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Gunawardena HP, Jayatilake MM, Brelsford JD, Nanda H. Diagnostic utility of N-terminal TMPP labels for unambiguous identification of clipped sites in therapeutic proteins. Sci Rep 2023; 13:18602. [PMID: 37903854 PMCID: PMC10616084 DOI: 10.1038/s41598-023-45446-z] [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: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Protein therapeutics are susceptible to clipping via enzymatic and nonenzymatic mechanisms that create neo-N-termini. Typically, neo-N-termini are identified by chemical derivatization of the N-terminal amine with (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) followed by proteolysis and mass spectrometric analysis. Detection of the TMPP-labeled peptide is achieved by mapping the peptide sequence to the product ion spectrum derived from collisional activation. The site-specific localization of the TMPP tag enables unambiguous determination of the true N-terminus or neo-N-termini. In addition to backbone product ions, TMPP reporter ions at m/z 573, formed via collision-induced dissociation, can be diagnostic for the presence of a processed N-termini. However, reporter ions generated by collision-induced dissociation may be uninformative because of their low abundance. We demonstrate a novel high-throughput LC-MS method for the facile generation of the TMPP reporter ion at m/z 533 and, in some instances m/z 590, upon electron transfer dissociation. We further demonstrate the diagnostic utility of TMPP labeled peptides derived from a total cell lysate shows high degree of specificity towards selective N-terminal labeling over labeling of lysine and tyrosine and highly-diagnostic Receiver Operating Characteristic's (ROC) of TMPP reporter ions of m/z 533 and m/z 590. The abundant generation of these reporters enables subsequent MS/MS by intensity and m/z-dependent triggering of complementary ion activation modes such as collision-induced dissociation, high-energy collision dissociation, or ultraviolet photo dissociation for subsequent peptide sequencing.
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Affiliation(s)
- Harsha P Gunawardena
- Janssen Research and Development LLC, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA.
| | - Meth M Jayatilake
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Jeffery D Brelsford
- Janssen Research and Development LLC, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA
| | - Hirsh Nanda
- Janssen Research and Development LLC, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA
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Analysis of Fragmentation Pathways of Peptide Modified with Quaternary Ammonium and Phosphonium Group as Ionization Enhancers. Molecules 2021; 26:molecules26226964. [PMID: 34834054 PMCID: PMC8623324 DOI: 10.3390/molecules26226964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022] Open
Abstract
Peptide modification by a quaternary ammonium group containing a permanent positive charge is a promising method of increasing the ionization efficiency of the analyzed compounds, making ultra-sensitive detection even at the attomolar level possible. Charge-derivatized peptides may undergo both charge remote (ChR) and charge-directed (ChD) fragmentation. A series of model peptide conjugates derivatized with N,N,N-triethyloammonium (TEA), 1-azoniabicyclo[2.2.2]octane (ABCO), 2,4,6-triphenylopyridinium (TPP) and tris(2,4,6-trimetoxyphenylo)phosphonium (TMPP) groups were analyzed by their fragmentation pathways both in collision-induced dissociation (CID) and electron-capture dissociation (ECD) mode. The effect of the fixed-charge tag type and peptide sequence on the fragmentation pathways was investigated. We found that the aspartic acid effect plays a crucial role in the CID fragmentation of TPP and TEA peptide conjugates whereas it was not resolved for the peptides derivatized with the phosphonium group. ECD spectra are mostly dominated by cn ions. ECD fragmentation of TMPP-modified peptides results in the formation of intense fragments derived from this fixed-charge tag, which may serve as reporter ion.
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Abstract
INTRODUCTION The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required. AREAS COVERED We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis. EXPERT OPINION N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
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Misal SA, Li S, Tang H, Radivojac P, Reilly JP. Identification of N-terminal protein processing sites by chemical labeling mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1015-1023. [PMID: 30884002 PMCID: PMC6522274 DOI: 10.1002/rcm.8435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/01/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Proteins undergo post-translational modifications and proteolytic processing that can affect their biological function. Processing often involves the loss of single residues. Cleavage of signal peptides from the N-terminus is commonly associated with translocation. Recent reports have suggested that other processing sites also exist. METHODS The secreted proteins from S. aureus N315 were precipitated with trichloroacetic acid (TCA) and amidinated with S-methyl thioacetimidate (SMTA). Amidinated proteins were digested with trypsin and analyzed with a high-resolution orbitrap mass spectrometer. RESULTS Sixteen examples of Staphylococcus aureus secretory proteins that lose an N-terminal signal peptide during their export were identified using this amidination approach. The N-termini of proteins with and without methionine were identified. Unanticipated protein cleavages due to sortase and an unknown protease were also uncovered. CONCLUSIONS A simple N-terminal amidination based mass spectrometry approach is described that facilitates identification of the N-terminus of a mature protein and the discovery of unexpected processing sites.
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Affiliation(s)
- Santosh A Misal
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Sujun Li
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - Haixu Tang
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - Predrag Radivojac
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
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DeGraan-Weber N, Ward SA, Reilly JP. A Novel Triethylphosphonium Charge Tag on Peptides: Synthesis, Derivatization, and Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1889-1900. [PMID: 28560565 PMCID: PMC5709245 DOI: 10.1007/s13361-017-1694-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Charge tagging is a peptide derivatization process that commonly localizes a positive charge on the N-terminus. Upon low energy activation (e.g., collision-induced dissociation or post-source decay) of charge tagged peptides, relatively few fragment ions are produced due to the absence of mobile protons. In contrast, high energy fragmentation, such as 157 nm photodissociation, typically leads to a series of a-type ions. Disadvantages of existing charge tags are that they can produce mobile protons or that they are undesirably large and bulky. Here, we investigate a small triethylphosphonium charge tag with two different linkages: amide (158 Da) and amidine bonds (157 Da). Activation of peptides labeled with a triethylphosphonium charge tag through an amide bond can lead to loss of the charge tag and the production of protonated peptides. This enables low intensity fragment ions from both the protonated and charge tagged peptides to be observed. Triethylphosphonium charge tagged peptides linked through an amidine bond are more stable. Post-source decay and photodissociation yield product ions that primarily contain the charge tag. Certain amidine induced fragments are also observed. The previously reported tris(trimethoxyphenyl) phosphonium acetic acid N-hydroxysuccinimidyl ester charge tag shows a similar fragment ion distribution, but the mass of the triethylphosphonium tag label is 415 Da smaller. Graphical Abstract ᅟ.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Sarah A Ward
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA.
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DeGraan-Weber N, Zhang J, Reilly JP. Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2041-2053. [PMID: 27613306 PMCID: PMC5748252 DOI: 10.1007/s13361-016-1487-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 05/21/2023]
Abstract
Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. Graphical Abstract ᅟ.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Jun Zhang
- Pre-Pivotal Drug Product Technologies, Amgen Inc., Thousand Oaks, CA, 91320, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light‐Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dustin D. Holden
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH Hanna-Kunath-Strasse 11 28199 Bremen Germany
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - James D. Sanders
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc. 355 River Oaks Pkwy San Jose CA 95134 USA
| | - Jennifer S. Brodbelt
- Department of Chemistry The University of Texas at Austin 105 E. 24th St Austin TX 78712 USA
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Holden DD, Makarov A, Schwartz JC, Sanders JD, Zhuk E, Brodbelt JS. Ultraviolet Photodissociation Induced by Light-Emitting Diodes in a Planar Ion Trap. Angew Chem Int Ed Engl 2016; 55:12417-21. [PMID: 27605434 DOI: 10.1002/anie.201605850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/02/2016] [Indexed: 11/09/2022]
Abstract
The first application of light-emitting diodes (LEDs) for ultraviolet photodissociation (UVPD) mass spectrometry is reported. LEDs provide a compact, low cost light source and have been incorporated directly into the trapping cell of an Orbitrap mass spectrometer. MS/MS efficiencies of over 50 % were obtained using an extended irradiation period, and UVPD was optimized by modulating the ion trapping parameters to maximize the overlap between the ion cloud and the irradiation volume.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199, Bremen, Germany
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA
| | - Eugene Zhuk
- Thermo Fisher Scientific Inc., 355 River Oaks Pkwy, San Jose, CA, 95134, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St, Austin, TX, 78712, USA.
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Hoffmann WD, Jackson GP. Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1939-43. [PMID: 25231159 DOI: 10.1007/s13361-014-0989-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/23/2014] [Accepted: 07/27/2014] [Indexed: 05/04/2023]
Abstract
A kiloelectronvolt beam of helium ions is used to ionize and fragment precursor peptide ions starting in the 1+ charge state. The electron affinity of helium cations (24.6 eV) exceeds the ionization potential of protonated peptides and can therefore be used to abstract an electron from--or charge exchange with--the isolated precursor ions. Kiloelectronvolt energies are used, (1) to overcome the Coulombic repulsion barrier between the cationic reactants, (2) to overcome ion-defocussing effects in the ion trap, and (3) to provide additional activation energy. Charge transfer dissociation (CTD) of the [M+H](+) precursor of Substance P gives product ions such as [M+H](2+•) and a dominant series of a ions in both the 1+ and 2+ charge states. These observations, along with the less-abundant a + 1 ions, are consistent with ultraviolet photodissociation (UVPD) results of others and indicate that C-C(α) cleavages are possible through charge exchange with helium ions. Although the efficiencies and timescale of CTD are not yet suitable for on-line chromatography, this new approach to ion activation provides an additional potential tool for the interrogation of gas phase ions.
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Affiliation(s)
- William D Hoffmann
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, 26506, USA
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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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Bertaccini D, Vaca S, Carapito C, Arsène-Ploetze F, Van Dorsselaer A, Schaeffer-Reiss C. An Improved Stable Isotope N-Terminal Labeling Approach with Light/Heavy TMPP To Automate Proteogenomics Data Validation: dN-TOP. J Proteome Res 2013; 12:3063-70. [DOI: 10.1021/pr4002993] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Diego Bertaccini
- Laboratoire de Spectrométrie
de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France
| | - Sebastian Vaca
- Laboratoire de Spectrométrie
de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie
de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France
| | - Florence Arsène-Ploetze
- Laboratoire de Génétique
Moléculaire, Génomique et Microbiologie, Université de Strasbourg, CNRS UMR7156, Strasbourg,
France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie
de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie
de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France
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