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McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH. THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:280-305. [PMID: 32608033 PMCID: PMC7989064 DOI: 10.1002/mas.21642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 05/06/2023]
Abstract
Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | | | - Joanna K Denton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
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2
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Rautenbach M, Kumar V, Vosloo JA, Masoudi Y, van Wyk RJ, Stander MA. Oligomerisation of tryptocidine C, a Trp-rich cyclodecapeptide from the antimicrobial tyrothricin complex. Biochimie 2020; 181:123-133. [PMID: 33333170 DOI: 10.1016/j.biochi.2020.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/17/2020] [Accepted: 12/12/2020] [Indexed: 01/07/2023]
Abstract
Tryptocidine C (TpcC, cyclo[D-Phe1-Pro2-Trp3-D-Trp4-Asn5-Gln6-Trp7-Val8-Orn9-Leu10]) is a broad-spectrum antimicrobial peptide in the tyrothricin complex produced by a soil bacterium, Brevibacillus parabrevis. Electrospray mass spectrometric studies reveal the oligomerisation of TpcC into dimers and higher oligomers, analogous to tyrocidine C (TrcC, Trp7 replaced by Tyr7). Ion mobility mass spectrometry (IMMS) further confirms the formation of stable peptide dimers and tetramers with diameters of 2.7 nm and 3.3 nm, respectively, calculated from collisional cross section (CCS). Molecular dynamic simulations and docking studies support the formation of amphipathic dimers, with a diameter of 2.5 ± 0.07 nm calculated from low energy model CCS. Circular dichroism and IMMS studies point towards dynamic hydrogen-bonded conformational changes up to 28-33 μM after which the structures become more static (or in equilibrium). Fluorescence studies indicate aromatic stacking of Trp residues with a CMC of 18 μM in aqueous solutions. The concentration and time dependent interaction of Trp in oligomers indicate cooperativity in the TpcC oligomerisation that leads to the formation of higher order microscopic structures. Scanning electron microscopy studies unequivocally shows that TpcC forms nanospheres with a mean diameter of 25 nm. Repeated smaller oligomeric units, possibly dimers and tetramers, self-assemble to form these nanospheres.
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Affiliation(s)
- Marina Rautenbach
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa.
| | - Vikas Kumar
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa.
| | - J Arnold Vosloo
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Yasamin Masoudi
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Rosalind J van Wyk
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Marietjie A Stander
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa; LC-MS Unit of the Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa
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3
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Haler JRN, Massonnet P, Far J, Upert G, Gilles N, Mourier G, Quinton L, De Pauw E. Can IM-MS Collision Cross Sections of Biomolecules Be Rationalized Using Collision Cross-Section Trends of Polydisperse Synthetic Homopolymers? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:990-995. [PMID: 32233380 DOI: 10.1021/jasms.9b00106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the past, we developed a method inferring physicochemical properties from ion mobility mass spectrometry (IM-MS) data from polydisperse synthetic homopolymers. We extend here the method to biomolecules that are generally monodisperse. Similarities in the IM-MS behavior were illustrated on proteins and peptides. This allows one to identify ionic species for which intramolecular interactions lead to specific structures.
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Affiliation(s)
- Jean R N Haler
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
| | - Philippe Massonnet
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, 6211 LK Maastricht, The Netherlands
| | - Johann Far
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
| | - Gregory Upert
- Commissariat à l'Energie Atomique CEA, DRF/SIMOPRO, 91191 Gif sur Yvette, France
| | - Nicolas Gilles
- Commissariat à l'Energie Atomique CEA, DRF/SIMOPRO, 91191 Gif sur Yvette, France
| | - Gilles Mourier
- Commissariat à l'Energie Atomique CEA, DRF/SIMOPRO, 91191 Gif sur Yvette, France
| | - Loïc Quinton
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, University of Liège, MolSys Research unit, Quartier Agora, Allée du Six Aout 11, B-4000 Liège, Belgium
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4
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Moghadamchargari Z, Huddleston J, Shirzadeh M, Zheng X, Clemmer DE, M Raushel F, Russell DH, Laganowsky A. Intrinsic GTPase Activity of K-RAS Monitored by Native Mass Spectrometry. Biochemistry 2019; 58:3396-3405. [PMID: 31306575 DOI: 10.1021/acs.biochem.9b00532] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations in RAS are associated with many different cancers and have been a therapeutic target for more than three decades. RAS cycles from an active to inactive state by both intrinsic and GTPase-activating protein (GAP)-stimulated hydrolysis. The activated enzyme interacts with downstream effectors, leading to tumor proliferation. Mutations in RAS associated with cancer are insensitive to GAP, and the rate of inactivation is limited to their intrinsic hydrolysis rate. Here, we use high-resolution native mass spectrometry (MS) to determine the kinetics and transition state thermodynamics of intrinsic hydrolysis for K-RAS and its oncogenic mutants. MS data reveal heterogeneity where both 2'-deoxy and 2'-hydroxy forms of GDP (guanosine diphosphate) and GTP (guanosine triphosphate) are bound to the recombinant enzyme. Intrinsic GTPase activity is directly monitored by the loss in mass of K-RAS bound to GTP, which corresponds to the release of phosphate. The rates determined from MS are in direct agreement with those measured using an established solution-based assay. Our results show that the transition state thermodynamics for the intrinsic GTPase activity of K-RAS is both enthalpically and entropically unfavorable. The oncogenic mutants G12C, Q61H, and G13D unexpectedly exhibit a 2'-deoxy GTP intrinsic hydrolysis rate higher than that for GTP.
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Affiliation(s)
- Zahra Moghadamchargari
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Jamison Huddleston
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mehdi Shirzadeh
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Xueyun Zheng
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana , 47405 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David H Russell
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Arthur Laganowsky
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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5
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Rautenbach M, Vlok NM, Eyéghé-Bickong HA, van der Merwe MJ, Stander MA. An Electrospray Ionization Mass Spectrometry Study on the "In Vacuo" Hetero-Oligomers Formed by the Antimicrobial Peptides, Surfactin and Gramicidin S. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1623-1637. [PMID: 28560564 DOI: 10.1007/s13361-017-1685-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
It was previously observed that the lipopeptide surfactants in surfactin (Srf) have an antagonistic action towards the highly potent antimicrobial cyclodecapeptide, gramicidin S (GS). This study reports on some of the molecular aspects of the antagonism as investigated through complementary electrospray ionization mass spectrometry techniques. We were able to detect stable 1:1 and 2:1 hetero-oligomers in a mixture of surfactin and gramicidin S. The noncovalent interaction between GS and Srf, with the proposed equilibrium: GS~Srf↔GS+Srf correlated to apparent K d values of 6-9 μM in gas-phase and 1 μM in aqueous solution. The apparent K d values decreased with a longer incubation time and indicated a slow oligomerization equilibrium. Furthermore, the low μM K dapp values of GS~Srf↔GS+Srf fell within the biological concentration range and related to the 2- to 3-fold increase in [GS] needed for bacterial growth inhibition in the presence of Srf. Competition studies indicated that neither Na+ nor Ca2+ had a major effect on the stability of preformed heterodimers and that GS in fact out-competed Ca2+ and Na+ from Srf. Traveling wave ion mobility mass spectrometry revealed near symmetrical peaks of the heterodimers correlating to a compact dimer conformation that depend on specific interactions. Collision-induced dissociation studies indicated that the peptide interaction is most probably between one Orn residue in GS and the Asp residue, but not the Glu residue in Srf. We propose that flanking hydrophobic residues in both peptides stabilize the antagonistic and inactive peptide hetero-oligomers and shield the specific polar interactions in an aqueous environment. Graphical Abstract ᅟ.
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Affiliation(s)
- Marina Rautenbach
- BIOPEP® Peptide Group, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa.
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa.
| | - N Maré Vlok
- BIOPEP® Peptide Group, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
| | - Hans A Eyéghé-Bickong
- BIOPEP® Peptide Group, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
| | - Marthinus J van der Merwe
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- LCMS Central Analytical Facility, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
| | - Marietjie A Stander
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- LCMS Central Analytical Facility, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
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6
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Liu Y, Cong X, Liu W, Laganowsky A. Characterization of Membrane Protein-Lipid Interactions by Mass Spectrometry Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:579-586. [PMID: 27924494 DOI: 10.1007/s13361-016-1555-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/06/2016] [Accepted: 11/03/2016] [Indexed: 05/21/2023]
Abstract
Lipids in the biological membrane can modulate the structure and function of integral and peripheral membrane proteins. Distinguishing individual lipids that bind selectively to membrane protein complexes from an ensemble of lipid-bound species remains a daunting task. Recently, ion mobility mass spectrometry (IM-MS) has proven to be invaluable for interrogating the interactions between protein and individual lipids, where the complex undergoes collision induced unfolding followed by quantification of the unfolding pathway to assess the effect of these interactions. However, gas-phase unfolding experiments for membrane proteins are typically performed on the entire ensemble (apo and lipid bound species), raising uncertainty to the contribution of individual lipids and the species that are ejected in the unfolding process. Here, we describe the application of mass spectrometry ion mobility mass spectrometry (MS-IM-MS) for isolating ions corresponding to lipid-bound states of a model integral membrane protein, ammonia channel (AmtB) from Escherichia coli. Free of ensemble effects, MS-IM-MS reveals that bound lipids are ejected as neutral species; however, no correlation was found between the lipid-induced stabilization of complex and their equilibrium binding constants. In comparison to data obtained by IM-MS, there are surprisingly limited differences in stability measurements from IM-MS and MS-IM-MS. The approach described here to isolate ions of membrane protein complexes will be useful for other MS methods, such as surface induced dissociation or collision induced dissociation to determine the stoichiometry of hetero-oligomeric membrane protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Yang Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Xiao Cong
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Arthur Laganowsky
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA.
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7
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Straus RN, Jockusch RA. Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:358-369. [PMID: 27943124 DOI: 10.1007/s13361-016-1528-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Rita N Straus
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Rebecca A Jockusch
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
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8
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Fuller DR, Glover MS, Pierson NA, Kim D, Russell DH, Clemmer DE. Cis→Trans Isomerization of Pro(7) in Oxytocin Regulates Zn(2+) Binding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1376-82. [PMID: 27154022 PMCID: PMC5161230 DOI: 10.1007/s13361-016-1410-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/11/2016] [Accepted: 04/14/2016] [Indexed: 05/28/2023]
Abstract
Ion mobility/mass spectrometry techniques are employed to investigate the binding of Zn(2+) to the nine-residue peptide hormone oxytocin (OT, Cys(1)-Tyr(2)-Ile(3)-Gln(4)-Asn(5)-Cys(6)-Pro(7)-Leu(8)-Gly(9)-NH2, having a disulfide bond between Cys(1) and Cys(6) residues). Zn(2+) binding to OT is known to increase the affinity of OT for its receptor [Pearlmutter, A. F., Soloff, M. S.: Characterization of the metal ion requirement for oxytocin-receptor interaction in rat mammary gland membranes. J. Biol. Chem. 254, 3899-3906 (1979)]. In the absence of Zn(2+), we find evidence for two primary OT conformations, which arise because the Cys(6)-Pro(7) peptide bond exists in both the trans- and cis-configurations. Upon addition of Zn(2+), we determine binding constants in water of KA = 1.43 ± 0.24 and 0.42 ± 0.12 μM(-1), for the trans- and cis-configured populations, respectively. The Zn(2+) bound form of OT, having a cross section of Ω = 235 Å(2), has Pro(7) in the trans-configuration, which agrees with a prior report [Wyttenbach, T., Liu, D., Bowers, M. T.: Interactions of the hormone oxytocin with divalent metal ions. J. Am. Chem. Soc. 130, 5993-6000 (2008)], in which it was proposed that Zn(2+) binds to the peptide ring and is further coordinated by interaction of the C-terminal, Pro(7)-Leu(8)-Gly(9)-NH2, tail. The present work shows that the cis-configuration of OT isomerizes to the trans-configuration upon binding Zn(2+). In this way, the proline residue regulates Zn(2+) binding to OT and, hence, is important in receptor binding. Graphical Abstract ᅟ.
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Affiliation(s)
- Daniel R Fuller
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Nicholas A Pierson
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
- Merck Research Laboratories, Rahway, NJ, 07065, USA
| | - DoYong Kim
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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9
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Chudinov AV, Martynovich YG, Sulimenkov IV, Brusov VS, Filatov VV, Pikhtelev AR, Kozlovskiy VI. Study of the dependence of peptide collision cross section on the ion bunch drift velocity in nitrogen. JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1134/s1061934815140051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Pal S, Ghosh U, Ampapathi RS, Chakraborty TK. Recent Studies on Gramicidin S Analog Structure and Antimicrobial Activity. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/7081_2015_188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Shahangi F, Chermahini AN, Farrokhpour H, Teimouri A. Selective complexation of alkaline earth metal ions with nanotubular cyclopeptides: DFT theoretical study. RSC Adv 2015. [DOI: 10.1039/c4ra08302d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The interaction of alkaline earth metal cations including Be2+, Mg2+, Ca2+, Sr2+ and Ba2+ with cyclic peptides containing 3 or 4 (S) alanine molecules (CyAla3 and CyAla4) was investigated by density functional theory (DFT-CAM-B3LYP and DFT-B3LYP).
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Affiliation(s)
- Fereshte Shahangi
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
| | | | - Hossein Farrokhpour
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
| | - Abbas Teimouri
- Chemistry Department
- Payame Noor University
- 19395-4697 Tehran
- Iran
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12
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Chudinov AV, Martynovich YG, Sulimenkov IV, Pikhtelev AR, Brusov VS, Filatov VV, Kozlovskii VI. Study of electrospray ion mobility dependence on the ion bunch drift velocity in the radio frequency quadrupole. JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1134/s1061934814130048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Gelb AS, Jarratt RE, Huang Y, Dodds ED. A Study of Calibrant Selection in Measurement of Carbohydrate and Peptide Ion-Neutral Collision Cross Sections by Traveling Wave Ion Mobility Spectrometry. Anal Chem 2014; 86:11396-402. [DOI: 10.1021/ac503379e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Abby S. Gelb
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Rebecca E. Jarratt
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Yuting Huang
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Eric D. Dodds
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
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14
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Harvey SR, Porrini M, Konijnenberg A, Clarke DJ, Tyler RC, Langridge-Smith PRR, MacPhee CE, Volkman BF, Barran PE. Dissecting the Dynamic Conformations of the Metamorphic Protein Lymphotactin. J Phys Chem B 2014; 118:12348-59. [DOI: 10.1021/jp504997k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Massimiliano Porrini
- Institut Européen de Chimie et Biologie (IECB), CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN), 33607 Pessac Cedex, France
| | | | | | - Robert C. Tyler
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | | | | | - Brian F. Volkman
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Perdita E. Barran
- School
of Chemistry,
Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
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15
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Jafari Chermahini Z, Najafi Chermahini A, Dabbagh HA, Teimouri A. Metal ion binding of s-block cations and nanotubular cyclic (proline)4: A theoretical study. Struct Chem 2014. [DOI: 10.1007/s11224-014-0525-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Zinnel NF, Russell DH. Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification. Anal Chem 2014; 86:4791-8. [PMID: 24754452 DOI: 10.1021/ac403929u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.
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Affiliation(s)
- Nathanael F Zinnel
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
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17
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Ahmed A, Cho Y, Giles K, Riches E, Lee JW, Kim HI, Choi CH, Kim S. Elucidating Molecular Structures of Nonalkylated and Short-Chain Alkyl (n < 5, (CH2)n) Aromatic Compounds in Crude Oils by a Combination of Ion Mobility and Ultrahigh-Resolution Mass Spectrometries and Theoretical Collisional Cross-Section Calculations. Anal Chem 2014; 86:3300-7. [DOI: 10.1021/ac4032737] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Arif Ahmed
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
| | - Yunju Cho
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
| | | | | | - Jong Wha Lee
- Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Hugh I. Kim
- Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Cheol Ho Choi
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
- Green-Nano Materials
Research Center, Daegu, 702-701 Republic of Korea
| | - Sunghwan Kim
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
- Green-Nano Materials
Research Center, Daegu, 702-701 Republic of Korea
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18
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Dilger JM, Valentine SJ, Glover MS, Clemmer DE. A database of alkaline-earth-coordinated peptide cross sections: insight into general aspects of structure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:768-79. [PMID: 23512423 DOI: 10.1007/s13361-013-0579-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 05/18/2023]
Abstract
A database of 1470 collision cross sections (666 doubly- and 804 triply-charged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M(2+)) correspond to Mg(2+), Ca(2+), or Ba(2+)] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M(2+)-coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M(2+)-coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M(2+) binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition.
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Affiliation(s)
- Jonathan M Dilger
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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19
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Brunelli NA, Neidholdt EL, Giapis KP, Flagan RC, Beauchamp JL. Continuous flow ion mobility separation with mass spectrometric detection using a nano-radial differential mobility analyzer at low flow rates. Anal Chem 2013; 85:4335-41. [PMID: 23544674 DOI: 10.1021/ac3032417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a hybrid mass-mobility instrument in which a continuous-flow ion mobility classifier is used as a front-end separation device for mass spectrometric analysis of ions generated with an electrospray ionization source. Using nitrogen as a carrier gas, the resolving power of the nano-radial differential mobility analyzer (nRDMA) for nanometer-sized ions is 5-7 for tetraalkylammonium ions. Data are presented demonstrating the ability of the system to resolve the different aggregation and charge states of tetraalkylammonium ions and protonated peptides using a quadrupole ion trap (QIT) mass spectrometer to analyze the mobility-classified ions. Specifically, data are presented for the two charge states of the decapeptide Gramicidin S. A key feature of the new instrument is the ability to continuously transmit ions with specific mobilities to the mass spectrometer for manipulation and analysis.
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Affiliation(s)
- N A Brunelli
- California Institute of Technology, Pasadena, California 91125, United States.
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20
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Fasciotti M, Lalli PM, Heerdt G, Steffen RA, Corilo YE, de Sá GF, Daroda RJ, Reis FDAM, Morgon NH, Pereira RCL, Eberlin MN, Klitzke CF. Structure-drift time relationships in ion mobility mass spectrometry. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0129-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Ponthus J, Riches E. Evaluating the multiple benefits offered by ion mobility-mass spectrometry in oil and petroleum analysis. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0128-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Hyung SJ, Ruotolo BT. Integrating mass spectrometry of intact protein complexes into structural proteomics. Proteomics 2012; 12:1547-64. [PMID: 22611037 DOI: 10.1002/pmic.201100520] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MS analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other MS approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative MS approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly advancing area.
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Affiliation(s)
- Suk-Joon Hyung
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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23
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Recent advances in metabolite identification and quantitative bioanalysis by LC–Q-TOF MS. Bioanalysis 2012; 4:937-59. [DOI: 10.4155/bio.12.43] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The need for rapid, sensitive and effective identification and quantitation of drugs and metabolites to accelerate drug discovery and development has given MS its central position in drug metabolism and pharmacokinetic research. This review attempts to orient the readers with respect to hybrid Q-TOF MS, which enables accurate mass measurement and generates information-rich datasets. The key properties of the Q-TOF MS system, including mass accuracy, resolution, scan speed and dynamic range, are herein discussed. Developments on tandem separation techniques (e.g., UHPLC® and ion mobility spectrometry), data acquisition and data-mining methods (e.g., mass defect, product/neutral loss, isotope pattern filters and background subtraction) that facilitate qualitative and quantitative analysis are then examined. The performance and versatility of LC–Q-TOF MS are thoroughly illustrated by its applications in metabolite identification and quantitative bioanalysis. Future perspectives are also discussed.
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24
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Goodwin CR, Fenn LS, Derewacz DK, Bachmann BO, McLean JA. Structural mass spectrometry: rapid methods for separation and analysis of peptide natural products. JOURNAL OF NATURAL PRODUCTS 2012; 75:48-53. [PMID: 22216918 PMCID: PMC3267852 DOI: 10.1021/np200457r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A significant challenge in natural product discovery is the initial discrimination of discrete secondary metabolites alongside functionally similar primary metabolic cellular components within complex biological samples. A property that has yet to be fully exploited for natural product identification and characterization is the gas-phase collision cross section, or, more generally, the mobility-mass correlation. Peptide natural products possess many of the properties that distinguish natural products, as they are frequently characterized by a high degree of intramolecular bonding and possess extended and compact conformations among other structural modifications. This report describes a rapid structural mass spectrometry technique based on ion mobility-mass spectrometry for the comparison of peptide natural products to their primary metabolic congeners using mobility-mass correlation. This property is empirically determined using ion mobility-mass spectrometry, applied to the analysis of linear versus modified peptides, and used to discriminate peptide natural products in a crude microbial extract. Complementary computational approaches are utilized to understand the structural basis for the separation of primary metabolism derived linear peptides from secondary metabolite cyclic and modified cyclic species. These findings provide a platform for enhancing the identification of secondary metabolic peptides with distinct mobility-mass ratios within complex biological samples.
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Affiliation(s)
- Cody R. Goodwin
- Vanderbilt University Department of Chemistry, Nashville, TN, United States of America
- Vanderbilt Institute for Chemical Biology, Nashville, TN, United States of America
- Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN, United States of America
| | - Larissa S. Fenn
- Vanderbilt University Department of Chemistry, Nashville, TN, United States of America
| | - Dagmara K. Derewacz
- Vanderbilt University Department of Chemistry, Nashville, TN, United States of America
- Vanderbilt Institute for Chemical Biology, Nashville, TN, United States of America
| | - Brian O. Bachmann
- Vanderbilt University Department of Chemistry, Nashville, TN, United States of America
- Vanderbilt Institute for Chemical Biology, Nashville, TN, United States of America
- ,
| | - John A. McLean
- Vanderbilt University Department of Chemistry, Nashville, TN, United States of America
- Vanderbilt Institute for Chemical Biology, Nashville, TN, United States of America
- Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN, United States of America
- ,
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25
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Li X, Guo L, Casiano-Maldonado M, Zhang D, Wesdemiotis C. Top-Down Multidimensional Mass Spectrometry Methods for Synthetic Polymer Analysis. Macromolecules 2011. [DOI: 10.1021/ma200542p] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Li Guo
- Department of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Donghui Zhang
- Department of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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26
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Harvey SR, Macphee CE, Barran PE. Ion mobility mass spectrometry for peptide analysis. Methods 2011; 54:454-61. [PMID: 21669288 DOI: 10.1016/j.ymeth.2011.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/04/2011] [Accepted: 05/22/2011] [Indexed: 02/03/2023] Open
Abstract
The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Examples are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.
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Affiliation(s)
- Sophie R Harvey
- The School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
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27
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Quantitative evaluation of protein conformation in pharmaceuticals using cross-linking reactions coupled with LC–MS/MS analysis. J Pharm Biomed Anal 2011; 55:574-82. [DOI: 10.1016/j.jpba.2011.01.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/28/2011] [Accepted: 01/31/2011] [Indexed: 11/22/2022]
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28
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Chen L, Shao Q, Gao YQ, Russell DH. Molecular Dynamics and Ion Mobility Spectrometry Study of Model β-Hairpin Peptide, Trpzip1. J Phys Chem A 2011; 115:4427-35. [DOI: 10.1021/jp110014j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Liuxi Chen
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Qiang Shao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yi-Qin Gao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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29
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An LK, Li RL, Zuo YL, Gu LQ. Solvent-free thermocyclization of the unactivated linear gramicidin S precursor and analogues. Org Lett 2011; 13:34-7. [PMID: 21121629 DOI: 10.1021/ol102800j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A convenient thermocyclization of the linear gramicidin S precursor and its analogues is demonstrated. With the preorganized β-sheet conformation, the unactivated linear precursors can cyclize into the corresponding head-to-tail cyclic products in high yield after being heated under solvent-free conditions.
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Affiliation(s)
- Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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30
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Fernandez-Lima FA, Blase RC, Russell DH. A Study of Ion-Neutral Collision Cross Section Values for Low Charge States of Peptides, Proteins, and Peptide/Protein Complexes. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2010; 298:111-118. [PMID: 21503273 PMCID: PMC3077763 DOI: 10.1016/j.ijms.2009.10.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we report ion-helium collision cross sections (CCS) for a number of peptide, small protein, and peptide/protein ionic complexes. The CCS values reported here are compared to previously reported results.[1, 2] We also compare values for low charge state species, i.e., [M + H](+) and [M + 2H](2+), formed by MALDI with values for high charge state species formed by ESI, and the measured CCSs are compared with predicted CCS for solid-state and solution phase structures and calculated structures obtained by using a protein-protein structure algorithm generator, based on a combined Biomolecular complex Generation with Global Evaluation and Ranking[3] and Multi Dimensional Scaling[4].
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31
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Ahmed A, Cho YJ, No MH, Koh J, Tomczyk N, Giles K, Yoo JS, Kim S. Application of the Mason−Schamp Equation and Ion Mobility Mass Spectrometry To Identify Structurally Related Compounds in Crude Oil. Anal Chem 2010; 83:77-83. [DOI: 10.1021/ac101934q] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Arif Ahmed
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Yun Ju Cho
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Myoung-han No
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Jaesuk Koh
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Nicholas Tomczyk
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Kevin Giles
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Jong Shin Yoo
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
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Kupser P, Pagel K, Oomens J, Polfer N, Koksch B, Meijer G, von Helden G. Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase. J Am Chem Soc 2010; 132:2085-93. [DOI: 10.1021/ja909842j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Kupser
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Jos Oomens
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Nick Polfer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Beate Koksch
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg
4-6, 14195 Berlin, Germany, Institut für Chemie und Biochemie,
Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,
and FOM Institute for Plasmaphysics, Edisonbaan 14, 3439 MN Nieuwegein,
The Netherlands
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33
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Uetrecht C, Rose RJ, van Duijn E, Lorenzen K, Heck AJR. Ion mobility mass spectrometry of proteins and proteinassemblies. Chem Soc Rev 2010; 39:1633-55. [DOI: 10.1039/b914002f] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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34
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Fernandez-Lima FA, Becker C, McKenna AM, Rodgers RP, Marshall AG, Russell DH. Petroleum Crude Oil Characterization by IMS-MS and FTICR MS. Anal Chem 2009; 81:9941-7. [DOI: 10.1021/ac901594f] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco A. Fernandez-Lima
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Christopher Becker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Amy M. McKenna
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Ryan P. Rodgers
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Alan G. Marshall
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
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Jackson S, Ugarov M, Post J, Egan T, Langlais D, Schultz JA, Woods A. A study of phospholipids by ion mobility TOFMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1655-62. [PMID: 18703352 PMCID: PMC2630282 DOI: 10.1016/j.jasms.2008.07.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 07/09/2008] [Accepted: 07/10/2008] [Indexed: 05/04/2023]
Abstract
Combining matrix-assisted laser desorption/ionization (MALDI) mass spectrometry with ion mobility (IM) results in the fast sorting of biomolecules in complex mixtures along trend lines. In this two-dimensional (2D) analysis of biological families, lipids, peptides, and nucleotides are separated from each other by differences in their ion mobility drift times in a timescale of hundreds of microseconds. Molecular ions of similar chemical type fall along trend lines when plotted in 2D plots of ion mobility drift time as a function of m/z. In this study, MALDI-IM MS is used to analyze species from all of the major phospholipid classes. Complex samples, including tissue extracts and sections, were probed to demonstrate the effects that radyl chain length, degree of unsaturation, and class/head group have upon an ion's cross section in the gas phase. We illustrate how these changes can be used to identify individual lipid species in complex mixtures, as well as the effects of cationization on ion cross section and ionization efficiency.
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Affiliation(s)
| | | | | | | | | | | | - Amina Woods
- NIDA IRP, NIH, Houston TX
- corresponding author: Amina S. Woods, Ph.D., NIDA IRP, NIH, 5500 Nathan Shock Drive, Baltimore, MD 21224, Tel: 410-550-1507, Fax: 410-550-6859, e-mail:
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Ruotolo BT, Benesch JLP, Sandercock AM, Hyung SJ, Robinson CV. Ion mobility–mass spectrometry analysis of large protein complexes. Nat Protoc 2008; 3:1139-52. [DOI: 10.1038/nprot.2008.78] [Citation(s) in RCA: 865] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Nedvěd J, Sulc M, Jegorov A, Giannakopulos A, Havlicek V. Application of Fungal Cyclic Peptides and Metabolites. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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39
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Riba-Garcia I, Giles K, Bateman RH, Gaskell SJ. Evidence for structural variants of a- and b-type peptide fragment ions using combined ion mobility/mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:609-613. [PMID: 18313327 DOI: 10.1016/j.jasms.2008.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/03/2008] [Accepted: 01/08/2008] [Indexed: 05/26/2023]
Abstract
Tandem mass spectrometry (MS/MS) of peptides plays a key role in the field of proteomics, and an understanding of the fragmentation mechanisms involved is vital for data interpretation. Not all the fragment ions observed by low-energy collision-induced dissociation of protonated peptides are readily explained by the generally accepted structures for a- and b-ions. The possibility of a macrocyclic structure for b-type ions has been recently proposed. In this study, we have undertaken investigations of linear protonated YAGFL-NH(2), N-acetylated-YAGFL-NH(2), and cyclo-(YAGFL) peptides and their fragments using a combination of ion mobility (IM) separation and mass spectrometry. The use of IM in this work both gives insight into relative structural forms of the ion species and crucial separation of isobaric species. Our study provides compelling evidence for the formation of a stable macrocyclic structure for the b(5) ion generated by fragmentation of protonated linear YAGFL-NH(2). Additionally we demonstrate that the a(4) ion fragment of protonated YAGFL-NH(2) has at least two structures; one of which is attributable to a macrocyclic structure on the basis of its subsequent fragmentation. More generally, this work emphasizes the value of combined IM-MS/MS in probing the detailed fragmentation mechanisms of peptide ions, and illustrates the use of combined ion mobility/collisional activation/mass spectrometry analysis in achieving an effective enhancement of the resolution of the mobility separator.
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Affiliation(s)
- Isabel Riba-Garcia
- Michael Barber Centre for Mass Spectrometry, School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
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40
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Hadjar O, Wang P, Futrell JH, Dessiaterik Y, Zhu Z, Cowin JP, Iedema MJ, Laskin J. Design and Performance of an Instrument for Soft Landing of Biomolecular Ions on Surfaces. Anal Chem 2007; 79:6566-74. [PMID: 17668931 DOI: 10.1021/ac070600h] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A new ion deposition apparatus was designed and constructed in our laboratory. Our research objectives were to investigate interactions of biomolecules with hydrophilic and hydrophobic surfaces and to carry out exploratory experiments aimed at highly selective deposition of spatially defined and uniquely selected biological molecules on surfaces. The apparatus includes a high-transmission electrospray ion source, a quadrupole mass filter, a bending quadrupole that deflects the ion beam and prevents neutral molecules originating in the ion source from impacting the surface, an ultrahigh vacuum (UHV) chamber for ion deposition by soft landing, and a vacuum lock system for introducing surfaces into the UHV chamber without breaking vacuum. Ex situ analysis of surfaces following soft landing of mass-selected peptide ions was performed using 15 keV Ga+ time-of-flight secondary ion mass spectrometry and grazing incidence infrared reflection-absorption spectroscopy. It is shown that these two techniques are highly complementary methods for characterization of surfaces prepared with a range of doses of mass-selected biomolecular ions. We also demonstrated that soft landing of peptide ions on surfaces can be utilized for controlled preparation of peptide films of known coverage for fundamental studies of matrix effects in SIMS.
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Affiliation(s)
- Omar Hadjar
- Pacific Northwest National Laboratory, Fundamental Science Directorate and Environmental Molecular Sciences Laboratory, Richland, WA 99352, USA
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41
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Shvartsburg AA, Li F, Tang K, Smith RD. Distortion of ion structures by field asymmetric waveform ion mobility spectrometry. Anal Chem 2007; 79:1523-8. [PMID: 17297950 DOI: 10.1021/ac061306c] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Field asymmetric waveform ion mobility spectrometry (FAIMS) is emerging as a major analytical tool, especially in conjunction with mass spectrometry (MS), conventional ion mobility spectrometry (IMS), or both. In particular, FAIMS is used to separate protein or peptide conformers prior to characterization by IMS, MS/MS, or H/D exchange. High electric fields in FAIMS induce ion heating, previously estimated at <10 degrees C on average and believed too weak to affect ion geometries. Here we use a FAIMS/IMS/MS system to compare the IMS spectra for ESI-generated ubiquitin ions that have and have not passed FAIMS and find that some unfolding occurs for most charge states. These data and their comparison with the reported protein unfolding in a Paul trap imply that at least some structural transitions observed in FAIMS, or previously in an ion trap, are not spontaneous. The observed unfolding is similar to that produced by heating of approximately 50 degrees C above room temperature, consistent with the calculated heating of ions at FAIMS waveform peaks. Hence, the ion isomerization in FAIMS likely proceeds in steps during the "hot" periods, especially right after entering the device. The process distorts ion geometries and causes ion losses by a "self-cleaning" mechanism and thus should be suppressed as much as possible. We propose achieving that via cooling FAIMS by the amount of ion heating; in most cases, cooling by approximately 75 degrees C should suffice.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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42
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Kaur-Atwal G, Weston DJ, Green PS, Crosland S, Bonner PLR, Creaser CS. Analysis of tryptic peptides using desorption electrospray ionisation combined with ion mobility spectrometry/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:1131-8. [PMID: 17318928 DOI: 10.1002/rcm.2941] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A novel method is reported for rapid protein identification by the analysis of tryptic peptides using desorption electrospray ionisation (DESI) coupled with hyphenated ion mobility spectrometry and quadrupole time-of-flight mass spectrometry (IMS/Q-ToF-MS). Confident protein identification is demonstrated for the analysis of tryptically digested bovine serum albumin (BSA), with no sample pre-treatment or clean-up. Electrophoretic ion mobility separation of ions generated by DESI allowed examination of charge-state and mobility distributions for tryptic peptide mixtures. Selective interrogation of singly charged ions allowed isobaric peptide responses to be distinguished, along with a reduction in spectral noise. The mobility-selected singly charged peptide responses were presented as a pseudo-peptide mass fingerprint (p-PMF) for protein database searching. Comparative data are shown for electrospray ionisation (ESI) of the BSA digest, without sample clean-up, from which confident protein identification could not be made. Implications for the robustness of the DESI method, together with potential insights into mechanisms for DESI of proteolytic digests, are discussed.
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Affiliation(s)
- Gushinder Kaur-Atwal
- School of Biomedical and Natural Sciences, Interdisciplinary Biomedical Research Centre, Nottingham Trent University, Nottingham NG11 8NS, UK
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43
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Abstract
The structures and properties of unsolvated peptides large enough to possess secondary structure have been examined by experiments and simulations. Some of the factors that stabilize unsolvated helices and sheets have been identified. The charge, in particular, plays a critical role in stabilizing alpha-helices and destabilizing beta-sheets. Some helices are much more stable in vacuum than in aqueous solution. Factors like helix propensity, context, and the incorporation of specific stabilizing interactions have been examined. The helix propensities in vacuum differ from those found in solution. Studies of the hydration of unsolvated peptides can be performed one water molecule at a time. The first few water molecules only bind weakly to unsolvated peptides, and they bind much more strongly to some conformations than to others. The most favorable binding locations are not the protonation sites, but clefts or pockets where a water molecule can establish a network of hydrogen bonds. Non-covalent interactions between secondary structure elements leads to the formation of tertiary structure. Helical peptides assemble into complexes with a variety of intriguing structures. The intramolecular coupling of helices to make antiparallel coiled-coil geometries has also been investigated with model peptides.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University 800 East Kirkwood Avenue, Bloomington 47405, Indiana, USA.
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Jegorov A, Hajduch M, Sulc M, Havlicek V. Nonribosomal cyclic peptides: specific markers of fungal infections. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:563-76. [PMID: 16770826 DOI: 10.1002/jms.1042] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Some cyclic peptides and depsipeptides are synthesized in microorganisms by large multienzymes called nonribosomal peptide synthetases. The structures of peptide products originating in this way are complex and diverse and are microorganism-specific. This work proposes the use of fungal cyclic peptides and depsipeptides as extremely specific markers of fungal infections. Since a reliable molecular tool for diagnosing fungal infections at an early stage is still missing, we present mass spectrometry as a new, modern, broadband (with respect to fungal strain) and specific tool for clinical mycologists. More than 40 different fungal species can be rapidly characterized according to specific families of cyclic peptides, and in some cases, a particular fungal strain can be identified on the basis of its cyclopeptide profile. This paper is also aimed at initiating discussion on the biological role of these secondary metabolites, especially of those synthesized by medically important strains. Proven cytotoxic, anti-inflammatory or immunosuppressive activities of some cyclic peptides indicate that these molecules may contribute to the synergistic array of fungal virulence factors and support microbial invasion during fungal infection. In addition to an overview on recent mass spectrometric protocols for cyclic peptide sequencing, the structures of new peptides from Paecilomyces and Pseudallescheria are presented.
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Affiliation(s)
- Alexandr Jegorov
- IVAX Pharmaceuticals, Branisovska 31, CZ-370 05 Ceske Budejovice, Czech Republic
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45
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Weston DJ, Bateman R, Wilson ID, Wood TR, Creaser CS. Direct Analysis of Pharmaceutical Drug Formulations Using Ion Mobility Spectrometry/Quadrupole-Time-of-Flight Mass Spectrometry Combined with Desorption Electrospray Ionization. Anal Chem 2005; 77:7572-80. [PMID: 16316164 DOI: 10.1021/ac051277q] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel approach to the rapid analysis of pharmaceutical drug formulations using hyphenated ion mobility spectrometry (IMS) and time-of-flight mass spectrometry (ToF-MS) that requires no sample pretreatment or chromatographic separation is described. A modified quadrupole time-of-flight mass spectrometer containing an ion mobility drift cell was used for gas-phase electrophoretic separation of ions prior to ToF-MS detection. The generation of sample ions directly from tablets and cream formulations was effected by desorption electrospray ionization (DESI) using a modified electrospray ion source. The analysis of a range of over-the-counter and prescription tablet formulations is described, including histamine H2 receptor antagonist (ranitidine), analgesic (paracetamol), opiate (codeine), and aromatase inhibitor anticancer (anastrozole) drugs. The successful determination of active drugs from soft formulations, such as an antiseptic cream (chlorhexidine) and a nicotine-containing skin patch, is also presented. Limits of detection for the active drugs using the DESI/IMS/ToF-MS method fell within the high-picomole to nanomole range. In all cases, the use of ion mobility drift tube separation showed increased selectivity for active drug responses (present as low as 0.14% w/w) over excipient responses such as poly(ethylene glycol). Tandem mass spectrometric analysis of precursor ions separated by IMS allowed positive confirmation of active drugs with little loss of ion mobility efficiency. The ability to analyze hard or soft pharmaceutical formulations directly by DESI combined with ion mobility spectrometry/mass spectrometry in approximately 2 min demonstrates the potential applicability of this novel method to pharmaceutical screening of low-molecular-weight drug formulations with high selectivity over the formulation vehicle.
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Affiliation(s)
- Daniel J Weston
- School of Biomedical and Natural Sciences, Interdisciplinary Biomedical Research Centre, Nottingham Trent University, UK
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Sawyer HA, Marini JT, Stone EG, Ruotolo BT, Gillig KJ, Russell DH. The structure of gas-phase bradykinin fragment 1-5 (RPPGF) ions: an ion mobility spectrometry and H/D exchange ion-molecule reaction chemistry study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:893-905. [PMID: 15878286 DOI: 10.1016/j.jasms.2005.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 02/28/2005] [Accepted: 03/05/2005] [Indexed: 05/02/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) data is interpreted as evidence that gas-phase bradykinin fragment 1-5 (BK1-5, RPPGF) [M + H](+) ions exist as three distinct structural forms, and the relative abundances of the structural forms depend on the solvent used to prepare the matrix-assisted laser desorption ionization (MALDI) samples. Samples prepared from organic rich solvents (90% methanol/10% water) yield ions having an ion mobility arrival-time distribution (ATD) that is dominated by a single peak; conversely, samples prepared using mostly aqueous solvents (10% methanol/90% water) yield an ATD composed of three distinct peaks. The BK1-5 [M + H](+) ions were also studied by gas-phase hydrogen/deuterium (H/D) exchange ion-molecule reactions and this data supports our interpretation of the IM-MS data. Plausible structures for BK1-5 ions were generated by molecular dynamics (MD). Candidate MD-generated structures correlated to measured cross-sections suggest a compact conformer containing a beta-turn whereas a more extended, open form does not contain such an interaction. This study illustrates the importance of intra-molecular interactions in the stabilization of the gas-phase ions, and these results clearly illustrate that solution-phase parameters (i.e., MALDI sample preparation) greatly influence the structures of gas-phase ions.
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Affiliation(s)
- Holly A Sawyer
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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Ruotolo BT, McLean JA, Gillig KJ, Russell DH. The influence and utility of varying field strength for the separation of tryptic peptides by ion mobility-mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:158-165. [PMID: 15694766 DOI: 10.1016/j.jasms.2004.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Revised: 10/26/2004] [Accepted: 10/28/2004] [Indexed: 05/24/2023]
Abstract
The influence of field strength on the separation of tryptic peptides by drift tube-based ion mobility-mass spectrometry is reported. Operating the ion mobility drift tube at elevated field strengths (expressed in V cm(-1) torr(-1)) reduces separation times and increases ion transmission efficiencies. Several accounts in the literature suggest that performing ion mobility separation at elevated field strength can change the selectivity of ion separation. To evaluate the field strength dependant selectivity of ion mobility separation, we examined a data set of 65 singly charged tryptic peptide ion signals (mass range 500-2500 m/z) at six different field strengths and four different drift gas compositions (He, N2, Ar, and CH4). Our results clearly illustrate that changing the field strength from low field (15 V cm(-1) torr(-1)) to high field (66 V cm(-1) torr(-1)) does not significantly alter the selectivity or peak capacity of IM-MS. The implications of these results are discussed in the context of separation methodologies that rely on the field strength dependence of ion mobility for separation selectivity, e.g., high-field asymmetric ion mobility spectrometry (FAIMS).
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Affiliation(s)
- Brandon T Ruotolo
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University College Station, Texas 77843, USA
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Ruotolo BT, Russell DH. Gas-Phase Conformations of Proteolytically Derived Protein Fragments: Influence of Solvent on Peptide Conformation. J Phys Chem B 2004. [DOI: 10.1021/jp0490296] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brandon T. Ruotolo
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - David H. Russell
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
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