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Karunaratne E, Hill DW, Dührkop K, Böcker S, Grant DF. Combining Experimental with Computational Infrared and Mass Spectra for High-Throughput Nontargeted Chemical Structure Identification. Anal Chem 2023; 95:11901-11907. [PMID: 37540774 DOI: 10.1021/acs.analchem.3c00937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
The inability to identify the structures of most metabolites detected in environmental or biological samples limits the utility of nontargeted metabolomics. The most widely used analytical approaches combine mass spectrometry and machine learning methods to rank candidate structures contained in large chemical databases. Given the large chemical space typically searched, the use of additional orthogonal data may improve the identification rates and reliability. Here, we present results of combining experimental and computational mass and IR spectral data for high-throughput nontargeted chemical structure identification. Experimental MS/MS and gas-phase IR data for 148 test compounds were obtained from NIST. Candidate structures for each of the test compounds were obtained from PubChem (mean = 4444 candidate structures per test compound). Our workflow used CSI:FingerID to initially score and rank the candidate structures. The top 1000 ranked candidates were subsequently used for IR spectra prediction, scoring, and ranking using density functional theory (DFT-IR). Final ranking of the candidates was based on a composite score calculated as the average of the CSI:FingerID and DFT-IR rankings. This approach resulted in the correct identification of 88 of the 148 test compounds (59%). 129 of the 148 test compounds (87%) were ranked within the top 20 candidates. These identification rates are the highest yet reported when candidate structures are used from PubChem. Combining experimental and computational MS/MS and IR spectral data is a potentially powerful option for prioritizing candidates for final structure verification.
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Affiliation(s)
- Erandika Karunaratne
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Dennis W Hill
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Kai Dührkop
- Chair for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena 07743, Germany
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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2
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Abdul-Khalek N, Wimmer R, Overgaard MT, Gregersen Echers S. Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS: A deep learning approach. Comput Struct Biotechnol J 2023; 21:3715-3727. [PMID: 37560124 PMCID: PMC10407266 DOI: 10.1016/j.csbj.2023.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
Accurate and absolute quantification of peptides in complex mixtures using quantitative mass spectrometry (MS)-based methods requires foreground knowledge and isotopically labeled standards, thereby increasing analytical expenses, time consumption, and labor, thus limiting the number of peptides that can be accurately quantified. This originates from differential ionization efficiency between peptides and thus, understanding the physicochemical properties that influence the ionization and response in MS analysis is essential for developing less restrictive label-free quantitative methods. Here, we used equimolar peptide pool repository data to develop a deep learning model capable of identifying amino acids influencing the MS1 response. By using an encoder-decoder with an attention mechanism and correlating attention weights with amino acid physicochemical properties, we obtain insight on properties governing the peptide-level MS1 response within the datasets. While the problem cannot be described by one single set of amino acids and properties, distinct patterns were reproducibly obtained. Properties are grouped in three main categories related to peptide hydrophobicity, charge, and structural propensities. Moreover, our model can predict MS1 intensity output under defined conditions based solely on peptide sequence input. Using a refined training dataset, the model predicted log-transformed peptide MS1 intensities with an average error of 9.7 ± 0.5% based on 5-fold cross validation, and outperformed random forest and ridge regression models on both log-transformed and real scale data. This work demonstrates how deep learning can facilitate identification of physicochemical properties influencing peptide MS1 responses, but also illustrates how sequence-based response prediction and label-free peptide-level quantification may impact future workflows within quantitative proteomics.
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Affiliation(s)
- Naim Abdul-Khalek
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
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3
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Jordan HA, Thomas SN. Novel proteomic technologies to address gaps in pre-clinical ovarian cancer biomarker discovery efforts. Expert Rev Proteomics 2023; 20:439-450. [PMID: 38116719 DOI: 10.1080/14789450.2023.2295861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION An estimated 20,000 women in the United States will receive a diagnosis of ovarian cancer in 2023. Late-stage diagnosis is associated with poor prognosis. There is a need for novel diagnostic biomarkers for ovarian cancer to improve early-stage detection and novel prognostic biomarkers to improve patient treatment. AREAS COVERED This review provides an overview of the clinicopathological features of ovarian cancer and the currently available biomarkers and treatment options. Two affinity-based platforms using proximity extension assays (Olink) and DNA aptamers (SomaLogic) are described in the context of highly reproducible and sensitive multiplexed assays for biomarker discovery. Recent developments in ion mobility spectrometry are presented as novel techniques to apply to the biomarker discovery pipeline. Examples are provided of how these aforementioned methods are being applied to biomarker discovery efforts in various diseases, including ovarian cancer. EXPERT OPINION Translating novel ovarian cancer biomarkers from candidates in the discovery phase to bona fide biomarkers with regulatory approval will have significant benefits for patients. Multiplexed affinity-based assay platforms and novel mass spectrometry methods are capable of quantifying low abundance proteins to aid biomarker discovery efforts by enabling the robust analytical interrogation of the ovarian cancer proteome.
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Affiliation(s)
- Helen A Jordan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Stefani N Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
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4
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Chatterjee P, Dutta SS, Chakraborty T. Tautomers and Rotamers of Curcumin: A Combined UV Spectroscopy, High-Performance Liquid Chromatography, Ion Mobility Mass Spectrometry, and Electronic Structure Theory Study. J Phys Chem A 2022; 126:1591-1604. [PMID: 35239351 DOI: 10.1021/acs.jpca.1c08612] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The structures of tautomers and rotameric forms of curcumin, the bioactive compound present in spice plant turmeric, have been investigated using ion mobility mass spectrometry (IMMS) in conjunction with high-performance liquid chromatography (HPLC) and UV-visible spectroscopy. Two tautomeric forms of this β-diketone compound, keto-enol and diketo, have been chromatographically separated, and the electronic absorption spectra for these two tautomeric forms in methanol solution have been recorded separately for the first time. The molecular identity of the HPLC-separated solution fractions is established unambiguously by recording the mass and fragmentation spectra simultaneously. The ion mobility spectrum for the deprotonated curcumin anion, [Cur-H]-, corresponding to the diketo tautomer, displays only one peak (P), and the collision cross-section (CCS) value is measured to be 185.9 Å2. However, the ion mobility spectrum corresponding to the HPLC-separated keto-enol tautomer shows three distinctly separated peaks, P, Q, and R, with CCS values of 185.9, 194.8, and 203.4 Å2, respectively, whereby peak R appears to be the most intense one, followed by peaks P and Q. The theoretically calculated CCS values of different isomers of [Cur-H]-, optimized by electronic structure theory methods, display satisfactory correlation with the experimentally observed values, corroborating our assignments. The spectral attributes also indicate the occurrence of structural rearrangements in the electrospray ionization process. With the aid of the electronic structure calculation, low-energy pathways for the occurrence of the structural isomerization to surpass the energy barrier are suggested, which are consistent with the assignments of the peaks observed in the IM spectra.
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Affiliation(s)
- Piyali Chatterjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhra Sankar Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
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5
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Karunaratne E, Hill DW, Pracht P, Gascón JA, Grimme S, Grant DF. High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra. Anal Chem 2021; 93:10688-10696. [PMID: 34288660 PMCID: PMC8404482 DOI: 10.1021/acs.analchem.1c02244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The high-throughput identification of unknown metabolites in biological samples remains challenging. Most current non-targeted metabolomics studies rely on mass spectrometry, followed by computational methods that rank thousands of candidate structures based on how closely their predicted mass spectra match the experimental mass spectrum of an unknown. We reasoned that the infrared (IR) spectra could be used in an analogous manner and could add orthologous structure discrimination; however, this has never been evaluated on large data sets. Here, we present results of a high-throughput computational method for predicting IR spectra of candidate compounds obtained from the PubChem database. Predicted spectra were ranked based on their similarity to gas-phase experimental IR spectra of test compounds obtained from the NIST. Our computational workflow (IRdentify) consists of a fast semiempirical quantum mechanical method for initial IR spectra prediction, ranking, and triaging, followed by a final IR spectra prediction and ranking using density functional theory. This approach resulted in the correct identification of 47% of 258 test compounds. On average, there were 2152 candidate structures evaluated for each test compound, giving a total of approximately 555,200 candidate structures evaluated. We discuss several variables that influenced the identification accuracy and then demonstrate the potential application of this approach in three areas: (1) combining IR and mass spectra rankings into a single composite rank score, (2) identifying the precursor and fragment ions using cryogenic ion vibrational spectroscopy, and (3) the incorporation of a trimethylsilyl derivatization step to extend the method compatibility to less-volatile compounds. Overall, our results suggest that matching computational with experimental IR spectra is a potentially powerful orthogonal option for adding significant high-throughput chemical structure discrimination when used with other non-targeted chemical structure identification methods.
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Affiliation(s)
- Erandika Karunaratne
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Dennis W Hill
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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6
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Belova L, Caballero-Casero N, van Nuijs ALN, Covaci A. Ion Mobility-High-Resolution Mass Spectrometry (IM-HRMS) for the Analysis of Contaminants of Emerging Concern (CECs): Database Compilation and Application to Urine Samples. Anal Chem 2021; 93:6428-6436. [PMID: 33845572 DOI: 10.1021/acs.analchem.1c00142] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ion mobility mass spectrometry (IM-MS)-derived collision cross section (CCS) values can serve as a valuable additional identification parameter within the analysis of compounds of emerging concern (CEC) in human matrices. This study introduces the first comprehensive database of DTCCSN2 values of 148 CECs and their metabolites including bisphenols, alternative plasticizers (AP), organophosphate flame retardants (OP), perfluoroalkyl chemicals (PFAS), and others. A total of 311 ions were included in the database, whereby the DTCCSN2 values for 113 compounds are reported for the first time. For 105 compounds, more than one ion is reported. Moreover, the DTCCSN2 values of several isomeric CECs and their metabolites are reported to allow a distinction between isomers. Comprehensive quality assurance guidelines were implemented in the workflow of acquiring DTCCSN2 values to ensure reproducible experimental conditions. The reliability and reproducibility of the complied database were investigated by analyzing pooled human urine spiked with 30 AP and OP metabolites at two concentration levels. For all investigated metabolites, the DTCCSN2 values measured in urine showed a percent error of <1% in comparison to database values. DTCCSN2 values of OP metabolites showed an average percent error of 0.12% (50 ng/mL in urine) and 0.15% (20 ng/mL in urine). For AP metabolites, these values were 0.10 and 0.09%, respectively. These results show that the provided database can be of great value for enhanced identification of CECs in environmental and human matrices, which can advance future suspect screening studies on CECs.
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Affiliation(s)
- Lidia Belova
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | | | | | - Adrian Covaci
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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7
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Chatterjee P, Dutta SS, Chakraborty T. Isomers and Rotamers of DCM in Methanol and in Gas Phase Probed by Ion Mobility Mass Spectrometry in Combination with High Performance Liquid Chromatography. J Phys Chem B 2020; 124:4498-4511. [PMID: 32380830 DOI: 10.1021/acs.jpcb.0c00097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
An integrated method of ion mobility mass spectrometry and high-performance liquid chromatography (HPLC) has been used to investigate the isomeric distribution of a popular fluorescent dye DCM (4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran) in methanol solution. Chromatographic separation of DCM isomers in methanol has been performed by probing the molecular mass (DCMH+), and two distinctly separated peaks are observed at retention times 3.73 (peak-I) and 3.87 (peak-II) min, where the latter one appears nearly twice as intense as the former. However, peak-I appears much weaker compared to peak-II if the chromatogram is recorded by optical probing at the absorption maximum of this dye (467 nm). The ion mobility (IM) spectra of DCMH+ ions corresponding to each of the LC-separated factions show three common peaks A, B, and C, with collision cross-section (CCS) values of 174, 185, and 197 Å2, respectively, but their relative intensities in the two IM spectra appear in opposite sequences. The three IM peaks have been assigned by considering the theoretically calculated CCS values of 13 possible isomers of DCMH+ ions. The IM spectral features also reveal that isomeric interconversions occur during the ESI process. Electronic structure calculations have been used to optimize the geometries of the four isomers of solvated DCM and the corresponding protomeric structures of DCMH+. The isomerization pathways and associated energy barriers have also been calculated. The gas-phase protomers are found to follow a completely different sequence of stability as compared to the neutral isomers. The analysis reveals that peak-I corresponds to one of the cis isomers, whereas peak-II arises due to cumulative contributions of the other three isomers. The absorption spectrum of DCM in methanol is simulated from the computed spectral profiles of the isomers which indicates a distribution of trans1, trans2, cis1, and cis2 isomers as 33.5, 61.5, 2.0, and 3.0%, respectively. The fragmentation behavior of DCMH+ ions in a collision-induced dissociation experiment has been found to be isomer dependent.
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Affiliation(s)
- Piyali Chatterjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhra Sankar Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja S C Mullick Road, Jadavpur, Kolkata 700032, India
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8
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Oranzi NR, Lei J, Kemperman RHJ, Chouinard CD, Holmquist B, Garrett TJ, Yost RA. Rapid Quantitation of 25-Hydroxyvitamin D2 and D3 in Human Serum Using Liquid Chromatography/Drift Tube Ion Mobility-Mass Spectrometry. Anal Chem 2019; 91:13555-13561. [DOI: 10.1021/acs.analchem.9b02683] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas R. Oranzi
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Jiajun Lei
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Robin H. J. Kemperman
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Christopher D. Chouinard
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, Florida 32901, United States
| | | | - Timothy J. Garrett
- Department of Pathology, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A. Yost
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
- Department of Pathology, University of Florida, Gainesville, Florida 32610, United States
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9
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Emhofer L, Himmelsbach M, Buchberger W, Klampfl CW. High-performance liquid chromatography drift-tube ion-mobility quadrupole time-of-flight/mass spectrometry for the identity confirmation and characterization of metabolites from three statins (lipid-lowering drugs) in the model plant cress (Lepidium sativum) after uptake from water. J Chromatogr A 2019; 1592:122-132. [DOI: 10.1016/j.chroma.2019.01.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 10/27/2022]
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10
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Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES. Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples. Trends Analyt Chem 2019; 116:292-299. [PMID: 31798197 DOI: 10.1016/j.trac.2019.04.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.
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Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A &M University, College Station, TX
| | - James N Dodds
- Department of Chemistry, NC State University, Raleigh, NC
| | - Jeremy Ash
- Department of Chemistry, NC State University, Raleigh, NC
| | - Denis Fourches
- Department of Chemistry, NC State University, Raleigh, NC
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Jason P Wendler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Erin S Baker
- Department of Chemistry, NC State University, Raleigh, NC
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11
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Couvillion SP, Zhu Y, Nagy G, Adkins JN, Ansong C, Renslow RS, Piehowski PD, Ibrahim YM, Kelly RT, Metz TO. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst 2019; 144:794-807. [PMID: 30507980 PMCID: PMC6349538 DOI: 10.1039/c8an01574k] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass-spectrometry based omics technologies - namely proteomics, metabolomics and lipidomics - have enabled the molecular level systems biology investigation of organisms in unprecedented detail. There has been increasing interest for gaining a thorough, functional understanding of the biological consequences associated with cellular heterogeneity in a wide variety of research areas such as developmental biology, precision medicine, cancer research and microbiome science. Recent advances in mass spectrometry (MS) instrumentation and sample handling strategies are quickly making comprehensive omics analyses of single cells feasible, but key breakthroughs are still required to push through remaining bottlenecks. In this review, we discuss the challenges faced by single cell MS-based omics analyses and highlight recent technological advances that collectively can contribute to comprehensive and high throughput omics analyses in single cells. We provide a vision of the potential of integrating pioneering technologies such as Structures for Lossless Ion Manipulations (SLIM) for improved sensitivity and resolution, novel peptide identification tactics and standards free metabolomics approaches for future applications in single cell analysis.
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Affiliation(s)
- Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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12
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Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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13
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MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES. Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2182-2188. [PMID: 30047074 PMCID: PMC6191345 DOI: 10.1007/s13361-018-2028-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 05/04/2023]
Abstract
Recent advances in ion mobility spectrometry (IMS) have illustrated its power in determining the structural characteristics of a molecule, especially when coupled with other separations dimensions such as liquid chromatography (LC) and mass spectrometry (MS). However, these three separation techniques together greatly complicate data analyses, making better informatics tools essential for assessing the resulting data. In this manuscript, Skyline was adapted to analyze LC-IMS-CID-MS data from numerous instrument vendor datasets and determine the effect of adding the IMS dimension into the normal LC-MS molecular pipeline. For the initial evaluation, a tryptic digest of bovine serum albumin (BSA) was spiked into a yeast protein digest at seven different concentrations, and Skyline was able to rapidly analyze the MS and CID-MS data for 38 of the BSA peptides. Calibration curves for the precursor and fragment ions were assessed with and without the IMS dimension. In all cases, addition of the IMS dimension removed noise from co-eluting peptides with close m/z values, resulting in calibration curves with greater linearity and lower detection limits. This study presents an important informatics development since to date LC-IMS-CID-MS data from the different instrument vendors is often assessed manually and cannot be analyzed quickly. Because these evaluations require days for the analysis of only a few target molecules in a limited number of samples, it is unfeasible to evaluate hundreds of targets in numerous samples. Thus, this study showcases Skyline's ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly. Graphical Abstract ᅟ.
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Affiliation(s)
- Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brian S Pratt
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jarrett D Egertson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd. MSIN K8-98, P.O. Box 999, Richland, WA, 99352, USA
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd. MSIN K8-98, P.O. Box 999, Richland, WA, 99352, USA.
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14
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Oranzi NR, Polfer NC, Lei J, Yost RA. Influence of Experimental Conditions on the Ratio of 25-Hydroxyvitamin D3 Conformers for Validating a Liquid Chromatography/Ion Mobility-Mass Spectrometry Method for Routine Quantitation. Anal Chem 2018; 90:13549-13556. [DOI: 10.1021/acs.analchem.8b03668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicholas R. Oranzi
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Nicolas C. Polfer
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Jiajun Lei
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Richard A. Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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15
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The potential of ion mobility-mass spectrometry for non-targeted metabolomics. Curr Opin Chem Biol 2017; 42:9-15. [PMID: 29107931 DOI: 10.1016/j.cbpa.2017.10.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 12/31/2022]
Abstract
Non-targeted analysis of metabolites in hypothesis-generating workflows has proven its potential to answer essential questions that arise when dealing with complex biological systems. Nevertheless, tracking changes in perturbed systems via accurate quantification and the identification process itself represent the most critical challenges in these workflows. Recent advances in ion mobility-mass spectrometry have enabled this technique to increase the confidence of metabolite annotation by introducing a complementary conditional molecular descriptor, that is collision cross section.
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16
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Nielson CM, Wiedrick J, Shen J, Jacobs J, Baker ES, Baraff A, Piehowski P, Lee CG, Baratt A, Petyuk V, McWeeney S, Lim JY, Bauer DC, Lane NE, Cawthon PM, Smith RD, Lapidus J, Orwoll ES. Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics. J Bone Miner Res 2017; 32:1559-1567. [PMID: 28316103 PMCID: PMC5489383 DOI: 10.1002/jbmr.3125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/22/2017] [Accepted: 03/06/2017] [Indexed: 01/16/2023]
Abstract
Serum proteomics analysis may lead to the discovery of novel osteoporosis biomarkers. The Osteoporotic Fractures in Men (MrOS) study comprises men ≥65 years old in the US who have had repeated BMD measures and have been followed for incident fracture. High-throughput quantitative proteomic analysis was performed on baseline fasting serum samples from non-Hispanic white men using a multidimensional approach coupling liquid chromatography, ion-mobility separation, and mass spectrometry (LC-IMS-MS). We followed the participants for a mean of 4.6 years for changes in femoral neck bone mineral density (BMD) and for incident hip fracture. Change in BMD was determined from mixed effects regression models taking age and weight into account. Participants were categorized into three groups: BMD maintenance (no decline; estimated change ≥0 g/cm2 , n = 453); expected loss (estimated change 0 to 1 SD below the estimated mean change, -0.034 g/cm2 for femoral neck, n = 1184); and accelerated loss (estimated change ≥1 SD below mean change, n = 237). Differential abundance values of 3946 peptides were summarized by meta-analysis to determine differential abundance of each of 339 corresponding proteins for accelerated BMD loss versus maintenance. Using this meta-analytic standardized fold change at cutoffs of ≥1.1 or ≤0.9 (p < 0.10), 20 proteins were associated with accelerated BMD loss. Associations of those 20 proteins with incident hip fracture were tested using Cox proportional hazards models with age and BMI adjustment in 2473 men. Five proteins were associated with incident hip fracture (HR between 1.29 and 1.41 per SD increase in estimated protein abundance). Some proteins have been previously associated with fracture risk (eg, CD14 and SHBG), whereas others have roles in cellular senescence and aging (B2MG and TIMP1) and complement activation and innate immunity (CO7, CO9, CFAD). These findings may inform development of biomarkers for future research in bone biology and fracture prediction. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Carrie M Nielson
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
- Bone and Mineral Unit, Oregon Health & Science University, Portland, OR, USA
| | - Jack Wiedrick
- Biostatistics and Design Program, OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Jian Shen
- Bone and Mineral Unit, Oregon Health & Science University, Portland, OR, USA
| | - Jon Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aaron Baraff
- Division of Biostatistics, Oregon Health & Science University, Portland, OR, USA
| | - Paul Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Christine G Lee
- Research Service, Portland Veterans Affairs Medical Center, Portland, OR, USA
| | - Arie Baratt
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA
| | - Vladislav Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA
| | - Jeong Youn Lim
- Division of Biostatistics, Oregon Health & Science University, Portland, OR, USA
| | - Douglas C Bauer
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Nancy E Lane
- Department of Internal Medicine, University of California at Davis, Sacramento, CA, USA
| | - Peggy M Cawthon
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jodi Lapidus
- Biostatistics and Design Program, OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Eric S Orwoll
- Bone and Mineral Unit, Oregon Health & Science University, Portland, OR, USA
- Department of Medicine, Oregon Health & Science University, Portland, OR, USA
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17
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Zheng X, Wojcik R, Zhang X, Ibrahim YM, Burnum-Johnson KE, Orton DJ, Monroe ME, Moore RJ, Smith RD, Baker ES. Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:71-92. [PMID: 28301728 PMCID: PMC5627998 DOI: 10.1146/annurev-anchem-061516-045212] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits.
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Affiliation(s)
- Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Roza Wojcik
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Xing Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Anschutz Medical Campus, University of Colorado, Denver, Colorado 80045
| | - Yehia M Ibrahim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Daniel J Orton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Matthew E Monroe
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Ronald J Moore
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Erin S Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352;
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18
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Zhang X, Kew K, Reisdorph R, Sartain M, Powell R, Armstrong M, Quinn K, Cruickshank-Quinn C, Walmsley S, Bokatzian S, Darland E, Rain M, Imatani K, Reisdorph N. Performance of a High-Pressure Liquid Chromatography-Ion Mobility-Mass Spectrometry System for Metabolic Profiling. Anal Chem 2017; 89:6384-6391. [PMID: 28528542 DOI: 10.1021/acs.analchem.6b04628] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A commercial liquid chromatography/drift tube ion mobility-mass spectrometer (LC/IM-MS) was evaluated for its utility in global metabolomics analysis. Performance was assessed using 12 targeted metabolite standards where the limit of detection (LOD), linear dynamic range, resolving power, and collision cross section (Ω) are reported for each standard. Data were collected in three different instrument operation modes: flow injection analysis with IM-MS (FIA/IM-MS), LC/MS, and LC/IM-MS. Metabolomics analyses of human plasma and HaCaT cells were used to compare the above three operation modes. LC/MS provides linearity in response, data processing automation, improved limits of detection, and ease of use. Advantages of LC/IM-MS and FIA/IM-MS include the ability to develop mobility-mass trend lines for structurally similar biomolecules, increased peak capacity, reduction of chemical/matrix noise, improvement in signal-to-noise, and separations of isobar/isomer compounds that are not resolved by LC. We further tested the feasibility of incorporating IM-MS into conventional LC/MS metabolomics workflows. In general, the addition of ion mobility dimension has increased the separation of compounds in complex biological matrixes and has the potential to largely improve the throughput of metabolomics analysis.
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Affiliation(s)
- Xing Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Kimberly Kew
- Department of Chemistry, East Carolina University , Greenville, North Carolina 27858, United States
| | - Richard Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Mark Sartain
- Life Sciences Group, Agilent Technologies , Santa Clara, California 95051, United States
| | - Roger Powell
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Michael Armstrong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Kevin Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Charmion Cruickshank-Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Scott Walmsley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Samantha Bokatzian
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
| | - Ed Darland
- Life Sciences Group, Agilent Technologies , Santa Clara, California 95051, United States
| | - Matthew Rain
- Life Sciences Group, Agilent Technologies , Santa Clara, California 95051, United States
| | - Ken Imatani
- Life Sciences Group, Agilent Technologies , Santa Clara, California 95051, United States
| | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado 80045, United States
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19
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Distler U, Kuharev J, Navarro P, Tenzer S. Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics. Nat Protoc 2016; 11:795-812. [DOI: 10.1038/nprot.2016.042] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Thevis M, Dib J, Thomas A, Höppner S, Lagojda A, Kuehne D, Sander M, Opfermann G, Schänzer W. Complementing the characterization ofin vivogeneratedN-glucuronic acid conjugates of stanozolol by collision cross section computation and analysis. Drug Test Anal 2015; 7:1050-6. [DOI: 10.1002/dta.1907] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 09/25/2015] [Accepted: 09/25/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Mario Thevis
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
- European Monitoring Center for Emerging Doping Agents (EuMoCEDA); Cologne/Bonn Germany
| | - Josef Dib
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Andreas Thomas
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Sebastian Höppner
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Andreas Lagojda
- Bayer CropScience AG; Alfred-Nobel-Str. 50 40789 Monheim Germany
| | - Dirk Kuehne
- Bayer CropScience AG; Alfred-Nobel-Str. 50 40789 Monheim Germany
| | - Mark Sander
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Georg Opfermann
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Wilhelm Schänzer
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
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21
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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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22
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Baker ES, Burnum-Johnson KE, Ibrahim YM, Orton DJ, Monroe ME, Kelly RT, Moore RJ, Zhang X, Théberge R, Costello CE, Smith RD. Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics 2015; 15:2766-76. [PMID: 26046661 DOI: 10.1002/pmic.201500048] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/06/2015] [Accepted: 06/02/2015] [Indexed: 11/06/2022]
Abstract
Proteomic measurements with greater throughput, sensitivity, and structural information are essential for improving both in-depth characterization of complex mixtures and targeted studies. While LC separation coupled with MS (LC-MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution and rapid structural information has many benefits in proteomic analyses. Technical advances in ion transmission and data acquisition have made ion mobility separations an opportune technology to be easily and effectively incorporated into LC-MS proteomic measurements for enhancing their information content. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.
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Affiliation(s)
- Erin Shammel Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xing Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Roger Théberge
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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23
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Szabo Z, Janaky T. Challenges and developments in protein identification using mass spectrometry. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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24
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Webb IK, Chen TC, Danielson WF, Ibrahim YM, Tang K, Anderson GA, Smith RD. Implementation of dipolar resonant excitation for collision induced dissociation with ion mobility/time-of-flight MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:563-71. [PMID: 24470195 PMCID: PMC4113219 DOI: 10.1007/s13361-013-0815-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/19/2013] [Accepted: 12/19/2013] [Indexed: 05/26/2023]
Abstract
An ion mobility/time-of-flight mass spectrometer (IMS/TOF MS) platform that allows for resonant excitation collision induced dissociation (CID) is presented. Highly efficient, mass-resolved fragmentation without additional excitation of product ions was accomplished and over-fragmentation common in beam-type CID experiments was alleviated. A quadrupole ion guide was modified to apply a dipolar AC signal across a pair of rods for resonant excitation. The method was characterized with singly protonated methionine enkephalin and triply protonated peptide angiotensin I, yielding maximum CID efficiencies of 44% and 84%, respectively. The Mathieu q(x,y) parameter was set at 0.707 for these experiments to maximize pseudopotential well depths and CID efficiencies. Resonant excitation CID was compared with beam-type CID for the peptide mixture. The ability to apply resonant waveforms in mobility-resolved windows is demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge (m/z) ratios within a single IMS-MS analysis.
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25
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Crowell KL, Slysz GW, Baker ES, LaMarche BL, Monroe ME, Ibrahim YM, Payne SH, Anderson GA, Smith RD. LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. Bioinformatics 2013; 29:2804-5. [PMID: 24008421 DOI: 10.1093/bioinformatics/btt465] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing. RESULTS We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension. AVAILABILITY LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/LC-IMS-MS_Feature_Finder.php. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README). CONTACT rds@pnnl.gov. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kevin L Crowell
- Biological Sciences Division, Pacific Northwest National Laboratory, 999 Battelle Boulevard, Richland, WA 99352, USA and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 999 Battelle Boulevard, Richland, WA 99352, USA
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