tandem mass spectrometry on a quadrupole time-of-flight (QTOF) platform suggests that the TNH hexamer is a dimer composed of two αβγ trimers; furthermore, the results suggest that α-β interact most strongly (Blackwell et al. Anal. Chem. 2011, 83, 2862-2865). Here, multiple complementary MS based approaches and homology modeling have been applied to refine the structure of TNH. Solution-phase organic solvent disruption coupled with native MS agrees with the previous SID results. By coupling surface induced dissociation with ion mobility mass spectrometry (SID/IM), further information on the intersubunit contacts and relative interfacial strengths are obtained. The results show that TNH is a dimer of αβγ trimers, that within the trimer the α, β subunits bind most strongly, and that the primary contact between the two trimers is through a γ-γ interface. Collisional cross sections (CCSs) measured from IM experiments are used as constraints for postulating the arrangement of the subunits represented by coarse-grained spheres. Covalent labeling (surface mapping) together with protein complex homology modeling and docking of trimers to form hexamer are utilized with all the above information to propose the likely quaternary structure of TNH, with chemical cross-linking providing cross-links consistent with the proposed structure. The novel feature of this approach is the use of SID-MS with ion mobility to define complete connectivity and relative interfacial areas of a heterohexameric protein complex, providing much more information than is available from solution disruption. That information, when combined with CCS-guided coarse-grained modeling and covalent labeling restraints for homology modeling and trimer-trimer docking, provides atomic models of a previously uncharacterized heterohexameric protein complex.
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Affiliation(s)
- Yang Song
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Micah
T. Nelp
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721, United
States
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department
of Chemistry and Biochemistry, The University
of Arizona, Tucson, Arizona 85721, United
States
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
- Address: 260 Biomedical Research
Tower, 460 West 12th Avenue, Columbus, OH 43210, USA. Phone: 614-292-8687. E-mail:
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279
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Cajka T, Fiehn O. Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics. Anal Chem 2015; 88:524-45. [PMID: 26637011 DOI: 10.1021/acs.analchem.5b04491] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomas Cajka
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States
| | - Oliver Fiehn
- UC Davis Genome Center-Metabolomics, University of California Davis , 451 Health Sciences Drive, Davis, California 95616, United States.,King Abdulaziz University , Faculty of Science, Biochemistry Department, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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280
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Meier F, Beck S, Grassl N, Lubeck M, Park MA, Raether O, Mann M. Parallel Accumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device. J Proteome Res 2015; 14:5378-87. [PMID: 26538118 DOI: 10.1021/acs.jproteome.5b00932] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In liquid chromatography-mass spectrometry (LC-MS)-based proteomics, many precursors elute from the column simultaneously. In data-dependent analyses, these precursors are fragmented one at a time, whereas the others are discarded entirely. Here we employ trapped ion mobility spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF) mass spectrometer to remove this limitation. In TIMS, all precursor ions are accumulated in parallel and released sequentially as a function of their ion mobility. Instead of selecting a single precursor mass with the quadrupole mass filter, we here implement synchronized scans in which the quadrupole is mass positioned with sub-millisecond switching times at the m/z values of appropriate precursors, such as those derived from a topN precursor list. We demonstrate serial selection and fragmentation of multiple precursors in single 50 ms TIMS scans. Parallel accumulation-serial fragmentation (PASEF) enables hundreds of MS/MS events per second at full sensitivity. Modeling the effect of such synchronized scans for shotgun proteomics, we estimate that about a 10-fold gain in sequencing speed should be achievable by PASEF without a decrease in sensitivity.
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Affiliation(s)
- Florian Meier
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Scarlet Beck
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Niklas Grassl
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Markus Lubeck
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Melvin A Park
- Bruker Daltonics Inc., 40 Manning Road, Billerica, Massachusetts 01821, United States
| | - Oliver Raether
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
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281
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May JC, Dodds JN, Kurulugama RT, Stafford GC, Fjeldsted JC, McLean JA. Broadscale resolving power performance of a high precision uniform field ion mobility-mass spectrometer. Analyst 2015; 140:6824-33. [PMID: 26191544 PMCID: PMC4586486 DOI: 10.1039/c5an00923e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An extensive study of two current ion mobility resolving power theories ("conditional" and "semi-empirical") was undertaken using a recently developed drift tube ion mobility-mass spectrometer. The current study investigates the quantitative agreement between experiment and theory at reduced pressure (4 Torr) for a wide range of initial ion gate widths (100 to 500 μs), and ion mobility values (K0 from 0.50 to 3.0 cm(2) V(-1) s(-1)) representing measurements obtained in helium, nitrogen, and carbon dioxide drift gas. Results suggest that the conditional resolving power theory deviates from experimental results for low mobility ions (e.g., high mass analytes) and for initial ion gate widths beyond 200 μs. A semi-empirical resolving power theory provided close-correlation of predicted resolving powers to experimental results across the full range of mobilities and gate widths investigated. Interpreting the results from the semi-empirical theory, the performance of the current instrumentation was found to be highly linear for a wide range of analytes, with optimal resolving powers being accessible for a narrow range of drift fields between 14 and 17 V cm(-1). While developed using singly-charged ion mobility data, preliminary results suggest that the semi-empirical theory has broader applicability to higher-charge state systems.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Institute for Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235-1822, USA.
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282
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Sherrod SD, McLean JA. Systems-Wide High-Dimensional Data Acquisition and Informatics Using Structural Mass Spectrometry Strategies. Clin Chem 2015; 62:77-83. [PMID: 26453699 DOI: 10.1373/clinchem.2015.238261] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/12/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND Untargeted multiomics data sets are obtained for samples in systems, synthetic, and chemical biology by integrating chromatographic separations with ion mobility-mass spectrometry (IM-MS) analysis. The data sets are interrogated using bioinformatics strategies to organize the data for identification prioritization. CONTENT The use of big data approaches for data mining of massive data sets in systems-wide analyses is presented. Untargeted biological data across multiomics dimensions are obtained using a variety of chromatography strategies with structural MS. Separation timescales for different techniques and the resulting data deluge when combined with IM-MS are presented. Data mining self-organizing map strategies are used to rapidly filter the data, highlighting those features describing uniqueness to the query. Examples are provided in longitudinal analyses in synthetic biology and human liver exposure to acetaminophen, and in chemical biology for natural product discovery from bacterial biomes. CONCLUSIONS Matching the separation timescales of different forms of chromatography with IM-MS provides sufficient multiomics selectivity to perform untargeted systems-wide analyses. New data mining strategies provide a means for rapidly interrogating these data sets for feature prioritization and discovery in a range of applications in systems, synthetic, and chemical biology.
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Affiliation(s)
- Stacy D Sherrod
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN.
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283
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Causon TJ, Hann S. Theoretical evaluation of peak capacity improvements by use of liquid chromatography combined with drift tube ion mobility-mass spectrometry. J Chromatogr A 2015; 1416:47-56. [DOI: 10.1016/j.chroma.2015.09.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/05/2015] [Accepted: 09/03/2015] [Indexed: 10/23/2022]
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284
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Foley CD, Zhang B, Alb AM, Trimpin S, Grayson SM. Use of Ion Mobility Spectrometry-Mass Spectrometry to Elucidate Architectural Dispersity within Star Polymers. ACS Macro Lett 2015; 4:778-782. [PMID: 35596476 DOI: 10.1021/acsmacrolett.5b00299] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The power of ion mobility spectrometry-mass spectrometry (IMS-MS) as an analytical technology for differentiating macromolecular architecture is demonstrated. The presence of architectural dispersity within a sample is probed by sequentially measuring both the drift time and the mass-to-charge ratio for every component within a polymer sample. The utility of this technology is demonstrated by investigating three poly(ethylene glycol) (PEG) architectures with closely related average molecular weights of about 9000 Da: a linear PEG, an unevenly branched miktoarm star PEG, and evenly branched homoarm star PEGs. The three architectures were readily distinguished when analyzed separately as "pure" architectures or when analyzed as mixtures. IMS-MS results are contrasted with matrix-assisted laser desorption/ionization-MS and viscometry measurements.
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Affiliation(s)
- Casey D. Foley
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | | | | | - Sarah Trimpin
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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285
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Donohoe GC, Arndt JR, Valentine SJ. Online deuterium hydrogen exchange and protein digestion coupled with ion mobility spectrometry and tandem mass spectrometry. Anal Chem 2015; 87:5247-54. [PMID: 25893550 DOI: 10.1021/acs.analchem.5b00277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Online deuterium hydrogen exchange (DHX) and pepsin digestion (PD) is demonstrated using drift tube ion mobility spectrometry (DTIMS) coupled with linear ion trap (LTQ) mass spectrometry (MS) with electron transfer dissociation (ETD) capabilities. DHX of deuterated ubiquitin, followed by subsequent quenching and digestion, is performed within ∼60 s, yielding 100% peptide sequence coverage. The high reproducibility of the IMS separation allows spectral feature matching between two-dimensional IMS-MS datasets (undeuterated and deuterated) without the need for dataset alignment. Extracted ion drift time distributions (XIDTDs) of deuterated peptic peptides are mobility-matched to corresponding XIDTDs of undeuterated peptic peptides that were identified using collision-induced dissociation (CID). Matching XIDTDs allows a straightforward identification and deuterium retention evaluation for labeled peptides. Aside from the mobility separation, the ion trapping capabilities of the LTQ, combined with ETD, are demonstrated to provide single-residue resolution. Deuterium retention for the c- series ions across residues M(1)-L(15) and N(25)-R(42) are in good agreement with the known secondary structural elements within ubiquitin.
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Affiliation(s)
- Gregory C Donohoe
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - James R Arndt
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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286
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Applications of ion-mobility mass spectrometry for lipid analysis. Anal Bioanal Chem 2015; 407:4995-5007. [PMID: 25893801 DOI: 10.1007/s00216-015-8664-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 12/28/2022]
Abstract
The high chemical complexity of the lipidome is one of the major challenges in lipidomics research. Ion-mobility spectrometry (IMS), a gas-phase electrophoretic technique, makes possible the separation of ions in the gas phase according to their charge, shape, and size. IMS can be combined with mass spectrometry (MS), adding three major benefits to traditional lipidomic approaches. First, IMS-MS allows the determination of the collision cross section (CCS), a physicochemical measure related to the conformational structure of lipid ions. The CCS is used to improve the confidence of lipid identification. Second, IMS-MS provides a new set of hybrid fragmentation experiments. These experiments, which combine collision-induced dissociation with ion-mobility separation, improve the specificity of MS/MS-based approaches. Third, IMS-MS improves the peak capacity and signal-to-noise ratio of traditional analytical approaches. In doing so, it allows the separation of complex lipid extracts from interfering isobaric species. Developing in parallel with advances in instrumentation, informatics solutions enable analysts to process and exploit IMS-MS data for qualitative and quantitative applications. Here we review the current approaches for lipidomics research based on IMS-MS, including liquid chromatography-MS and direct-MS analyses of "shotgun" lipidomics and MS imaging.
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