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Deschamps E, Calabrese V, Schmitz I, Hubert-Roux M, Castagnos D, Afonso C. Advances in Ultra-High-Resolution Mass Spectrometry for Pharmaceutical Analysis. Molecules 2023; 28:molecules28052061. [PMID: 36903305 PMCID: PMC10003995 DOI: 10.3390/molecules28052061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Pharmaceutical analysis refers to an area of analytical chemistry that deals with active compounds either by themselves (drug substance) or when formulated with excipients (drug product). In a less simplistic way, it can be defined as a complex science involving various disciplines, e.g., drug development, pharmacokinetics, drug metabolism, tissue distribution studies, and environmental contamination analyses. As such, the pharmaceutical analysis covers drug development to its impact on health and the environment. Moreover, due to the need for safe and effective medications, the pharmaceutical industry is one of the most heavily regulated sectors of the global economy. For this reason, powerful analytical instrumentation and efficient methods are required. In the last decades, mass spectrometry has been increasingly used in pharmaceutical analysis both for research aims and routine quality controls. Among different instrumental setups, ultra-high-resolution mass spectrometry with Fourier transform instruments, i.e., Fourier transform ion cyclotron resonance (FTICR) and Orbitrap, gives access to valuable molecular information for pharmaceutical analysis. In fact, thanks to their high resolving power, mass accuracy, and dynamic range, reliable molecular formula assignments or trace analysis in complex mixtures can be obtained. This review summarizes the principles of the two main types of Fourier transform mass spectrometers, and it highlights applications, developments, and future perspectives in pharmaceutical analysis.
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Affiliation(s)
- Estelle Deschamps
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Valentina Calabrese
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100 Villeurbanne, France
| | - Isabelle Schmitz
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Marie Hubert-Roux
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Denis Castagnos
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- Correspondence:
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2
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Lin Y, Agarwal AM, Anderson LC, Marshall AG. Discovery of a biomarker for β-Thalassemia by HPLC-MS and improvement from Proton Transfer Reaction - Parallel Ion Parking. J Mass Spectrom Adv Clin Lab 2023; 28:20-26. [PMID: 36814695 PMCID: PMC9939715 DOI: 10.1016/j.jmsacl.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
β-thalassemia is a quantitative hemoglobin (Hb) disorder resulting in reduced production of Hb A and increased levels of Hb A2. Diagnosis of β-thalassemia can be problematic when combined with other structural Hb variants, so that the separation approaches in routine clinical centers are not sufficiently decisive to obtain accurate results. Here, we separate the intact Hb subunits by high-performance liquid chromatography, followed by top-down tandem mass spectrometry of intact subunits to distinguish Hb variants. Proton transfer reaction-parallel ion parking (PTR-PIP), in which a radical anion removes protons from multiply charged precursor ions and produces charge-reduced ions spanning a limited m/z range, was used to increase the signal-to-noise ratio of the subunits of interest. We demonstrate that the δ/β ratio can act as a biomarker to identify β-thalassemia in normal electrospray ionization MS1 and PTR-PIP MS1. The application of PTR-PIP significantly increases the sensitivity and specificity of the HPLC-MS method to identify δ/β ratio as a thalassemia biomarker.
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Key Words
- ACN, Acetonitrile
- AUC, Areas under the curve
- CID, Collision-induced dissociation
- ESI, Electrospray ionization
- ETD, Electron-transfer dissociation
- FA, Formic acid
- FN, False-negative
- FP, False-positive
- FT-ICR
- FT-ICR, MS Fourier transform ion cyclotron resonance mass spectrometer
- FTMS
- Fourier transform ion cyclotron resonance
- Hb A, Normal adult Hb
- Hb, Hemoglobin
- HbA1d, Hb β with glutathione
- IFCC, International Federation of Clinical Chemistry and Laboratory Medicine
- IQR, Interquartile range
- J, Youden Index
- MCW, Methanol/chloroform/water
- MS, Mass spectrometry
- PTM, Post-translational modification
- PTR-PIP, Proton transfer reaction-parallel ion parking
- ROC, Receiver operating characteristic
- S/N, Signal-to-noise ratios
- Se(c), Sensitivity, the probability of a true positive)
- Sp(c), Specificity, the probability of a true negative)
- TIC, Total ion chromatogram
- TN, True negative
- TP, True positive
- Top-down
- XIC, Extracted ion chromatograms
- m/z, Mass-to-charge ratios
- δ/β ratio
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Affiliation(s)
- Yuan Lin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States
| | - Archana M. Agarwal
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, United States,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, United States
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States,Corresponding authors at: Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States (A.G. Marshall).
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States,Corresponding authors at: Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32308, United States (A.G. Marshall).
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Caleb Bagley M, Garrard KP, Muddiman DC. The development and application of matrix assisted laser desorption electrospray ionization: The teenage years. Mass Spectrom Rev 2023; 42:35-66. [PMID: 34028071 DOI: 10.1002/mas.21696] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 05/24/2023]
Abstract
In the past 15 years, ambient ionization techniques have witnessed a significant incursion into the field of mass spectrometry imaging, demonstrating their ability to provide complementary information to matrix-assisted laser desorption ionization. Matrix-assisted laser desorption electrospray ionization is one such technique that has evolved since its first demonstrations with ultraviolet lasers coupled to Fourier transform-ion cyclotron resonance mass spectrometers to extensive use with infrared lasers coupled to orbitrap-based mass spectrometers. Concurrently, there have been transformative developments of this imaging platform due to the high level of control the principal group has retained over the laser technology, data acquisition software (RastirX), instrument communication, and image processing software (MSiReader). This review will discuss the developments of MALDESI since its first laboratory demonstration in 2005 to the most recent advances in 2021.
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Affiliation(s)
- Michael Caleb Bagley
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Kenneth P Garrard
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
- The Precision Engineering Consortium, North Carolina State University, Raleigh, North Carolina, USA
- Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina, USA
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
- Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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4
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Simon C, Dührkop K, Petras D, Roth VN, Böcker S, Dorrestein PC, Gleixner G. Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter. Environ Sci Technol 2022; 56:11027-11040. [PMID: 35834352 PMCID: PMC9352317 DOI: 10.1021/acs.est.2c01332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 05/30/2023]
Abstract
Ultrahigh-resolution Fourier transform mass spectrometry (FTMS) has revealed unprecedented details of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level, but we lack approaches to access the underlying structural complexity. We here explore the hypothesis that every DOM precursor ion is potentially linked with all emerging product ions in FTMS2 experiments. The resulting mass difference (Δm) matrix is deconvoluted to isolate individual precursor ion Δm profiles and matched with structural information, which was derived from 42 Δm features from 14 in-house reference compounds and a global set of 11 477 Δm features with assigned structure specificities, using a dataset of ∼18 000 unique structures. We show that Δm matching is highly sensitive in predicting potential precursor ion identities in terms of molecular and structural composition. Additionally, the approach identified unresolved precursor ions and missing elements in molecular formula annotation (P, Cl, F). Our study provides first results on how Δm matching refines structural annotations in van Krevelen space but simultaneously demonstrates the wide overlap between potential structural classes. We show that this effect is likely driven by chemodiversity and offers an explanation for the observed ubiquitous presence of molecules in the center of the van Krevelen space. Our promising first results suggest that Δm matching can both unfold the structural information encrypted in DOM and assess the quality of FTMS-derived molecular formulas of complex mixtures in general.
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Affiliation(s)
- Carsten Simon
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Kai Dührkop
- Chair
for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Daniel Petras
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, 9500 Gilman Drive, MC 0657, La Jolla, California 92093-0657, United States of America
- CMFI
Cluster of Excellence, Interfaculty Institute of Microbiology and
Medicine, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Vanessa-Nina Roth
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Sebastian Böcker
- Chair
for Bioinformatics, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Pieter C. Dorrestein
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California
San Diego, 9500 Gilman Drive, MC 0657, La Jolla, California 92093-0657, United States of America
| | - Gerd Gleixner
- Molecular
Biogeochemistry, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
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5
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Nagornov KO, Kozhinov AN, Gasilova N, Menin L, Tsybin YO. Characterization of the Time-Domain Isotopic Beat Patterns of Monoclonal Antibodies in Fourier Transform Mass Spectrometry. J Am Soc Mass Spectrom 2022; 33:1113-1125. [PMID: 35638743 DOI: 10.1021/jasms.1c00336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The time-domain transients in the Fourier transform mass spectrometry (FTMS) analysis of monoclonal antibodies (mAbs) are known to exhibit characteristic isotopic beat patterns. These patterns are defined by the isotopic distributions of all gaseous mAb ions present in the FTMS mass analyzer, originating from single or multiple charge states, and from single or multiple proteoforms. For an isolated charge state of a single proteoform, the mAb isotopic beat pattern resembles narrow splashes of signal amplitude (beats), spaced periodically in the time-domain transient, with broad (often exceeding 1 s) "valleys" between them. Here, we reinforce the importance of isotopic beat patterns for the accurate interpretation and presentation of FTMS data in the analysis of mAbs and other large biopolymers. An updated, mAb-grade version of the transient-mediated FTMS data simulation and visualization tool, FTMS Simulator is introduced and benchmarked. We then apply this tool to evaluate the charge-state dependent characteristics of isotopic beats in mAbs analyses with modern models of Orbitrap and ion cyclotron resonance (ICR) FTMS instruments, including detection of higher-order harmonics. We demonstrate the impact of the isotopic beat patterns on the analytical characteristics of the resulting mass spectra of individual and overlapping mAb proteoforms. The results reported here detail highly nonlinear dependences of resolution and signal-to-noise ratio on the time-domain transient period, absorption or magnitude mode spectra representation, and apodization functions. The provided description and the demonstrated ability to routinely conduct accurate simulations of FTMS data for large biopolymers should aid the end-users of Orbitrap and ICR FTMS instruments in the analysis of mAbs and other biopolymers, including viruses.
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Affiliation(s)
| | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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Bianco M, Ventura G, Calvano CD, Losito I, Cataldi TRI. A new paradigm to search for allergenic proteins in novel foods by integrating proteomics analysis and in silico sequence homology prediction: Focus on spirulina and chlorella microalgae. Talanta 2022; 240:123188. [PMID: 34990986 DOI: 10.1016/j.talanta.2021.123188] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
Since novel nutrient sources with high protein content, such as yeast, fungi, bacteria, algae, and insects, are increasingly introduced in the consumer market, safety evaluation studies on their potentially allergenic proteins are required. A pipeline for in silico establishing the sequence-based homology between proteins of spirulina (Arthrospira platensis) and chlorella (Chlorella vulgaris) micro-algae and those included in the AllergenOnline (AO) database (AllergenOnline.org) is described. The extracted proteins were first identified through tryptic peptides analysis by reversed-phase liquid chromatography and high resolution/accuracy Fourier-transform tandem mass spectrometry (RPLC-ESI-FTMS/MS), followed by a quest on the UniProt database. The AO database was subsequently interrogated to assess sequence similarity between identified microalgal proteins and known allergens, based on criteria established by the World Health Organization (WHO) and Food and Agriculture Organization (FAO). A direct search for microalgal proteins already included in allergen databases was also performed using the Allergome database. Six proteins exhibiting a significant homology with food allergens were identified in spirulina extracts. Five of them, i.e., two thioredoxins (D4ZSU6, K1VP15), a superoxide dismutase (C3V3P3), a glyceraldehyde-3-phosphate dehydrogenase (K1W168), and a triosephosphate isomerase (D5A635), resulted from the search on AO. The sixth protein, C-phycocyanin beta subunit (P72508), was directly obtained after examining the Allergome database. Two proteins exhibiting significant sequence homology with food allergens were retrieved in chlorella extracts, viz. calmodulin (A0A2P6TFR8), which is related to troponin c (D7F1Q2), and fructose-bisphosphate aldolase (A0A2P6TDD0). Specific serum screenings based on immunochemical tests should be undertaken to confirm or rule out the allergenicity of the identified proteins.
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Affiliation(s)
- Mariachiara Bianco
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Giovanni Ventura
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
| | - Cosima Damiana Calvano
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Ilario Losito
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Tommaso R I Cataldi
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
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7
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Nagornov KO, Tsybin OY, Nicol E, Kozhinov AN, Tsybin YO. Fourier transform ion cyclotron resonance mass spectrometry at the true cyclotron frequency. Mass Spectrom Rev 2022; 41:314-337. [PMID: 33462876 DOI: 10.1002/mas.21681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Ion cyclotron resonance (ICR) cells provide stability and coherence of ion oscillations in crossed electric and magnetic fields over extended periods of time. Using the Fourier transform enables precise measurements of ion oscillation frequencies. These precisely measured frequencies are converted into highly accurate mass-to-charge ratios of the analyte ions by calibration procedures. In terms of resolution and mass accuracy, Fourier transform ICR mass spectrometry (FT-ICR MS) offers the highest performance of any MS technology. This is reflected in its wide range of applications. However, in the most challenging MS application, for example, imaging, enhancements in the mass accuracy of fluctuating ion fluxes are required to continue advancing the field. One approach is to shift the ion signal power into the peak corresponding to the true cyclotron frequency instead of the reduced cyclotron frequency peak. The benefits of measuring the true cyclotron frequency include increased tolerance to electric fields within the ICR cell, which enhances frequency measurement precision. As a result, many attempts to implement this mode of FT-ICR MS operation have occurred. Examples of true cyclotron frequency measurements include detection of magnetron inter-harmonics of the reduced cyclotron frequency (i.e., the sidebands), trapping field-free (i.e., screened) ICR cells, and hyperbolic ICR cells with quadrupolar ion detection. More recently, ICR cells with spatially distributed ion clouds have demonstrated attractive performance characteristics for true cyclotron frequency ion detection. Here, we review the corresponding developments in FT-ICR MS over the past 40 years.
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Affiliation(s)
| | - Oleg Y Tsybin
- Ion Physics and Mass Spectrometry Laboratory, Peter The Great State Polytechnic University, Saint-Petersburg, Russia
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire, CNRS, UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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8
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Lin Y, Agarwal AM, Marshall AG, Anderson LC. Characterization of Structural Hemoglobin Variants by Top-Down Mass Spectrometry and R Programming Tools for Rapid Identification. J Am Soc Mass Spectrom 2022; 33:123-130. [PMID: 34955023 DOI: 10.1021/jasms.1c00291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hemoglobinopathies are one of the most prevalent genetic disorders, affecting millions throughout the world. These are caused by pathogenic variants in genes that control the production of hemoglobin (Hb) subunits. As the number of known Hb variants has increased, it has become more challenging to obtain unambiguous results from routine chromatographic assays employed in the clinical laboratory. Top-down proteomic analysis of Hb by mass spectrometry is a definitive method to directly characterize the sequences of intact subunits. Here, we apply "chimeric ion loading" to characterize Hb β subunit variants. In this technique, product ions derived from complementary dissociation techniques are accumulated in a multipole storage device before delivery to a 21 T Fourier-transform ion cyclotron resonance mass spectrometer for simultaneous detection. To further improve the efficiency of identification of Hb variants and localization of the mutation site(s), we developed an R programming script, "Variants Identifier", to search top-down data against a database containing accurate intact mass differences and diagnostic ions from investigated Hb variants. A second R script, "PredictDiag", was developed and employed to determine relevant diagnostic ions for additional Hb variants with known sequences. These two R scripts were successfully applied to the identification of a Hb δ-β fusion protein and other Hb variants. The combination of chimeric ion loading and the above R scripts enables rapid and reliable interpretation of top-down mass spectrometry data, regardless of activation type, for Hb variant identification.
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Affiliation(s)
- Yuan Lin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32308, United States
| | - Archana M Agarwal
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, United States
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32308, United States
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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Samarah LZ, Vertes A, Anderton CR. Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures. Methods Mol Biol 2022; 2437:61-75. [PMID: 34902140 DOI: 10.1007/978-1-0716-2030-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.
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Affiliation(s)
- Laith Z Samarah
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Akos Vertes
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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10
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Kline JT, Mullen C, Durbin KR, Oates RN, Huguet R, Syka JEP, Fornelli L. Sequential Ion-Ion Reactions for Enhanced Gas-Phase Sequencing of Large Intact Proteins in a Tribrid Orbitrap Mass Spectrometer. J Am Soc Mass Spectrom 2021; 32:2334-2345. [PMID: 33900069 DOI: 10.1021/jasms.1c00062] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Obtaining extensive sequencing of an intact protein is essential in order to simultaneously determine both the nature and exact localization of chemical and genetic modifications which distinguish different proteoforms arising from the same gene. To effectively achieve such characterization, it is necessary to take advantage of the analytical potential offered by the top-down mass spectrometry approach to protein sequence analysis. However, as a protein increases in size, its gas-phase dissociation produces overlapping, low signal-to-noise fragments. The application of advanced ion dissociation techniques such as electron transfer dissociation (ETD) and ultraviolet photodissociation (UVPD) can improve the sequencing results compared to slow-heating techniques such as collisional dissociation; nonetheless, even ETD- and UVPD-based approaches have thus far fallen short in their capacity to reliably enable extensive sequencing of proteoforms ≥30 kDa. To overcome this issue, we have applied proton transfer charge reduction (PTCR) to limit signal overlap in tandem mass spectra (MS2) produced by ETD (alone or with supplemental ion activation, EThcD). Compared to conventional MS2 experiments, following ETD/EThcD MS2 with PTCR MS3 prior to m/z analysis of deprotonated product ions in the Orbitrap mass analyzer proved beneficial for the identification of additional large protein fragments (≥10 kDa), thus improving the overall sequencing and in particular the coverage of the central portion of all four analyzed proteins spanning from 29 to 56 kDa. Specifically, PTCR-based data acquisition led to 39% sequence coverage for the 56 kDa glutamate dehydrogenase, which was further increased to 44% by combining fragments obtained via HCD followed by PTCR MS3.
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Affiliation(s)
- Jake T Kline
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | | | - Ryan N Oates
- Department of Chemistry and Biochemistry, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, Oklahoma 73019, United States
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Nagornov KO, Kozhinov AN, Nicol E, Tsybin OY, Touboul D, Brunelle A, Tsybin YO. Narrow Aperture Detection Electrodes ICR Cell with Quadrupolar Ion Detection for FT-ICR MS at the Cyclotron Frequency. J Am Soc Mass Spectrom 2020; 31:2258-2269. [PMID: 32966078 DOI: 10.1021/jasms.0c00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion signal detection at the true (unperturbed) cyclotron frequency instead of the conventional reduced cyclotron frequency has remained a formidable challenge since the inception of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Recently, routine FT-ICR MS at the true cyclotron frequency has become a reality with the implementation of ICR cells with narrow aperture detection electrodes (NADEL). Here, we describe the development and implementation of the next generation of these cells, namely, a 2xNADEL ICR cell, which comprises four flat detect and four ∼45° cylindrical excite electrodes, enabling independent ion excitation and quadrupolar ion detection. The performance of the 2xNADEL ICR cell was evaluated on two commercial FT-ICR MS platforms, 10 T LTQ FT from Thermo Scientific and 9.4 T SolariX XR from Bruker Daltonics. The cells provided accurate mass measurements in the analyses of singly and multiply charged peptides (root-mean-square, RMS, mass error Δm/m of 90 ppb), proteins (Δm/m = 200 ppb), and petroleum fractions (Δm/m < 200 ppb). Due to the reduced influence of measured frequency on the space charge and external (trapping) electric fields, the 2xNADEL ICR cells exhibited stable performance in a wide range of trapping potentials (1-20 V). Similarly, in a 13 h rat brain MALDI imaging experiment, the RMS mass error did not exceed 600 ppb even for low signal-to-noise ratio analyte peaks. Notably, the same set of calibration constants was applicable to Fourier spectra in all pixels, reducing the need for recalibration at the individual pixel level. Overall, these results support further experimental development and fundamentals investigation of this promising technology.
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Affiliation(s)
| | | | - Edith Nicol
- Laboratoire de Chimie Moléculaire, CNRS UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Oleg Yu Tsybin
- Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Alain Brunelle
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
- Laboratoire d'Archéologie Moléculaire et Structurale, LAMS UMR8220, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, 1015 Lausanne, Switzerland
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12
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Srzentić K, Fornelli L, Tsybin YO, Loo JA, Seckler H, Agar JN, Anderson LC, Bai DL, Beck A, Brodbelt JS, van der Burgt YEM, Chamot-Rooke J, Chatterjee S, Chen Y, Clarke DJ, Danis PO, Diedrich JK, D'Ippolito RA, Dupré M, Gasilova N, Ge Y, Goo YA, Goodlett DR, Greer S, Haselmann KF, He L, Hendrickson CL, Hinkle JD, Holt MV, Hughes S, Hunt DF, Kelleher NL, Kozhinov AN, Lin Z, Malosse C, Marshall AG, Menin L, Millikin RJ, Nagornov KO, Nicolardi S, Paša-Tolić L, Pengelley S, Quebbemann NR, Resemann A, Sandoval W, Sarin R, Schmitt ND, Shabanowitz J, Shaw JB, Shortreed MR, Smith LM, Sobott F, Suckau D, Toby T, Weisbrod CR, Wildburger NC, Yates JR, Yoon SH, Young NL, Zhou M. Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:1783-1802. [PMID: 32812765 PMCID: PMC7539639 DOI: 10.1021/jasms.0c00036] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product's primary structure accurately and reproducibly. The major objective of the present study is to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up (BU) approaches with regard to confirming protein integrity, sequencing variable domains, avoiding artifacts, and revealing modifications and their locations. We also aim to gather information on the common TD/MD MS methods and practices in the field. A panel of three mAbs was selected and centrally provided to 20 laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). Various MS instrument platforms and ion dissociation techniques were employed. The present study confirms that TD/MD MS tools are available in laboratories worldwide and provide complementary information to the BU approach that can be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. A primary limitation revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS.
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Affiliation(s)
- Kristina Srzentić
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Luca Fornelli
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Joseph A Loo
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Henrique Seckler
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Jeffrey N Agar
- Northeastern University, Boston, Massachusetts 02115, United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Dina L Bai
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Alain Beck
- Centre d'immunologie Pierre Fabre, 74160 Saint-Julien-en-Genevois, France
| | | | | | | | | | - Yunqiu Chen
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | - David J Clarke
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, Massachusetts 02142, United States
| | - Jolene K Diedrich
- The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ying Ge
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Young Ah Goo
- University of Maryland, Baltimore, Maryland 21201, United States
| | - David R Goodlett
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Sylvester Greer
- University of Texas at Austin, Austin, Texas 78712-1224, United States
| | | | - Lidong He
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | | | - Joshua D Hinkle
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Matthew V Holt
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Sam Hughes
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Donald F Hunt
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Neil L Kelleher
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Anton N Kozhinov
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Ziqing Lin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Alan G Marshall
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Florida State University, Tallahassee, Florida 32310-4005, United States
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Robert J Millikin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Simone Nicolardi
- Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Neil R Quebbemann
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | | | - Wendy Sandoval
- Genentech, Inc., South San Francisco, California 94080-4990, United States
| | - Richa Sarin
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | | | | | - Jared B Shaw
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Lloyd M Smith
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Frank Sobott
- University of Antwerp, 2000 Antwerp, Belgium
- University of Leeds, LS2 9JT Leeds, United Kingdom
| | | | - Timothy Toby
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Norelle C Wildburger
- Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - John R Yates
- The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sung Hwan Yoon
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicolas L Young
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Hu P, Cole DP. Routine Absorption Mode FTMS Data Display with an Ethoxylated Anionic Detergent as a Dual-Role (Mass and Phase) Calibrant. J Am Soc Mass Spectrom 2019; 30:468-475. [PMID: 30456597 DOI: 10.1007/s13361-018-2099-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Absorption mode display of Fourier transform mass spectrometry (FTMS) data is known to improve both peak shape and resolution. Most FTMS data, however, are shown in magnitude mode due to the lack of a routine for determining the phase of ions that are necessary for absorption mode display. Despite the recent development of phase calibration methods, the use of absorption mode processing as a routine has been inhibited by the lack of a good phase calibration standard, particularly a standard that can be used as both a mass and a phase calibrant. A dual-role calibrant will enable the consolidation of mass and phase calibration into a single step making phase calibration as accessible as mass calibration without any incremental increase in complexity in the calibration procedure. We tested a series of detergents and found Triton QS-15, an anionic detergent, suitable as a dual-role calibrant. Additionally, Triton QS-15 produces both positive and negative ion series and thus can be used as a calibrant in both ionization modes. The establishment of a phase calibration routine helps to enable the application of FTMS in areas that require extreme mass resolution. One of the areas is the separation of the fine isotopic peaks of molecules with a large molecular mass (e.g., > 500 u). For data acquired using an ion cyclotron resonance instrument with a small magnet (e.g., 7 Tesla), there may not be adequate mass resolution to establish a useful isotopic fine structure if the data is displayed in the historical magnitude mode. A mere switch to the absorption mode display makes the isotopic fine structure (IFS) readily available for molecular formula determination. Graphical Abstract x.
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Affiliation(s)
- Peifeng Hu
- Baxter Healthcare Corporation, 25212 W Illinois Rt. 120, Round Lake, IL, 60073, USA.
| | - D Paul Cole
- Baxter Healthcare Corporation, 25212 W Illinois Rt. 120, Round Lake, IL, 60073, USA
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14
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Srzentić K, Zhurov KO, Lobas AA, Nikitin G, Fornelli L, Gorshkov MV, Tsybin YO. Chemical-Mediated Digestion: An Alternative Realm for Middle-down Proteomics? J Proteome Res 2018; 17:2005-2016. [PMID: 29722266 DOI: 10.1021/acs.jproteome.7b00834] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein digestion in mass spectrometry (MS)-based bottom-up proteomics targets mainly lysine and arginine residues, yielding primarily 0.6-3 kDa peptides for the proteomes of organisms of all major kingdoms. Recent advances in MS technology enable analysis of complex mixtures of increasingly longer (>3 kDa) peptides in a high-throughput manner supporting the development of a middle-down proteomics (MDP) approach. Generating longer peptides is a paramount step in launching an MDP pipeline, but the quest for the selection of a cleaving agent that would provide the desired 3-15 kDa peptides remains open. Recent bioinformatics studies have shown that cleavage at the rarely occurring amino acid residues such as methionine (Met), tryptophan (Trp), or cysteine (Cys) would be suitable for MDP approach. Interestingly, chemical-mediated proteolytic cleavages uniquely allow targeting these rare amino acids, for which no specific proteolytic enzymes are known. Herein, as potential candidates for MDP-grade proteolysis, we have investigated the performance of chemical agents previously reported to target primarily Met, Trp, and Cys residues: CNBr, BNPS-Skatole (3-bromo-3-methyl-2-(2-nitrophenyl)sulfanylindole), and NTCB (2-nitro-5-thiobenzoic acid), respectively. Figures of merit such as digestion reproducibility, peptide size distribution, and occurrence of side reactions are discussed. The NTCB-based MDP workflow has demonstrated particularly attractive performance, and NTCB is put forward here as a potential cleaving agent for further MDP development.
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Affiliation(s)
- Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | | | - Anna A Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia
| | - Gennady Nikitin
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Luca Fornelli
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy per. , Dolgoprudny, Moscow 141707 , Russia
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park , Lausanne 1015 , Switzerland
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15
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Nagornov KO, Kozhinov AN, Tsybin YO. Cyclotron Phase-Coherent Ion Spatial Dispersion in a Non-Quadratic Trapping Potential is Responsible for FT-ICR MS at the Cyclotron Frequency. J Am Soc Mass Spectrom 2018; 29:63-77. [PMID: 29119518 DOI: 10.1007/s13361-017-1821-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) at the cyclotron frequency instead of the reduced cyclotron frequency has been experimentally demonstrated using narrow aperture detection electrode (NADEL) ICR cells. Here, based on the results of SIMION simulations, we provide the initial mechanistic insights into the cyclotron frequency regime generation in FT-ICR MS. The reason for cyclotron frequency regime is found to be a new type of a collective motion of ions with a certain dispersion in the initial characteristics, such as pre-excitation ion velocities, in a highly non-quadratic trapping potential as realized in NADEL ICR cells. During ion detection, ions of the same m/z move in phase for cyclotron ion motion but out of phase for magnetron (drift) ion motion destroying signals at the fundamental and high order harmonics that comprise reduced cyclotron frequency components. After an initial magnetron motion period, ion clouds distribute into a novel type of structures - ion slabs, elliptical cylinders, or star-like structures. These structures rotate at the Larmor (half-cyclotron) frequency on a plane orthogonal to the magnetic field, inducing signals at the true cyclotron frequency on each of the narrow aperture detection electrodes. To eliminate the reduced cyclotron frequency peak upon dipolar ion detection, a number of slabs or elliptical cylinders organizing a star-like configuration are formed. In a NADEL ICR cell with quadrupolar ion detection, a single slab or an elliptical cylinder is sufficient to minimize the intensity of the reduced cyclotron frequency components, particularly the second harmonic. Graphical Abstract ᅟ.
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Affiliation(s)
| | | | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, 1015, Lausanne, Switzerland.
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16
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Tian S, Yu G, He H, Zhao Y, Liu P, Marshall AG, Demeler B, Stagg SM, Li H. Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p. Structure 2017; 25:1519-1529.e4. [PMID: 28919439 PMCID: PMC6625358 DOI: 10.1016/j.str.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/11/2017] [Accepted: 08/07/2017] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of structural information on the ScR2TP complex, however, prevents a mechanistic understanding of this biological process. We characterized the structure of the ScR2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 binding proteins, Tah1p and Pih1p, and its interaction with the snoRNP protein Nop58p by a combination of analytical ultracentrifugation, isothermal titration calorimetry, chemical crosslinking, hydrogen-deuterium exchange, and cryoelectron microscopy methods. We find that Pih1p-Tah1p interacts with Rvb1/2p cooperatively through the nucleotide-sensitive domain of Rvb1/2p. Nop58p further binds Pih1p-Tahp1 on top of the dome-shaped R2TP. Consequently, nucleotide binding releases Pih1p-Tah1p from Rvb1/2p, which offers a mechanism for nucleotide-driven binding and release of snoRNP intermediates.
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Affiliation(s)
- Shaoxiong Tian
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Peilu Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Ion Cyclotron Resonance Program, The National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Scott M Stagg
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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17
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Weisbrod CR, Kaiser NK, Syka JEP, Early L, Mullen C, Dunyach JJ, English AM, Anderson LC, Blakney GT, Shabanowitz J, Hendrickson CL, Marshall AG, Hunt DF. Front-End Electron Transfer Dissociation Coupled to a 21 Tesla FT-ICR Mass Spectrometer for Intact Protein Sequence Analysis. J Am Soc Mass Spectrom 2017; 28:1787-1795. [PMID: 28721671 PMCID: PMC5711562 DOI: 10.1007/s13361-017-1702-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 05/13/2023]
Abstract
High resolution mass spectrometry is a key technology for in-depth protein characterization. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enables high-level interrogation of intact proteins in the most detail to date. However, an appropriate complement of fragmentation technologies must be paired with FTMS to provide comprehensive sequence coverage, as well as characterization of sequence variants, and post-translational modifications. Here we describe the integration of front-end electron transfer dissociation (FETD) with a custom-built 21 tesla FT-ICR mass spectrometer, which yields unprecedented sequence coverage for proteins ranging from 2.8 to 29 kDa, without the need for extensive spectral averaging (e.g., ~60% sequence coverage for apo-myoglobin with four averaged acquisitions). The system is equipped with a multipole storage device separate from the ETD reaction device, which allows accumulation of multiple ETD fragment ion fills. Consequently, an optimally large product ion population is accumulated prior to transfer to the ICR cell for mass analysis, which improves mass spectral signal-to-noise ratio, dynamic range, and scan rate. We find a linear relationship between protein molecular weight and minimum number of ETD reaction fills to achieve optimum sequence coverage, thereby enabling more efficient use of instrument data acquisition time. Finally, real-time scaling of the number of ETD reactions fills during method-based acquisition is shown, and the implications for LC-MS/MS top-down analysis are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
- Chad R Weisbrod
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA.
| | - Nathan K Kaiser
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | | | - Lee Early
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | | | - A Michelle English
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Lissa C Anderson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Greg T Blakney
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory (NHMFL), 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, McCormick Road, P.O. Box 400319, Charlottesville, VA, 22904-4319, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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18
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He L, Anderson LC, Barnidge DR, Murray DL, Hendrickson CL, Marshall AG. Analysis of Monoclonal Antibodies in Human Serum as a Model for Clinical Monoclonal Gammopathy by Use of 21 Tesla FT-ICR Top-Down and Middle-Down MS/MS. J Am Soc Mass Spectrom 2017; 28:827-838. [PMID: 28247297 DOI: 10.1007/s13361-017-1602-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/07/2017] [Accepted: 01/11/2017] [Indexed: 05/27/2023]
Abstract
With the rapid growth of therapeutic monoclonal antibodies (mAbs), stringent quality control is needed to ensure clinical safety and efficacy. Monoclonal antibody primary sequence and post-translational modifications (PTM) are conventionally analyzed with labor-intensive, bottom-up tandem mass spectrometry (MS/MS), which is limited by incomplete peptide sequence coverage and introduction of artifacts during the lengthy analysis procedure. Here, we describe top-down and middle-down approaches with the advantages of fast sample preparation with minimal artifacts, ultrahigh mass accuracy, and extensive residue cleavages by use of 21 tesla FT-ICR MS/MS. The ultrahigh mass accuracy yields an RMS error of 0.2-0.4 ppm for antibody light chain, heavy chain, heavy chain Fc/2, and Fd subunits. The corresponding sequence coverages are 81%, 38%, 72%, and 65% with MS/MS RMS error ~4 ppm. Extension to a monoclonal antibody in human serum as a monoclonal gammopathy model yielded 53% sequence coverage from two nano-LC MS/MS runs. A blind analysis of five therapeutic monoclonal antibodies at clinically relevant concentrations in human serum resulted in correct identification of all five antibodies. Nano-LC 21 T FT-ICR MS/MS provides nonpareil mass resolution, mass accuracy, and sequence coverage for mAbs, and sets a benchmark for MS/MS analysis of multiple mAbs in serum. This is the first time that extensive cleavages for both variable and constant regions have been achieved for mAbs in a human serum background. Graphical Abstract ᅟ.
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Affiliation(s)
- Lidong He
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32310, USA
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - David R Barnidge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - David L Murray
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Christopher L Hendrickson
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32310, USA
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32310, USA.
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL, 32310, USA.
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19
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Nagornov KO, Kozhinov AN, Tsybin YO. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry at the Cyclotron Frequency. J Am Soc Mass Spectrom 2017; 28:768-780. [PMID: 28213728 DOI: 10.1007/s13361-017-1598-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 12/29/2016] [Accepted: 01/07/2017] [Indexed: 06/06/2023]
Abstract
The phenomenon of ion cyclotron resonance allows for determining mass-to-charge ratio, m/z, of an ensemble of ions by means of measurements of their cyclotron frequency, ω c . In Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), the ω c quantity is usually unavailable for direct measurements: the resonant state is located close to the reduced cyclotron frequency (ω+), whereas the ω c and the corresponding m/z values may be calculated via theoretical derivation from an experimental estimate of the ω+ quantity. Here, we describe an experimental observation of a new resonant state, which is located close to the ω c frequency and is established because of azimuthally-dependent trapping electric fields of the recently developed ICR cells with narrow aperture detection electrodes. We show that in mass spectra, peaks close to ω+ frequencies can be reduced to negligible levels relative to peaks close to ω c frequencies. Due to reduced errors with which the ω c quantity is obtained, the new resonance provides a means of cyclotron frequency measurements with precision greater than that achieved when ω+ frequency peaks are employed. The described phenomenon may be considered for a development into an FT-ICR MS technology with increased mass accuracy for applications in basic research, life, and environmental sciences. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Anton N Kozhinov
- Spectroswiss Sàrl, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Yury O Tsybin
- Spectroswiss Sàrl, EPFL Innovation Park, 1015, Lausanne, Switzerland.
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20
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Park SG, Anderson GA, Bruce JE. Parallel Spectral Acquisition with Orthogonal ICR Cells. J Am Soc Mass Spectrom 2017; 28:515-524. [PMID: 28058592 PMCID: PMC5352489 DOI: 10.1007/s13361-016-1573-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/21/2016] [Accepted: 11/27/2016] [Indexed: 05/22/2023]
Abstract
FT-based high performance mass analyzers yield increased resolving power and mass measurement accuracy, yet require increased duration of signal acquisition that can limit many applications. The implementation of stronger magnetic fields, multiple detection electrodes for harmonic signal detection, and an array of multiple mass analyzers arranged along the magnetic field axis have been used to decrease required acquisition time. The results presented here show that multiple ion cyclotron resonance (ICR) mass analyzers can also be implemented orthogonal to the central magnetic field axis. The orthogonal ICR cell system presented here consisting of two cells (master and slave cells) was constructed with printed circuit boards and installed within a single superconducting magnet and vacuum system. A master cell was positioned, as is normally done with ICR cells, on the central magnetic field axis and a slave cell was located off this central axis, but directly adjacent and alongside the master cell. To achieve ion transfer between cells, ions that were initially trapped in the master cell were drifted across the magnetic field into the slave cell with application of a small DC field applied perpendicularly to the magnetic field axis. A subsequent population of ions was injected and accumulated in the master cell. Simultaneous excitation of cyclotron motion of ions in both cells was carried out; ICR signals from each cell were independently amplified and recorded in parallel. Presented here are the initial results of successful parallel spectral acquisition with this orthogonal dual ICR cell array. Graphical Abstract ᅟ.
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Affiliation(s)
- Sung-Gun Park
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA
| | | | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, 98109, USA.
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21
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Anderson LC, DeHart CJ, Kaiser NK, Fellers RT, Smith DF, Greer JB, LeDuc RD, Blakney GT, Thomas PM, Kelleher NL, Hendrickson CL. Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry. J Proteome Res 2016; 16:1087-1096. [PMID: 27936753 DOI: 10.1021/acs.jproteome.6b00696] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Successful high-throughput characterization of intact proteins from complex biological samples by mass spectrometry requires instrumentation capable of high mass resolving power, mass accuracy, sensitivity, and spectral acquisition rate. These limitations often necessitate the performance of hundreds of LC-MS/MS experiments to obtain reasonable coverage of the targeted proteome, which is still typically limited to molecular weights below 30 kDa. The National High Magnetic Field Laboratory (NHMFL) recently installed a 21 T FT-ICR mass spectrometer, which is part of the NHMFL FT-ICR User Facility and available to all qualified users. Here we demonstrate top-down LC-21 T FT-ICR MS/MS of intact proteins derived from human colorectal cancer cell lysate. We identified a combined total of 684 unique protein entries observed as 3238 unique proteoforms at a 1% false discovery rate, based on rapid, data-dependent acquisition of collision-induced and electron-transfer dissociation tandem mass spectra from just 40 LC-MS/MS experiments. Our identifications included 372 proteoforms with molecular weights over 30 kDa detected at isotopic resolution, which substantially extends the accessible mass range for high-throughput top-down LC-MS/MS.
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Affiliation(s)
- Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Caroline J DeHart
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Nathan K Kaiser
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Donald F Smith
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Joseph B Greer
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Greg T Blakney
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry and Molecular Biosciences and the Division of Hematology-Oncology, Northwestern University , Evanston, Illinois 60208, United States
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32304, United States
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22
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Shaw JB, Lin TY, Leach FE, Tolmachev AV, Tolić N, Robinson EW, Koppenaal DW, Paša-Tolić L. 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox. J Am Soc Mass Spectrom 2016; 27:1929-1936. [PMID: 27734325 DOI: 10.1007/s13361-016-1507-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
We provide the initial performance evaluation of a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer operating at the Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory. The spectrometer constructed for the 21T system employs a commercial dual linear ion trap mass spectrometer coupled to a FTICR spectrometer designed and built in-house. Performance gains from moving to higher magnetic field strength are exemplified by the measurement of peptide isotopic fine structure, complex natural organic matter mixtures, and large proteins. Accurate determination of isotopic fine structure was demonstrated for doubly charged Substance P with minimal spectral averaging, and 8158 molecular formulas assigned to Suwannee River Fulvic Acid standard with root-mean-square (RMS) error of 10 ppb. We also demonstrated superior performance for intact proteins; namely, broadband isotopic resolution of the entire charge state distribution of apo-transferrin (78 kDa) and facile isotopic resolution of monoclonal antibody under a variety of acquisition parameters (e.g., 6 s time-domains with absorption mode processing yielded resolution of approximately 1 M at m/z = 2700). Graphical Abstract ᅟ.
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Affiliation(s)
- Jared B Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Tzu-Yung Lin
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Franklin E Leach
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Aleksey V Tolmachev
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Errol W Robinson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Ave. (K8-98), P.O. Box 999, Richland, WA, 99352, USA.
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23
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Yang B, Feng YJ, Vu H, McCormick B, Rowley J, Pedro L, Crowther GJ, Van Voorhis WC, Forster PI, Quinn RJ. Bioaffinity Mass Spectrometry Screening. ACTA ACUST UNITED AC 2016; 21:194-200. [PMID: 26773071 DOI: 10.1177/1087057115622605] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS or ESI-FTMS) was used to screen 192 natural product extracts and a 659-member natural product-based fragment library for bindings to a potential malaria drug target, Plasmodium falciparum Rab11a (PfRab11a, PF13_0119). One natural product extract and 11 fragments showed binding activity. A new natural product, arborside E, was identified from the active extract of Psydrax montigena as a weak binder. Its binding activity and inhibitory activity against PfRab11a were confirmed by ESI-FTMS titration experiments and an orthogonal enzyme assay.
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Affiliation(s)
- Ben Yang
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Yun Jiang Feng
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Hoan Vu
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brendan McCormick
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Jessica Rowley
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Liliana Pedro
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | | | | | - Paul I Forster
- Queensland Herbarium, DSITI, Brisbane Botanic Gardens, Queensland, Australia
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
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24
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Dang X, Singh A, Spetman BD, Nolan KD, Isaacs JS, Dennis JH, Dalton S, Marshall AG, Young NL. Label-Free Relative Quantitation of Isobaric and Isomeric Human Histone H2A and H2B Variants by Fourier Transform Ion Cyclotron Resonance Top-Down MS/MS. J Proteome Res 2016; 15:3196-203. [PMID: 27431976 DOI: 10.1021/acs.jproteome.6b00414] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone variants are known to play a central role in genome regulation and maintenance. However, many variants are inaccessible by antibody-based methods or bottom-up tandem mass spectrometry due to their highly similar sequences. For many, the only tractable approach is with intact protein top-down tandem mass spectrometry. Here, ultra-high-resolution FT-ICR MS and MS/MS yield quantitative relative abundances of all detected HeLa H2A and H2B isobaric and isomeric variants with a label-free approach. We extend the analysis to identify and relatively quantitate 16 proteoforms from 12 sequence variants of histone H2A and 10 proteoforms of histone H2B from three other cell lines: human embryonic stem cells (WA09), U937, and a prostate cancer cell line LaZ. The top-down MS/MS approach provides a path forward for more extensive elucidation of the biological role of many previously unstudied histone variants and post-translational modifications.
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Affiliation(s)
- Xibei Dang
- Department of Chemistry and Biochemistry, Florida State University , 95 Chieftain Way, Tallahassee, Florida 32306-4390, United States
| | - Amar Singh
- Department of Biochemistry and Molecular Biology, University of Georgia , 724 Biological Sciences Building, Athens, Georgia 30602-2607, United States
| | - Brian D Spetman
- Department of Biological Science, Florida State University , 319 Stadium Drive, Tallahassee, Florida 32306-4295, United States
| | - Krystal D Nolan
- Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina , 173 Ashley Avenue, Charleston, South Carolina 29425, United States
| | - Jennifer S Isaacs
- Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina , 173 Ashley Avenue, Charleston, South Carolina 29425, United States
| | - Jonathan H Dennis
- Department of Biological Science, Florida State University , 319 Stadium Drive, Tallahassee, Florida 32306-4295, United States
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, University of Georgia , 724 Biological Sciences Building, Athens, Georgia 30602-2607, United States
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University , 95 Chieftain Way, Tallahassee, Florida 32306-4390, United States.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States
| | - Nicolas L Young
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, United States.,Verna & Marrs McLean Dept. of Biochemistry & Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, Texas 77030-3411, United States
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25
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Ghaste M, Mistrik R, Shulaev V. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics. Int J Mol Sci 2016; 17:ijms17060816. [PMID: 27231903 PMCID: PMC4926350 DOI: 10.3390/ijms17060816] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 02/02/2023] Open
Abstract
Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.
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Affiliation(s)
- Manoj Ghaste
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
| | | | - Vladimir Shulaev
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
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26
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Lim L, Yan F, Bach S, Pihakari K, Klein D. Fourier Transform Mass Spectrometry: The Transformation of Modern Environmental Analyses. Int J Mol Sci 2016; 17:E104. [PMID: 26784175 DOI: 10.3390/ijms17010104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/21/2015] [Accepted: 12/28/2015] [Indexed: 12/16/2022] Open
Abstract
Unknown compounds in environmental samples are difficult to identify using standard mass spectrometric methods. Fourier transform mass spectrometry (FTMS) has revolutionized how environmental analyses are performed. With its unsurpassed mass accuracy, high resolution and sensitivity, researchers now have a tool for difficult and complex environmental analyses. Two features of FTMS are responsible for changing the face of how complex analyses are accomplished. First is the ability to quickly and with high mass accuracy determine the presence of unknown chemical residues in samples. For years, the field has been limited by mass spectrometric methods that were based on knowing what compounds of interest were. Secondly, by utilizing the high resolution capabilities coupled with the low detection limits of FTMS, analysts also could dilute the sample sufficiently to minimize the ionization changes from varied matrices.
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27
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Takahashi K, Kozuka T, Anegawa A, Nagatani A, Mimura T. Development and Application of a High-Resolution Imaging Mass Spectrometer for the Study of Plant Tissues. Plant Cell Physiol 2015; 56:1329-38. [PMID: 26063395 DOI: 10.1093/pcp/pcv083] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/30/2015] [Indexed: 05/27/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) or imaging mass spectrometry (imaging MS) has been a powerful tool to map the spatial distribution of molecules on the surface of biological materials. This technique has frequently been applied to animal tissue slices for the purpose of mapping proteins, peptides, lipids, sugars or small metabolites to find disease-specific biomarkers or to study drug metabolism. Recently, it has also been applied to intact plant tissues or thin slices thereof using commercial mass spectrometers. The present work is concerned with the refinement of MALDI/laser desorption/ionization (LDI)-Fourier transform ion cyclotron resonance (FTICR)-MS incorporating certain specific features namely, ultra-high mass resolution (>100,000), ultra-high molecular mass accuracy (<1 p.p.m.) and high spatial resolution (<10 µm) for imaging MS of plant tissues. Employing an in-house built mass spectrometer, the imaging MS analysis of intact Arabidopsis thaliana tissues, namely etiolated seedlings and roots of seedlings, glued to a small transparent ITO (indium tin oxide)-coated conductive glass was performed. A matrix substance was applied to the vacuum-dried intact tissues by sublimation prior to the imaging MS analysis. The images of various small metabolites representing their two-dimensional distribution on the dried intact tissues were obtained with or without different matrix substances. The effects of MALDI matrices on the ionization of small metabolites during imaging MS acquisition are discussed.
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Affiliation(s)
- Katsutoshi Takahashi
- National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568 Japan
| | - Toshiaki Kozuka
- Kyoto University, Kyoto, 606-8502 Japan Hiroshima University, Hiroshima, 739-8526 Japan These authors contributed equally to this work
| | - Aya Anegawa
- Kobe University, Kobe, 657-8501 Japan These authors contributed equally to this work
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28
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Guan X, Noble KA, Tao Y, Roux KH, Sathe SK, Young NL, Marshall AG. Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry. J Mass Spectrom 2015; 50:812-819. [PMID: 26169135 DOI: 10.1002/jms.3589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution-phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX-MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope-contributing segments.
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Affiliation(s)
- Xiaoyan Guan
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Kyle A Noble
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Shridhar K Sathe
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
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29
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Koulman A, Prentice P, Wong MCY, Matthews L, Bond NJ, Eiden M, Griffin JL, Dunger DB. The development and validation of a fast and robust dried blood spot based lipid profiling method to study infant metabolism. Metabolomics 2014; 10:1018-1025. [PMID: 25177234 PMCID: PMC4145199 DOI: 10.1007/s11306-014-0628-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/27/2014] [Indexed: 01/21/2023]
Abstract
Early life exposures and metabolic programming are associated with later disease risk. In particular lipid metabolism is thought to play a key role in the development of the metabolic syndrome and insulin resistance in later life. Investigative studies of metabolic programming are limited by the ethics and practicalities of sample collection in small infants. Dried blood spots on filter paper, derived from heel pricks are considered as the most suitable option for this age group. We validated a novel lipid profiling method, based on high resolution mass spectrometry to successfully determine the lipid composition of infants using dried blood spots. The spotting and air drying of blood on paper has noticeable effects on many of the lipids, leading to lipid oxidation and hydrolysis, which demand careful interpretation of the obtained data. We compared the lipid profiles from plasma or whole blood samples and the results from dried blood spots to determine if these revealed the same inter-subject differences. The results from dried blood spots were no less reproducible than other lipid profiling methods which required comparatively larger sample volumes. Therefore, lipid profiles obtained from dried blood spots can be successfully used to monitor infancy lipid metabolism and we show significant differences in the lipid metabolism of infants at age 3 versus 12 months.
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Affiliation(s)
- Albert Koulman
- 0000 0004 0606 2472grid.415055.0Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL UK
| | - Philippa Prentice
- 0000000121885934grid.5335.0Department of Paediatrics, Addenbrooke’s Hospital, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Max C. Y. Wong
- 0000000121885934grid.5335.0Department of Paediatrics, Addenbrooke’s Hospital, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Lee Matthews
- 0000 0004 0606 2472grid.415055.0Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL UK
| | - Nicholas J. Bond
- 0000 0004 0606 2472grid.415055.0Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL UK
| | - Michael Eiden
- 0000 0004 0606 2472grid.415055.0Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL UK
| | - Julian L. Griffin
- 0000 0004 0606 2472grid.415055.0Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL UK
| | - David B. Dunger
- 0000000121885934grid.5335.0Department of Paediatrics, Addenbrooke’s Hospital, University of Cambridge, Cambridge, CB2 0QQ UK
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30
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Vo QV, Trenerry C, Rochfort S, Wadeson J, Leyton C, Hughes AB. Synthesis and anti-inflammatory activity of indole glucosinolates. Bioorg Med Chem 2013; 22:856-64. [PMID: 24360830 DOI: 10.1016/j.bmc.2013.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/21/2013] [Accepted: 12/02/2013] [Indexed: 11/24/2022]
Abstract
The nitronate and nitrovinyl methods to synthesize indole glucosinolates (GLs) have been investigated. The results were applied to generally the most prevalent natural indole glucosinolates to synthesize 4-methoxyglucobrassicin (MGB) and neo-glucobrassicin (NGB) in moderate overall yield for the first time. The anti-inflammatory activity of the synthetic indole GLs was determined by inhibition of TNF-α secretion in LPS-stimulated THP-1 cells. The data showed that glucobrassicin (GB) exhibited higher activity than other synthetic indolyl GLs.
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Affiliation(s)
- Quan V Vo
- Department of Chemistry, La Trobe University, Victoria 3086, Australia
| | - Craige Trenerry
- Department of Primary Industries, Knoxfield Centre, 621 Burwood Highway, Knoxfield 3180, Australia
| | - Simone Rochfort
- Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora 3083, Victoria, Australia; La Trobe University, Victoria 3086, Australia
| | - Jenny Wadeson
- Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora 3083, Victoria, Australia
| | - Carolina Leyton
- Department of Primary Industries, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora 3083, Victoria, Australia
| | - Andrew B Hughes
- Department of Chemistry, La Trobe University, Victoria 3086, Australia.
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31
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Gouveia MJ, Brindley PJ, Santos LL, da Costa JMC, Gomes P, Vale N. Mass spectrometry techniques in the survey of steroid metabolites as potential disease biomarkers: a review. Metabolism 2013; 62:1206-17. [PMID: 23664145 PMCID: PMC3755027 DOI: 10.1016/j.metabol.2013.04.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/13/2013] [Accepted: 04/02/2013] [Indexed: 01/31/2023]
Abstract
Mass spectrometric approaches have been fundamental to the identification of metabolites associated with steroid hormones, yet this topic has not been reviewed in depth in recent years. To this end, and given the increasing relevance of liquid chromatography-mass spectrometry (LC-MS) studies on steroid hormones and their metabolites, the present review addresses this subject. This review provides a timely summary of the use of various mass spectrometry-based analytical techniques during the evaluation of steroidal biomarkers in a range of human disease settings. The sensitivity and specificity of these technologies are clearly providing valuable new insights into breast cancer and cardiovascular disease. We aim to contribute to an enhanced understanding of steroid metabolism and how it can be profiled by LC-MS techniques.
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Affiliation(s)
- Maria João Gouveia
- Center for the Study of Animal Science, ICETA, University of Porto
- INSA, Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal
| | - Paul J. Brindley
- George Washington University School of Medicine & Health Sciences – Department of Microbiology, Immunology and Tropical Medicine, Ross Hali, 20037 Washington, DC, USA
| | - Lúcio Lara Santos
- Experimental Therapeutics and Pathology Research Group - IPO-Porto, Portuguese Institute of Oncology Francisco Gentil, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - José Manuel Correia da Costa
- Center for the Study of Animal Science, ICETA, University of Porto
- INSA, Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal
| | - Paula Gomes
- CIQUP, Chemistry and Biochemistry Department, Faculty of Sciences, University of Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Nuno Vale
- CIQUP, Chemistry and Biochemistry Department, Faculty of Sciences, University of Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal
- Corresponding author: CIQUP, Chemistry and Biochemistry Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal Tel.: +351 220402567; fax: + 351 220402563,
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32
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Vo QV, Trenerry C, Rochfort S, Wadeson J, Leyton C, Hughes AB. Synthesis and anti-inflammatory activity of aromatic glucosinolates. Bioorg Med Chem 2013; 21:5945-54. [PMID: 23978357 DOI: 10.1016/j.bmc.2013.07.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 07/19/2013] [Accepted: 07/30/2013] [Indexed: 11/26/2022]
Abstract
Aromatic GLs are important members of the glucosinolate family of compounds because of their potential biological activity and medicinal properties. This study has shown success in the high yielding synthesis of some important aromatic GLs as well as the results of testing for anti-inflammatory properties of the synthetic GLs. 3,4-Dimethoxyphenylglucosinolate was found to be the most active anti-inflammatory of the seven glucosinolates assayed.
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Affiliation(s)
- Quan V Vo
- Department of Chemistry, La Trobe University, Victoria 3086, Australia
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G Marshall A, T Blakney G, Chen T, K Kaiser N, M McKenna A, P Rodgers R, M Ruddy B, Xian F. Mass resolution and mass accuracy: how much is enough? Mass Spectrom (Tokyo) 2013; 2:S0009. [PMID: 24349928 DOI: 10.5702/massspectrometry.s0009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/28/2012] [Indexed: 11/23/2022] Open
Abstract
Accurate mass measurement requires the highest possible mass resolution, to ensure that only a single elemental composition contributes to the mass spectral peak in question. Although mass resolution is conventionally defined as the closest distinguishable separation between two peaks of equal height and width, the required mass resolving power can be ∼10× higher for equal width peaks whose peak height ratio is 100 : 1. Ergo, minimum resolving power requires specification of maximum dynamic range, and is thus 10-100× higher than the conventional definition. Mass resolving power also depends on mass-to-charge ratio. Mass accuracy depends on mass spectral signal-to-noise ratio and digital resolution. Finally, the reliability of elemental composition assignment can be improved by resolution of isotopic fine structure. Thus, the answer to the question of "how much is enough mass resolving power" requires that one first specify S/N ratio, dynamic range, digital resolution, mass-to-charge ratio, and (if available) isotopic fine structure. The highest available broadband mass resolving power and mass accuracy is from Fourier transform ion cyclotron resonance mass spectrometry. Over the past five years, FT-ICR MS mass accuracy has improved by about an order of magnitude, based on higher magnetic field strength, conditional averaging of time-domain transients, better mass calibration (spectral segmentation; inclusion of a space charge term); radially dispersed excitation; phase correction to yield absorption-mode display; and new ICR cell segmentation designs.
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Affiliation(s)
- Alan G Marshall
- Department of Chemistry & Biochemistry, Florida State University ; Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University
| | - Greg T Blakney
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University
| | - Tong Chen
- Department of Chemistry & Biochemistry, Florida State University
| | - Nathan K Kaiser
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University
| | - Amy M McKenna
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University
| | - Ryan P Rodgers
- Department of Chemistry & Biochemistry, Florida State University ; Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University
| | - Brian M Ruddy
- Department of Chemistry & Biochemistry, Florida State University
| | - Feng Xian
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University
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