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Kooij S, Chojnacka A, Bonn D, Corthals GL, van Rijn CJM. Electroless Ionization Mass Spectrometry Using a Compact Electrokinetic Ionization Source. Anal Chem 2024; 96:10978-10985. [PMID: 38917274 PMCID: PMC11238159 DOI: 10.1021/acs.analchem.4c01403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024]
Abstract
We introduce a new ionization technique for compact, portable mass spectrometers. It consists of a syringe with sample liquid capped by a self-ionizing spray nozzle containing a microfabricated nozzle chip. Interaction of the sample liquid with the nozzle wall results in electrical charging without the need for electronics. Elaborate cleaning procedures are redundant when disposable syringes and mass-fabricated spray nozzles are used. This self-named electroless spray ionization (ELI) technique shows comparable performance to conventional ionization techniques. In contrast to commonly used electrospray ionization, ELI exhibits excellent ionization efficiency for low-conductive solutions such as water or acetonitrile. Due to its compact size and the absence of high-voltage electronics, it can also be readily integrated in other ionization sources. Besides reviewing the main properties of ELI, we showcase the technique's potential for two on-site, ambient mass spectroscopy applications: perfume fingerprinting and fast screening of fungicides on citrus fruits.
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Affiliation(s)
- Stefan Kooij
- Van
der Waals-Zeeman Institute, University of
Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Aleksandra Chojnacka
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Daniel Bonn
- Van
der Waals-Zeeman Institute, University of
Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Garry L. Corthals
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Cees J. M. van Rijn
- Van
der Waals-Zeeman Institute, University of
Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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2
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Intracluster Sulphur Dioxide Oxidation by Sodium Chlorite Anions: A Mass Spectrometric Study. Molecules 2021; 26:molecules26237114. [PMID: 34885696 PMCID: PMC8659277 DOI: 10.3390/molecules26237114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
The reactivity of [NaL·ClO2]− cluster anions (L = ClOx−; x = 0–3) with sulphur dioxide has been investigated in the gas phase by ion–molecule reaction experiments (IMR) performed in an in-house modified Ion Trap mass spectrometer (IT-MS). The kinetic analysis revealed that SO2 is efficiently oxidised by oxygen-atom (OAT), oxygen-ion (OIT) and double oxygen transfer (DOT) reactions. The main difference from the previously investigated free reactive ClO2− is the occurrence of intracluster OIT and DOT processes, which are mediated by the different ligands of the chlorite anion. This gas-phase study highlights the importance of studying the intrinsic properties of simple reacting species, with the aim of elucidating the elementary steps of complex processes occurring in solution, such as the oxidation of sulphur dioxide.
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3
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Itze-Mayrhofer C, Brem G. Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids. J Proteomics 2020; 225:103884. [PMID: 32593762 DOI: 10.1016/j.jprot.2020.103884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 02/06/2023]
Abstract
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
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Affiliation(s)
- Corina Itze-Mayrhofer
- Institute of Animal Breeding and Genetics, Group Molecular Reproduction IFA-Tulln, University of Veterinary Medicine, Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
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4
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Persaud RR, Dieke NE, Jing X, Lambert S, Parsa N, Hartmann E, Vincent JB, Cassady CJ, Dixon DA. Mechanistic Study of Enhanced Protonation by Chromium(III) in Electrospray Ionization: A Superacid Bound to a Peptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:308-318. [PMID: 32031389 DOI: 10.1021/jasms.9b00078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Addition of trivalent chromium, Cr(III), to solutions undergoing electrospray ionization (ESI) enhances protonation and leads to formation of [M + 2H]2+ for peptides that normally produce [M + H]+. This effect is explored using electronic structure calculations at the density functional theory (DFT) level to predict the energetics of various species that are potentially important to the mechanism. Gas- and solution-phase reaction free energies for glycine and its anion reacting with [Cr(III)(H2O)6]3+ and for dehydration of these species have been predicted, where glycine is used as a simple model for a peptide. For comparison, calculations were also performed with Fe(III), Al(III), Sc(III), Y(III), and La(III). Removal of water from these complexes, as would occur during the ESI desolvation process, results in species that are highly acidic. The calculated pKa of Cr(III) with a single solvation shell is -10.8, making [Cr(III)(H2O)6]3+ a superacid that is more acidic than sulfuric acid (pKa = -8.8). Binding to glycine requires removal of two aqua ligands, which gives [Cr(III)(H2O)4]3+ that has an extremely acidic pKa of -28.8. Removal of additional water further enhances acidity, reaching a pKa of -84.7 for [Cr(III)(H2O)]3+. A mechanism for enhanced protonation is proposed that incorporates computational and experiment results, as well as information on the known chemistry of Cr(III), which is substitutionally inert. The initial step involves binding of [Cr(III)(H2O)4]3+ to the deprotonated C-terminus of a peptide. As the drying process during ESI strips water from the complex, the resulting superacid transfers protons to the bound peptide, eventually leading to formation of [M + 2H]2+.
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Affiliation(s)
- Rudradatt R Persaud
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Nnenna E Dieke
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Xinyao Jing
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Skyler Lambert
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Nicholas Parsa
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Elizabeth Hartmann
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - John B Vincent
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - Carolyn J Cassady
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
| | - David A Dixon
- Department of Chemistry & Biochemistry , The University of Alabama , Tuscaloosa , Alabama 35487-0336 , United States
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5
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Tsypin M, Asmellash S, Meyer K, Touchet B, Roder H. Extending the information content of the MALDI analysis of biological fluids via multi-million shot analysis. PLoS One 2019; 14:e0226012. [PMID: 31815946 PMCID: PMC6901224 DOI: 10.1371/journal.pone.0226012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 11/18/2019] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Reliable measurements of the protein content of biological fluids like serum or plasma can provide valuable input for the development of personalized medicine tests. Standard MALDI analysis typically only shows high abundance proteins, which limits its utility for test development. It also exhibits reproducibility issues with respect to quantitative measurements. In this paper we show how the sensitivity of MALDI profiling of intact proteins in unfractionated human serum can be substantially increased by exposing a sample to many more laser shots than are commonly used. Analytical reproducibility is also improved. METHODS To assess what is theoretically achievable we utilized spectra from the same samples obtained over many years and combined them to generate MALDI spectral averages of up to 100,000,000 shots for a single sample, and up to 8,000,000 shots for a set of 40 different serum samples. Spectral attributes, such as number of peaks and spectral noise of such averaged spectra were investigated together with analytical reproducibility as a function of the number of shots. We confirmed that results were similar on MALDI instruments from different manufacturers. RESULTS We observed an expected decrease of noise, roughly proportional to the square root of the number of shots, over the whole investigated range of the number of shots (5 orders of magnitude), resulting in an increase in the number of reliably detected peaks. The reproducibility of the amplitude of these peaks, measured by CV and concordance analysis also improves with very similar dependence on shot number, reaching median CVs below 2% for shot numbers > 4 million. Measures of analytical information content and association with biological processes increase with increasing number of shots. CONCLUSIONS We demonstrate that substantially increasing the number of laser shots in a MALDI-TOF analysis leads to more informative and reliable data on the protein content of unfractionated serum. This approach has already been used in the development of clinical tests in oncology.
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Affiliation(s)
- Maxim Tsypin
- Biodesix Inc., Boulder, Colorado, United States of America
| | | | - Krista Meyer
- Biodesix Inc., Boulder, Colorado, United States of America
| | | | - Heinrich Roder
- Biodesix Inc., Boulder, Colorado, United States of America
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6
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Ngounou Wetie AG, Sokolowska I, Channaveerappa D, Dupree EJ, Jayathirtha M, Woods AG, Darie CC. Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:121-142. [DOI: 10.1007/978-3-030-15950-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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YU JJ, LIU P, ZENG Z, CHEN Y, GAO W, LI M, WANG CG, HUANG ZX, ZHOU Z, LI L. Development and Characterization of A Linear Matrix-assisted Laser Desorption Ionization Mass Spectrometer. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(17)61077-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Hattan SJ, Parker KC, Vestal ML, Yang JY, Herold DA, Duncan MW. Analysis and Quantitation of Glycated Hemoglobin by Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:532-541. [PMID: 26733405 DOI: 10.1007/s13361-015-1316-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 06/05/2023]
Abstract
Measurement of glycated hemoglobin is widely used for the diagnosis and monitoring of diabetes mellitus. Matrix assisted laser desorption/ionization (MALDI) time of flight (TOF) mass spectrometry (MS) analysis of patient samples is used to demonstrate a method for quantitation of total glycation on the β-subunit of hemoglobin. The approach is accurate and calibrated with commercially available reference materials. Measurements were linear (R(2) > 0.99) across the clinically relevant range of 4% to 20% glycation with coefficients of variation of ≤ 2.5%. Additional and independent measurements of glycation of the α-subunit of hemoglobin are used to validate β-subunit glycation measurements and distinguish hemoglobin variants. Results obtained by MALDI-TOF MS were compared with those obtained in a clinical laboratory using validated HPLC methodology. MALDI-TOF MS sample preparation was minimal and analysis times were rapid making the method an attractive alternative to methodologies currently in practice.
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Affiliation(s)
| | | | | | - Jane Y Yang
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093-0612, USA
| | - David A Herold
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093-0612, USA
- VA San Diego Healthcare System, PALMS, MS 113, San Diego, CA, 92161, USA
| | - Mark W Duncan
- Division of Endocrinology, Metabolism, and Diabetes, University of Colorado School of Medicine, MS 8106, Aurora, CO, 80045, USA
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9
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Cenci L, Anesi A, Busato M, Guella G, Bossi AM. Molecularly imprinted polymers coupled to matrix assisted laser desorption ionization mass spectrometry for femtomoles detection of cardiac troponin I peptides. J Mol Recognit 2015; 29:41-50. [PMID: 26373625 DOI: 10.1002/jmr.2494] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/21/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022]
Abstract
Molecularly imprinted polymers (MIPs) were combined to MALDI-TOF-MS to evaluate a selective enrichment (SE) method for the determination of clinically relevant biomarkers from complex biological samples. The concept was proven with the myocardial injury marker Troponin I (cTnI). In a first part, MIP materials entailed for the recognition of cTnI epitopes (three peptides selected) were prepared and characterized in dimensions (0.7-2μm), dissociation constants (58-817 nM), kinetics of binding (5-60 min), binding capacity (ca. 1.5 µg/mg polymer), imprinting factors (3 > IF > 5) and selectivity for the peptide epitope. Then, the MIPs, incubated with cTnI peptides and spotted on the target with the DHB matrix, were assayed for the desorption of the peptides in MALDI-TOF-MS. The measured detection limit was ca. 300 femtomols. Finally, the MIP-SE MALDI-TOF-MS was tested for its ability to enrich in the cTnI peptides from a complex sample, mimic of serum (i.e. 81 peptides of digested albumin). The MIP-SE MALDI-TOF-MS successfully enriched in cTnI peptides from the complex sample proving the technique could offer a flexible platform to prepare entailed materials suitable for diagnostic purposes.
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Affiliation(s)
- Lucia Cenci
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, 37134, Verona, Italy
| | - Andrea Anesi
- University of Trento, Department of Physics, Via Sommarive 14, 38123, Trento, Italy
| | - Mirko Busato
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, 37134, Verona, Italy
| | - Graziano Guella
- University of Trento, Department of Physics, Via Sommarive 14, 38123, Trento, Italy
| | - Alessandra Maria Bossi
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, 37134, Verona, Italy
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10
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Feng C, Commodore JJ, Cassady CJ. The use of chromium(III) to supercharge peptides by protonation at low basicity sites. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:347-58. [PMID: 25395012 PMCID: PMC4323856 DOI: 10.1007/s13361-014-1020-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 05/16/2023]
Abstract
The addition of chromium(III) nitrate to solutions of peptides with seven or more residues greatly increases the formation of doubly protonated peptides, [M + 2H](2+), by electrospray ionization. The test compound heptaalanine has only one highly basic site (the N-terminal amino group) and undergoes almost exclusive single protonation using standard solvents. When Cr(III) is added to the solution, abundant [M + 2H](2+) forms, which involves protonation of the peptide backbone or the C-terminus. Salts of Al(III), Mn(II), Fe(III), Fe(II), Cu(II), Zn (II), Rh(III), La(III), Ce(IV), and Eu(III) were also studied. Although several metal ions slightly enhance protonation, Cr(III) has by far the greatest ability to generate [M + 2H](2+). Cr(III) does not supercharge peptide methyl esters, which suggests that the mechanism involves interaction of Cr(III) with a carboxylic acid group. Other factors may include the high acidity of hexa-aquochromium(III) and the resistance of Cr(III) to reduction. Nitrate salts enhance protonation more than chloride salts and a molar ratio of 10:1 Cr(III):peptide produces the most intense [M + 2H](2+). Cr(III) also supercharges numerous other small peptides, including highly acidic species. For basic peptides, Cr(III) increases the charge state (2+ versus 1+) and causes the number of peptide molecules being protonated to double or triple. Chromium(III) does not supercharge the proteins cytochrome c and myoglobin. The ability of Cr(III) to enhance [M + 2H](2+) intensity may prove useful in tandem mass spectrometry because of the resulting overall increase in signal-to-noise ratio, the fact that [M + 2H](2+) generally dissociate more readily than [M + H](+), and the ability to produce [M + 2H](2+) precursors for electron-based dissociation techniques.
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Affiliation(s)
- Changgeng Feng
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | | | - Carolyn J. Cassady
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL, 35487, USA
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11
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Determination of sterols using liquid chromatography with off-line surface-assisted laser desorption/ionization mass spectrometry. J Chromatogr A 2014; 1358:102-9. [DOI: 10.1016/j.chroma.2014.06.077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 11/15/2022]
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12
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Chakraborty S, Ataman C, Courtney DG, Dandavino S, Shea H. A ToF-MS with a highly efficient electrostatic ion guide for characterization of ionic liquid electrospray sources. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1364-1373. [PMID: 24833357 DOI: 10.1007/s13361-014-0914-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 04/09/2014] [Accepted: 04/09/2014] [Indexed: 06/03/2023]
Abstract
We report on the development of a time-of-flight (ToF) mass spectrometer with a highly efficient electrostatic ion guide for enhancing detectability in ToF mass spectrometry. This 65-cm long ion guide consists of 13 cascaded stages of Einzel lens to collect a large fraction of emitted charges over a wide emission angle and energy spread for time-of-flight measurements. Simulations show that the ion guide can collect 100% of the charges with up to 23° emission half-angle or 30% energy spread irrespective of their specific charge. We demonstrate this ion guide as applied to electrospray ion sources. Experiments performed with tungsten needle electrospraying the ionic liquid EMI-BF4 showed that up to 80% of the emitted charges could be collected at the end of the flight tube. Flight times of monomers and dimers emitted from the needles were measured in both positive and negative emission polarities. The setup was also used to characterize the electrospray from microfabricated silicon capillary emitters and nearly 30% charges could be collected even from a 40(°) emission half-angle. This setup can thus increase the fraction of charge collection for ToF measurement and spray characteristics can be obtained from a very large fraction of the emission in real time.
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Affiliation(s)
- Subha Chakraborty
- Microsystems for Space Technologies Laboratory, EPFL, Neuchatel, Switzerland,
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13
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Grayson SM, Myers BK, Bengtsson J, Malkoch M. Advantages of monodisperse and chemically robust "SpheriCal" polyester dendrimers as a "universal" MS calibrant. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:303-309. [PMID: 24297473 DOI: 10.1007/s13361-013-0777-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 10/11/2013] [Accepted: 10/22/2013] [Indexed: 06/02/2023]
Abstract
The utilization of dendrimer calibrants as an alternative to peptides and proteins for high mass calibration is explored. These synthetic macromolecules exhibited a number of attractive advantages, including exceptional shelf-lives, broad compatibility with a wide range of matrices and solvents, and evenly spaced calibration masses across the mass range examined, 700-30,000 u. The exceptional purity of these dendrimers and the technical simplicity of this calibration platform validate their broad relevance for high molecular weight mass spectrometry.
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Affiliation(s)
- Scott M Grayson
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA,
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14
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Bednařík A, Kuba P, Moskovets E, Tomalová I, Krásenský P, Houška P, Preisler J. Rapid Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Imaging with Scanning Desorption Laser Beam. Anal Chem 2014; 86:982-6. [DOI: 10.1021/ac402823n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Antonín Bednařík
- Central
European Institute of Technology (CEITEC), Masaryk University, 625
00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
| | - Pavel Kuba
- Faculty
of Mechanical Engineering, Brno University of Technology, Technická
2896/2, 616 69 Brno, Czech Republic
| | - Eugene Moskovets
- MassTech, Inc. 6992
Columbia Gateway Drive, Suite No. 160, Columbia, Maryland 21046, United States
| | - Iva Tomalová
- Central
European Institute of Technology (CEITEC), Masaryk University, 625
00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
| | - Pavel Krásenský
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
| | - Pavel Houška
- Faculty
of Mechanical Engineering, Brno University of Technology, Technická
2896/2, 616 69 Brno, Czech Republic
| | - Jan Preisler
- Central
European Institute of Technology (CEITEC), Masaryk University, 625
00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00, Brno, Czech Republic
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15
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Abstract
Rather than providing a single specific protocol, the inclusive area of seed proteomics is reviewed; methods are described and compared and primary literature citations are provided. The limitations and challenges of proteomics as an approach to study seed biology are emphasized. The proteomic analysis of seeds encounters some specific problems that do not impinge on analyses of other plant cells, tissues, or organs. There are anatomic considerations. Seeds comprise the seed coat, the storage organ(s), and the embryonic axis. Are these to be studied individually or as a composite? The physiological status of the seeds must be considered; developing, mature, or germinating? If mature, are they quiescent or dormant? If mature and quiescent, then orthodox or recalcitrant? The genetic uniformity of the population of seeds being compared must be considered. Finally, seeds are protein-rich and the extreme abundance of the storage proteins results in a study-subject with a dynamic range that spans several orders of magnitude. This represents a problem that must be dealt with if the study involves analysis of proteins that are of "normal" to low abundance. Several different methods of prefractionation are described and the results compared.
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Affiliation(s)
- Ján A Miernyk
- USDA, Agricultural Research Service, Plant Genetics Research Unit, Department of Biochemistry, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
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16
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC. Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 2014; 71:205-28. [PMID: 23579629 PMCID: PMC11113707 DOI: 10.1007/s00018-013-1333-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
Abstract
Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as single entities but rather as a dynamic network of team players that have to communicate. Though genetic (yeast two-hybrid Y2H) and biochemical methods (co-immunoprecipitation Co-IP, affinity purification AP) were the methods of choice at the beginning of the study of protein-protein interactions (PPI), in more recent years there has been a shift towards proteomics-based methods and bioinformatics-based approaches. In this review, we first describe in depth PPIs and we make a strong case as to why unraveling the interactome is the next challenge in the field of proteomics. Furthermore, classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. The greatest emphasis is placed on proteomic methods, especially native techniques that were recently developed and that have been shown to be reliable. Finally, we point out the limitations of these methods and the need to set up a standard for the validation of PPI experiments.
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Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katrin Deinhardt
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
- Institute for Life Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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Tomalová I, Foltynová P, Kanický V, Preisler J. MALDI MS and ICP MS Detection of a Single CE Separation Record: A Tool for Metalloproteomics. Anal Chem 2013; 86:647-54. [DOI: 10.1021/ac402941e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Iva Tomalová
- Central
European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavla Foltynová
- Department
of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Viktor Kanický
- Central
European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Preisler
- Central
European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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18
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Rath CM, Yang JY, Alexandrov T, Dorrestein PC. Data-independent microbial metabolomics with ambient ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1167-1176. [PMID: 23568029 PMCID: PMC3715584 DOI: 10.1007/s13361-013-0608-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/29/2013] [Accepted: 02/05/2013] [Indexed: 05/29/2023]
Abstract
Atmospheric ionization methods are ideally suited for prolonged MS/MS analysis. Data-independent MS/MS is a complementary technique for analysis of biological samples as compared to data-dependent analysis. Here, we pair data-independent MS/MS with the ambient ionization method nanospray desorption electrospray ionization (nanoDESI) for untargeted analysis of bacterial metabolites. Proof-of-principle data and analysis are illustrated by sampling Bacillus subtilis and Pseudomonas aeruginosa directly from Petri dishes. We found that this technique enables facile comparisons between strains via MS and MS/MS plots which can be translated to chemically informative molecular maps through MS/MS networking. The development of novel techniques to characterize microbial metabolites allows rapid and efficient analysis of metabolic exchange factors. This is motivated by our desire to develop novel techniques to explore the role of interspecies interactions in the environment, health, and disease. This is a contribution to honor Professor Catherine C. Fenselau in receiving the prestigious ASMS Award for a Distinguished Contribution in Mass Spectrometry for her pioneering work on microbial mass spectrometry.
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Affiliation(s)
- Christopher M Rath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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19
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Champagne A, Boutry M. Proteomics of nonmodel plant species. Proteomics 2013; 13:663-73. [PMID: 23125178 DOI: 10.1002/pmic.201200312] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 01/10/2023]
Abstract
Until recently, large scale proteomic investigations in the plant field have only been possible for a few model species for which the whole genome sequence had been fully determined. In contrast, for many other species with a strong economic interest as sources of human food and animal feed, as well as industrial and pharmacological molecules, little was known about their genome sequence and identifying the proteome in these species was still considered challenging. However, progress has been made as a result of several recent advances in proteomics tools, e.g. in MS technology and data search programs, and the increasing availability of genomic and cDNA sequences from various species. Moreover, next-generation sequencing technologies now make it possible to rapidly determine, at a reasonable cost, the genome or RNA sequence of species not currently considered as models, thus considerably expanding the plant sequence databases. This review will show how these advances make it possible to identify a large set of proteins, even for species for which few sequences are currently available.
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Affiliation(s)
- Antoine Champagne
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, Louvain-la-Neuve, Belgium
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20
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Lavigne JP, Espinal P, Dunyach-Remy C, Messad N, Pantel A, Sotto A. Mass spectrometry: a revolution in clinical microbiology? Clin Chem Lab Med 2013; 51:257-70. [DOI: 10.1515/cclm-2012-0291] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/28/2012] [Indexed: 11/15/2022]
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22
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Stolowitz ML. On-target and nanoparticle-facilitated selective enrichment of peptides and proteins for analysis by MALDI-MS. Proteomics 2012; 12:3438-50. [DOI: 10.1002/pmic.201200252] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/27/2012] [Accepted: 09/20/2012] [Indexed: 01/09/2023]
Affiliation(s)
- Mark L. Stolowitz
- Canary Center at Stanford for Cancer Early Detection; Department of Radiology; Stanford University School of Medicine; Palo Alto CA USA
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23
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Li J, Inutan ED, Wang B, Lietz CB, Green DR, Manly CD, Richards AL, Marshall DD, Lingenfelter S, Ren Y, Trimpin S. Matrix assisted ionization: new aromatic and nonaromatic matrix compounds producing multiply charged lipid, peptide, and protein ions in the positive and negative mode observed directly from surfaces. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1625-43. [PMID: 22895857 DOI: 10.1007/s13361-012-0413-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 05/09/2012] [Accepted: 05/11/2012] [Indexed: 05/25/2023]
Abstract
Matrix assisted inlet ionization (MAII) is a method in which a matrix:analyte mixture produces mass spectra nearly identical to electrospray ionization without the application of a voltage or the use of a laser as is required in laserspray ionization (LSI), a subset of MAII. In MAII, the sample is introduced by, for example, tapping particles of dried matrix:analyte into the inlet of the mass spectrometer and, therefore, permits the study of conditions pertinent to the formation of multiply charged ions without the need of absorption at a laser wavelength. Crucial for the production of highly charged ions are desolvation conditions to remove matrix molecules from charged matrix:analyte clusters. Important factors affecting desolvation include heat, vacuum, collisions with gases and surfaces, and even radio frequency fields. Other parameters affecting multiply charged ion production is sample preparation, including pH and solvent composition. Here, findings from over 100 compounds found to produce multiply charged analyte ions using MAII with the inlet tube set at 450 °C are presented. Of the compounds tested, many have -OH or -NH(2) functionality, but several have neither (e.g., anthracene), nor aromaticity or conjugation. Binary matrices are shown to be applicable for LSI and solvent-free sample preparation can be applied to solubility restricted compounds, and matrix compounds too volatile to allow drying from common solvents. Our findings suggest that the physical properties of the matrix such as its morphology after evaporation of the solvent, its propensity to evaporate/sublime, and its acidity are more important than its structure and functional groups.
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Affiliation(s)
- Jing Li
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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Abstract
A newcomer to the -omics era, proteomics, is a broad instrument-intensive research area that has advanced rapidly since its inception less than 20 years ago. Although the 'wet-bench' aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techniques, including various improvements in two-dimensional gel electrophoresis and gel-free or off-gel protein focusing, it has been the seminal advances in MS that have led to the ascension of this field. Recent improvements in sensitivity, mass accuracy and fragmentation have led to achievements previously only dreamed of, including whole-proteome identification, and quantification and extensive mapping of specific PTMs (post-translational modifications). With such capabilities at present, one might conclude that proteomics has already reached its zenith; however, 'capability' indicates that the envisioned goals have not yet been achieved. In the present review we focus on what we perceive as the areas requiring more attention to achieve the improvements in workflow and instrumentation that will bridge the gap between capability and achievement for at least most proteomes and PTMs. Additionally, it is essential that we extend our ability to understand protein structures, interactions and localizations. Towards these ends, we briefly focus on selected methods and research areas where we anticipate the next wave of proteomic advances.
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25
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Fekete S, Veuthey JL, Guillarme D. New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications. J Pharm Biomed Anal 2012; 69:9-27. [PMID: 22475515 DOI: 10.1016/j.jpba.2012.03.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 12/22/2022]
Abstract
In the pharmaceutical field, there is considerable interest in the use of peptides and proteins for therapeutic purposes. There are various ways to characterize such complex samples, but during the last few years, a significant number of technological developments have been brought to the field of RPLC and RPLC-MS. Thus, the present review focuses first on the basics of RPLC for peptides and proteins, including the inherent problems, some possible solutions and some directions for developing a new RPLC method that is dedicated to biomolecules. Then the latest advances in RPLC, such as wide-pore core-shell particles, fully porous sub-2 μm particles, organic monoliths, porous layer open tubular columns and elevated temperature, are described and critically discussed in terms of both kinetic efficiency and selectivity. Numerous applications with real samples are presented that confirm the relevance of these different strategies. Finally, one of the key advantages of RPLC for peptides and proteins over other historical approaches is its inherent compatibility with MS using both MALDI and ESI sources.
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Affiliation(s)
- Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Bd d'Yvoy 20, 1211 Geneva 4, Switzerland.
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26
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Biomedical mass spectrometry in today's and tomorrow's clinical microbiology laboratories. J Clin Microbiol 2012; 50:1513-7. [PMID: 22357505 DOI: 10.1128/jcm.00420-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Clinical microbiology is a conservative laboratory exercise where base technologies introduced in the 19th century remained essentially unaltered. High-tech mass spectrometry (MS) has changed that. Within a few years following its adaptation to microbiological diagnostics, MS has been introduced, embraced, and broadly accepted by clinical microbiology laboratories throughout the world as an innovative tool for definitive bacterial species identification. Herein, we review the current state of the art with respect to this exciting new technology and discuss potential future applications.
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Pagnotti VS, Inutan ED, Marshall DD, McEwen CN, Trimpin S. Inlet ionization: a new highly sensitive approach for liquid chromatography/mass spectrometry of small and large molecules. Anal Chem 2011; 83:7591-4. [PMID: 21899326 DOI: 10.1021/ac201982r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Inlet ionization is a new approach for ionizing both small and large molecules in solids or liquid solvents with high sensitivity. The utility of solvent based inlet ionization mass spectrometry (MS) as a method for analysis of volatile and nonvolatile compounds eluting from a liquid chromatography (LC) column is demonstrated. This new LC/MS approach uses reverse phase solvent systems common to electrospray ionization MS. The first LC/MS analyses using this novel approach produced sharp chromatographic peaks and good quality full mass range mass spectra for over 25 peptides from injection of only 1 pmol of a tryptic digest of bovine serum albumin using an eluent flow rate of 55 μL min(-1). Similarly, full acquisition LC/MS/MS of the MH(+) ion of the drug clozapine, using the same solvent flow rate, produced a signal-to-noise ratio of 54 for the major fragment ion with injection of only 1 μL of a 2 ppb solution. LC/MS results were acquired on two different manufacturer's mass spectrometers using a Waters Corporation NanoAcquity liquid chromatograph.
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Affiliation(s)
- Vincent S Pagnotti
- Department of Chemistry and Biochemistry, University of the Science, Philadelphia, Pennsylvania, USA
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