1
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Kolbowski L, Belsom A, Pérez-López AM, Ly T, Rappsilber J. Light-Induced Orthogonal Fragmentation of Crosslinked Peptides. JACS AU 2023; 3:2123-2130. [PMID: 37654600 PMCID: PMC10466327 DOI: 10.1021/jacsau.3c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Crosslinking mass spectrometry provides pivotal information on the structure and interaction of proteins. MS-cleavable crosslinkers are regarded as a cornerstone for the analysis of complex mixtures. Yet they fragment under similar conditions as peptides, leading to mixed fragmentation spectra of the crosslinker and peptide. This hampers selecting individual peptides for their independent identification. Here, we introduce orthogonal cleavage using ultraviolet photodissociation (UVPD) to increase crosslinker over peptide fragmentation. We designed and synthesized a crosslinker that can be cleaved at 213 nm in a commercial mass spectrometer configuration. In an analysis of crosslinked Escherichia coli lysate, the crosslinker-to-peptide fragment intensity ratio increases from nearly 1 for a conventionally cleavable crosslinker to 5 for the UVPD-cleavable crosslinker. This largely increased the sensitivity of selecting the individual peptides for MS3, even more so with an improved doublet detection algorithm. Data are available via ProteomeXchange with identifier PXD040267.
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Affiliation(s)
- Lars Kolbowski
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
| | - Adam Belsom
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
| | - Ana M. Pérez-López
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
| | - Tony Ly
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
| | - Juri Rappsilber
- Chair
of Bioanalytics, Technische Universität
Berlin, 10623 Berlin, Germany
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
- Si-M/″Der
Simulierte Mensch″, a Science Framework of Technische Universität
Berlin and Charité - Universitätsmedizin Berlin, 10623 Berlin, Germany
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2
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Ghéczy N, Tao S, Pour-Esmaeil S, Szymańska K, Jarzębski AB, Walde P. Performance of a Flow-Through Enzyme Reactor Prepared from a Silica Monolith and an α-Poly(D-Lysine)-Enzyme Conjugate. Macromol Biosci 2023; 23:e2200465. [PMID: 36598452 DOI: 10.1002/mabi.202200465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/26/2022] [Indexed: 01/05/2023]
Abstract
Horseradish peroxidase (HRP) is covalently bound in aqueous solution to polycationic α-poly(D-lysine) chains of ≈1000 repeating units length, PDL, via a bis-aryl hydrazone bond (BAH). Under the experimental conditions used, about 15 HRP molecules are bound along the PDL chain. The purified PDL-BAH-HRP conjugate is very stable when stored at micromolar HRP concentration in a pH 7.2 phosphate buffer solution at 4 °C. When a defined volume of such a conjugate solution of desired HRP concentration (i.e., HRP activity) is added to a macro- and mesoporous silica monolith with pore sizes of 20-30 µm as well as below 30 nm, quantitative and stable noncovalent conjugate immobilization is achieved. The HRP-containing monolith can be used as flow-through enzyme reactor for bioanalytical applications at neutral or slightly alkaline pH, as demonstrated for the determination of hydrogen peroxide in diluted honey. The conjugate can be detached from the monolith by simple enzyme reactor washing with an aqueous solution of pH 5.0, enabling reloading with fresh conjugate solution at pH 7.2. Compared to previously investigated polycationic dendronized polymer-enzyme conjugates with approximately the same average polymer chain length, the PDL-BAH-HRP conjugate appears to be equally suitable for HRP immobilization on silica surfaces.
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Affiliation(s)
- Nicolas Ghéczy
- Laboratory for Multifunctional Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, CH-8093, Switzerland
| | - Siyuan Tao
- Laboratory for Multifunctional Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, CH-8093, Switzerland
| | - Sajad Pour-Esmaeil
- Laboratory for Multifunctional Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, CH-8093, Switzerland
| | - Katarzyna Szymańska
- Department of Chemical Engineering and Process Design, Silesian University of Technology, Gliwice, 44-100, Poland
| | - Andrzej B Jarzębski
- Institute of Chemical Engineering, Polish Academy of Sciences, Gliwice, 44-100, Poland
| | - Peter Walde
- Laboratory for Multifunctional Materials, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, Zürich, CH-8093, Switzerland
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3
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Chakrabarty JK, Bugarin A, Chowdhury SM. Evaluating the performance of an ETD-cleavable cross-linking strategy for elucidating protein structures. J Proteomics 2020; 225:103846. [PMID: 32480079 DOI: 10.1016/j.jprot.2020.103846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 01/08/2023]
Abstract
Chemical cross-linking is a powerful strategy for elucidating the structures of protein or protein complexes. The distance constraints obtained from cross-linked peptides represent the three-dimensional structures of the protein complexes. Unfortunately, structural analysis using cross-linking approach demands a significant amount of data to elucidate protein structures. This requires the development of several cleavable cross-linkers with different range of spacer chains. An Electron Transfer Dissociation (ETD) tandem mass spectrometry cleavable bond hydrazone was reported. Its fragmentation with conjugated peptides showed promise for the development of a new ETD cleavable cross-linker. However, no cross-linker was developed utilizing this ETD cleavable bond. For the first time, we attempted to develop an ETD cleavable cross-linker utilizing a hydrazone bond. We overcome the pitfall for the synthesis of this cross-linker and an easy synthesis scheme is reported. In this report, we evaluated the performance of this cross-linker called Hydrazone Incorporated ETD cleavable cross-linker (HI-ETD-XL) in model peptides and proteins. The characteristic fragmentation behavior of HI-ETD-XL during electron transfer dissociation and subsequent sequence identification of the peptide fragment ions by tandem mass spectrometry allowed the identification of cross-linked peptides unambiguously. We believe the availability of this ETD cleavable cross-linker will advance structural proteomics research significantly. SIGNIFICANCE: Many cellular processes rely on the structural dynamics of protein complexes. The detailed knowledge of the structure and dynamics of protein complexes is crucial for understanding their biological functions and regulations. However, most of the structure of these multiprotein entities remain uncharacterized and sometimes is very challenging to reveal with biophysical techniques alone. Chemical cross-linking combined with mass spectrometry (MS) has proven to be a dependable strategy in structural proteomics field. However, data complexity and false identifications are significant hindrances for unambiguous identification of cross-linked peptides. Confident identifications demand structural studies with cross-linkers with different properties and variable spacer chain lengths. This new ETD cleavable cross-linking workflow will provide additional confidence to overcome these drawbacks and allow us to pinpoint cross-linked peptides confidently.
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Affiliation(s)
| | - Alejandro Bugarin
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, USA; Department of Chemistry & Physics, Florida Gulf Coast University, FL, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, USA.
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4
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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5
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Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018; 90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
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6
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Xiao K, Yu F, Tian Z. Top-down protein identification using isotopic envelope fingerprinting. J Proteomics 2016; 152:41-47. [PMID: 27989944 DOI: 10.1016/j.jprot.2016.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/11/2016] [Accepted: 10/23/2016] [Indexed: 12/14/2022]
Abstract
For top-down protein database search and identification from tandem mass spectra, our isotopic envelope fingerprinting search algorithm and ProteinGoggle search engine have demonstrated their strength of efficiently resolving heavily overlapping data as well separating non-ideal data with non-ideal isotopic envelopes from ideal ones with ideal isotopic envelopes. Here we report our updated ProteinGoggle 2.0 for intact protein database search with full-capacity. The indispensable updates include users' optional definition of dynamic post-translational modifications and static chemical labeling during database creation, comprehensive dissociation methods and ion series, as well as a Proteoform Score for each proteoform. ProteinGoggle has previously been benchmarked with both collision-based dissociation (CID, HCD) and electron-based dissociation (ETD) data of either intact proteins or intact proteomes. Here we report our further benchmarking of the new version of ProteinGoggle with publically available photon-based dissociation (UVPD) data (http://hdl.handle.net/2022/17316) of intact E. coli ribosomal proteins. BIOLOGICAL SIGNIFICANCE Protein species (aka proteoforms) function at their molecular level, and diverse structures and biological roles of every proteoform come from often co-occurring proteolysis, amino acid variation and post-translational modifications. Complete and high-throughput capture of this combinatorial information of proteoforms has become possible in evolving top-down proteomics; yet, various methods and technologies, especially database search and bioinformatics identification tools, in the top-down pipeline are still in their infancy stages and demand intensive research and development.
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Affiliation(s)
- Kaijie Xiao
- School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China
| | - Fan Yu
- School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China
| | - Zhixin Tian
- School of Chemical Science and Engineering, Tongji University, Shanghai, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.
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7
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Crittenden CM, Parker WR, Jenner ZB, Bruns KA, Akin LD, McGee WM, Ciccimaro E, Brodbelt JS. Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:856-863. [PMID: 26864791 DOI: 10.1007/s13361-016-1355-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/13/2016] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the amine-containing portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.
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Affiliation(s)
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Zachary B Jenner
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Kerry A Bruns
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Lucas D Akin
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - William M McGee
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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8
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Aponte JR, Vasicek L, Swaminathan J, Xu H, Koag MC, Lee S, Brodbelt JS. Streamlining bottom-up protein identification based on selective ultraviolet photodissociation (UVPD) of chromophore-tagged histidine- and tyrosine-containing peptides. Anal Chem 2014; 86:6237-44. [PMID: 24897623 DOI: 10.1021/ac403654m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report a fast and highly efficient diazonium reaction that couples a nitroazobenzene chromophore to tyrosine and histidine residues, thus endowing peptides with high photoabsorption cross sections at 351 nm in the gas phase. Only the tagged peptides undergo ultraviolet photodissociation (UVPD) at 351 nm, as demonstrated for several Tyr- and His-containing peptides from protein digests. Additional selectivity is achieved by the integration of the UVPD-MS method with an in silico database search restricted to Tyr- and His-containing peptides. A modified MassMatrix algorithm condenses analysis by filtering the input database file to include Tyr/His-containing peptides only, thus reducing the search space and increasing confidence. In summary, derivatization of specific amino acid residues in conjunction with selective activation of the derivatized peptides provides a streamlined approach to shotgun proteomics.
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Affiliation(s)
- Julia R Aponte
- Department of Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
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9
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Brodbelt JS. Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem Soc Rev 2014; 43:2757-83. [PMID: 24481009 PMCID: PMC3966968 DOI: 10.1039/c3cs60444f] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.
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10
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Grotzky A, Altamura E, Adamcik J, Carrara P, Stano P, Mavelli F, Nauser T, Mezzenga R, Schlüter AD, Walde P. Structure and enzymatic properties of molecular dendronized polymer-enzyme conjugates and their entrapment inside giant vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10831-10840. [PMID: 23895383 DOI: 10.1021/la401867c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Macromolecular hybrid structures were prepared in which two types of enzymes, horseradish peroxidase (HRP) and bovine erythrocytes Cu,Zn-superoxide dismutase (SOD), were linked to a fluorescently labeled, polycationic, dendronized polymer (denpol). Two homologous denpols of first and second generation were used and compared, and the activities of HRP and SOD of the conjugates were measured in aqueous solution separately and in combination. In the latter case the efficiency of the two enzymes in catalyzing a two-step cascade reaction was evaluated. Both enzymes in the two types of conjugates were highly active and comparable to free enzymes, although the efficiency of the enzymes bound to the second-generation denpol was significantly lower (up to a factor of 2) than the efficiency of HRP and SOD linked to the first-generation denpol. Both conjugates were analyzed by atomic force microscopy (AFM), confirming the expected increase in object size compared to free denpols and demonstrating the presence of enzyme molecules localized along the denpol chains. Finally, giant phospholipid vesicles with diameters of up to about 20 μm containing in their aqueous interior pool a first-generation denpol-HRP conjugate were prepared. The HRP of the entrapped conjugate was shown to remain active toward externally added, membrane-permeable substrates, an important prerequisite for the development of vesicular multienzyme reaction systems.
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Affiliation(s)
- Andrea Grotzky
- Laboratory of Polymer Chemistry, Department of Materials, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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11
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O'Brien JP, Pruet JM, Brodbelt JS. Chromogenic chemical probe for protein structural characterization via ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:7391-7. [PMID: 23855605 DOI: 10.1021/ac401305f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A chemical probe/ultraviolet photodissociation (UVPD) mass spectrometry strategy for evaluating structures of proteins and protein complexes is reported, as demonstrated for lysozyme and beta-lactoglobulin with and without bound ligands. The chemical probe, NN, incorporates a UV chromophore that endows peptides with high cross sections at 351 nm, a wavelength not absorbed by unmodified peptides. Thus, NN-modified peptides can readily be differentiated from nonmodified peptides in complex tryptic digests created upon proteolysis of proteins after their exposure to the NN chemical probe. The NN chemical probe also affords two diagnostic reporter ions detected upon UVPD of the NN-modified peptide that provides a facile method for the identification of NN peptides within complex mixtures. Quantitation of the modified and unmodified peptides allows estimation of the surface accessibilities of lysine residues based on their relative reactivities with the NN chemical probe.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, United States
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12
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Cotham VC, Wine Y, Brodbelt JS. Selective 351 nm photodissociation of cysteine-containing peptides for discrimination of antigen-binding regions of IgG fragments in bottom-up liquid chromatography-tandem mass spectrometry workflows. Anal Chem 2013; 85:5577-85. [PMID: 23641966 DOI: 10.1021/ac400851x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite tremendous inroads in the development of more sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategies for mass spectrometry-based proteomics, there remains a significant need for enhancing the selectivity of MS/MS-based workflows for streamlined analysis of complex biological mixtures. Here, a novel LC-MS/MS platform based on 351 nm ultraviolet photodissociation (UVPD) is presented for the selective analysis of cysteine-peptide subsets in complex protein digests. Cysteine-selective UVPD is mediated through the site-specific conjugation of reduced cysteine residues with a 351 nm active chromogenic Alexa Fluor 350 (AF350) maleimide tag. Only peptides containing the AF350 chromophore undergo photodissociation into extensive arrays of b- and y-type fragment ions, thus providing a facile means for differentiating cysteine-peptide targets from convoluting peptide backgrounds. With the use of this approach in addition to strategic proteolysis, the selective analysis of diagnostic heavy-chain complementarity determining regions (CDRs) of single-chain antibody (scAb) fragments is demonstrated.
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Affiliation(s)
- Victoria C Cotham
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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13
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Ko BJ, Brodbelt JS. Enhanced electron transfer dissociation of peptides modified at C-terminus with fixed charges. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1991-2000. [PMID: 22895859 DOI: 10.1007/s13361-012-0458-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/21/2012] [Accepted: 07/21/2012] [Indexed: 06/01/2023]
Abstract
The impact of the conversion of carboxylates in peptides to basic or fixed charge sites on the outcome of electron transfer dissociation (ETD) is evaluated with respect to ETD efficiency and the number of diagnostic sequence ions. Four reagents, including benzylamine (BA), 1-benzylpiperazine (BZP), carboxymethyl trimethylammonium chloride hydrazide (GT), and (2-aminoethyl)trimethylammonium chloride hydrochloride (AETMA), were used for the carboxylate derivatization, with the first two replacing the acidic carboxylate groups with basic functionalities and the latter two introducing fixed charge sites. The ETD efficiencies and Xcorr scores were compared for both nonderivatized and derivatized tryptic and Glu-C peptides from cytochrome c. Derivatization of the carboxylate increases the average charge states, the number of fragment ions, and the dissociation efficiencies of peptides, especially for the fixed charge reagent, AETMA.
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Affiliation(s)
- Byoung Joon Ko
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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14
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Cleavable linkers in chemical biology. Bioorg Med Chem 2012; 20:571-82. [DOI: 10.1016/j.bmc.2011.07.048] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/08/2011] [Accepted: 07/23/2011] [Indexed: 01/11/2023]
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15
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Enjalbert Q, Simon R, Salvador A, Antoine R, Redon S, Ayhan MM, Darbour F, Chambert S, Bretonnière Y, Dugourd P, Lemoine J. Photo-SRM: laser-induced dissociation improves detection selectivity of Selected Reaction Monitoring mode. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3375-3381. [PMID: 22002689 DOI: 10.1002/rcm.5232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Selected Reaction Monitoring (SRM) carried out on triple-quadrupole mass spectrometers coupled to liquid chromatography has been a reference method to develop quantitative analysis of small molecules in biological or environmental matrices for years and is currently emerging as a promising tool in clinical proteomic. However, sensitive assays in complex matrices are often hampered by the presence of co-eluted compounds that share redundant transitions with the target species. On-the-fly better selection of the precursor ion by high-field asymmetric waveform ion mobility spectrometry (FAIMS) or increased quadrupole resolution is one way to escape from interferences. In the present work we document the potential interest of substituting classical gas-collision activation mode by laser-induced dissociation in the visible wavelength range to improve the specificity of the fragmentation step. Optimization of the laser beam pathway across the different quadrupoles to ensure high photo-dissociation yield in Q2 without detectable fragmentation in Q1 was assessed with sucrose tagged with a push-pull chromophore. Next, the proof of concept that photo-SRM ensures more specific detection than does conventional collision-induced dissociation (CID)-based SRM was carried out with oxytocin peptide. Oxytocin was derivatized by the thiol-reactive QSY® 7 C(5)-maleimide quencher on cysteine residues to shift its absorption property into the visible range. Photo-SRM chromatograms of tagged oxytocin spiked in whole human plasma digest showed better detection specificity and sensitivity than CID, that resulted in extended calibration curve linearity. We anticipate that photo-SRM might significantly improve the limit of quantification of classical SRM-based assays targeting cysteine-containing peptides.
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16
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Antoine R, Dugourd P. Visible and ultraviolet spectroscopy of gas phase protein ions. Phys Chem Chem Phys 2011; 13:16494-509. [PMID: 21811728 DOI: 10.1039/c1cp21531k] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.
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Brodbelt JS. Shedding light on the frontier of photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:197-206. [PMID: 21472579 DOI: 10.1007/s13361-010-0023-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
The development of new ion activation/dissociation methods is motivated by the need for more versatile ways to characterize structures of ions, especially in the growing arena of biological mass spectrometry in which better tools for determining sequences, modifications, interactions, and conformations of biopolymers are essential. Although most agree that collision-induced dissociation (CID) remains the gold standard for ion activation/dissociation, recent inroads in electron- and photon-based activation methods have cemented their role as outstanding alternatives. This article will focus on the impact of photodissociation, including its strengths and drawbacks as an analytical tool, and its potential for further development in the next decade. Moreover, the discussion will emphasize photodissociation in quadrupole ion traps, because that platform has been used for one of the greatest arrays of new applications over the past decade.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.
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Ko BJ, Brodbelt JS. Ultraviolet photodissociation of carboxylate-derivatized peptides in a quadrupole ion trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:49-56. [PMID: 21472543 DOI: 10.1007/s13361-010-0016-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
The fragmentation patterns obtained by ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer were compared for peptides modified at their C-termini and at acidic amino acids. Attachment of Alexa Fluor 350 or 7-amino-4-methyl-coumarin chromophores at the C-terminal and acidic residues enhances the UV absorptivity of the peptides and all fragment ions that retain the chromophore, such as the y ions that contain the chromophore-modified C-terminus. Whereas CID results in the formation of the typical array of mainly y-type and a/b-type fragment ions, UVPD produces predominantly a/b-type ions with greatly reduced abundances of y ions. Immonium ions, mostly ones from aromatic or basic amino acids, are also observed in the low m/z range upon UVPD. UVPD of peptides containing two chromophore moieties (with one at the C-terminus and another at an acidic residue) results in even more efficient photodissociation at the expense of the annihilation of almost all diagnostic b and y ions containing the chromophore.
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Affiliation(s)
- Byoung Joon Ko
- Department of Chemical Engineering, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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Yang L, Tang X, Weisbrod CR, Munske GR, Eng JK, von Haller PD, Kaiser NK, Bruce JE. A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies. Anal Chem 2010; 82:3556-66. [PMID: 20373789 DOI: 10.1021/ac902615g] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we present the results of proof-of-concept experiments using a novel photocleavable and mass spectrometry identifiable cross-linker pcPIR (photocleavable protein interaction reporter). pcPIR can be dissociated under UV irradiation either off- or online before the introduction to the mass spectrometers. Photo dissociation of cross-linkers is different from either the gas phase or the chemical cleavage of cross-linkers. Different types of cross-links can be identified using the pcPIR mass relationships, where the mass of cross-linked precursor equals the sum of the masses of the released products and reporter. Since pcPIR is cleaved prior to the entrance to the mass spectrometer, the released peptides are available to be sequenced with routine collision-induced dissociation (CID) MS/MS experiments and database search algorithms. In this report, the pcPIR strategy of identifying the cross-linked peptides with on- and off-line photocleavage coupled with novel targeted data dependent LC-MS/MS is demonstrated with the use of standard peptides, bovine serum albumin (BSA), and human hemoglobin tetramer protein complex.
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Affiliation(s)
- Li Yang
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
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Gardner MW, Brodbelt JS. Preferential Cleavage of N−N Hydrazone Bonds for Sequencing Bis-arylhydrazone Conjugated Peptides by Electron Transfer Dissociation. Anal Chem 2010; 82:5751-9. [DOI: 10.1021/ac100788a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myles W. Gardner
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
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Bakir M, Green O, Wilmot-Singh M. Synthesis, spectroscopic, and X-ray crystallographic analysis of manganese compounds of di-2-pyridyl ketone thiophene-2-carboxylic acid hydrazone (dpktch): The reaction of Mn(CO)5Br with dpktch. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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