New free radical-initiated peptide sequencing (FRIPS) mass spectrometry reagent with high conjugation efficiency enabling single-step peptide sequencing.


Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
09 06 2022
Historique:
received: 13 03 2022
accepted: 17 05 2022
entrez: 10 6 2022
pubmed: 11 6 2022
medline: 14 6 2022
Statut: epublish

Résumé

A newly designed TEMPO-FRIPS reagent, 4-(2,2,6,6-tetramethylpiperidine-1-oxyl) methyl benzyl succinic acid N-hydroxysuccinimide ester or p-TEMPO-Bn-Sc-NHS, was synthesized to achieve single-step free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) for a number of model peptides, including phosphopeptides. The p-TEMPO-Bn-Sc-NHS reagent was conjugated to target peptides, and the resulting peptides were subjected to collisional activation. The peptide backbone dissociation behaviors of the MS/MS and MS

Identifiants

pubmed: 35680949
doi: 10.1038/s41598-022-13624-0
pii: 10.1038/s41598-022-13624-0
pmc: PMC9184593
doi:

Substances chimiques

Free Radicals 0
Indicators and Reagents 0
Ions 0
Phosphopeptides 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

9494

Commentaires et corrections

Type : ErratumIn

Informations de copyright

© 2022. The Author(s).

Références

Borotto, N. B., Ileka, K. M., Tom, C. A. T. M. B., Martin, B. R. & Håkansson, K. Free radical initiated peptide sequencing for direct site localization of sulfation and phosphorylation with negative ion mode mass spectrometry. Anal. Chem. 90, 9682–9686 (2018).
pubmed: 30063332 pmcid: 6235672 doi: 10.1021/acs.analchem.8b02707
Halim, M. A. et al. Ultraviolet, infrared, and high-low energy photodissociation of post-translationally modified peptides. J. Am. Soc. Mass Spectrom. 29, 270–283 (2018).
pubmed: 28980177 doi: 10.1007/s13361-017-1794-9
Wiesner, J., Premsler, T. & Sickmann, A. Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 8, 4466–4483 (2008).
pubmed: 18972526 doi: 10.1002/pmic.200800329
Kim, M. S. & Pandey, A. Electron transfer dissociation mass spectrometry in proteomics. Proteomics 12, 530–542 (2012).
pubmed: 22246976 pmcid: 3664229 doi: 10.1002/pmic.201100517
Zhurov, K. O., Fornelli, L., Wodrich, M. D., Laskay, Ü. A. & Tsybin, Y. O. Principles of electron capture and transfer dissociation mass spectrometry applied to peptide and protein structure analysis. Chem. Soc. Rev. 42, 5014–5030 (2013).
pubmed: 23450212 doi: 10.1039/c3cs35477f
Tsybin, Y. O. et al. Structural analysis of intact monoclonal antibodies by electron transfer dissociation mass spectrometry. Anal. Chem. 83, 8919–8927 (2011).
pubmed: 22017162 doi: 10.1021/ac201293m
Floris, F. et al. Bottom-up two-dimensional electron-capture dissociation mass spectrometry of calmodulin. J. Am. Soc. Mass. Spectrom. 29, 207–210 (2018).
pubmed: 28975559 doi: 10.1007/s13361-017-1812-y
Han, L. & Costello, C. E. Electron transfer dissociation of milk oligosaccharides. J. Am. Soc. Mass. Spectrom. 22, 997–1013 (2011).
pubmed: 21953041 pmcid: 3606914 doi: 10.1007/s13361-011-0117-9
Halim, M. A. et al. 213 nm Ultraviolet photodissociation on peptide anions: Radical-directed fragmentation patterns. J. Am. Soc. Mass. Spectrom. 27, 474–486 (2016).
pubmed: 26545767 doi: 10.1007/s13361-015-1297-5
Brunet, C. et al. Gas phase photo-formation and vacuum UV photofragmentation spectroscopy of tryptophan and tyrosine radical-containing peptides. J. Phys. Chem. A 115, 8933–8939 (2011).
pubmed: 21744817 doi: 10.1021/jp205617x
Lacobucci, C., Hage, C., Schäfer, M. & Sinz, A. A novel MS-cleavable azo cross-linker for peptide structure analysis by free radical initiated peptide sequencing (FRIPS). J. Am. Soc. Mass. Spectrom. 28, 2039–2053 (2017).
doi: 10.1007/s13361-017-1744-6
Oh, H. B. & Moon, B. Radical-driven peptide backbone dissociation tandem mass spectrometry. Mass Spectrom. Rev. 34, 116–132 (2015).
pubmed: 24863492 doi: 10.1002/mas.21426
Masterson, D. S. et al. Lysine peroxycarbamates: free radical-promoted peptide cleavage. J. Am. Chem. Soc. 126, 720–721 (2004).
pubmed: 14733538 doi: 10.1021/ja038615u
Hodyss, R., Cox, H. A. & Beauchamp, J. L. Bioconjugates for tunable peptide fragmentation: free radical initiated peptide sequencing (FRIPS). J. Am. Chem. Soc. 127, 12436–12437 (2005).
pubmed: 16144360 doi: 10.1021/ja052042z
Sohn, C. H. et al. Mechanisms and energetics of free radical initiated disulfide bond cleavage in model peptides and insulin by mass spectrometry. Chem. Sci. 6, 4550–4560 (2015).
pubmed: 29142703 pmcid: 5666513 doi: 10.1039/C5SC01305D
Marshall, D. L., Hansen, C. S., Trevitt, A. J., Oh, H. B. & Blanksby, S. J. Photodissociation of TEMPO-modified peptides: new approaches to radical-directed dissociation of biomolecules. Phys. Chem. Chem. Phys. 16, 4871–4879 (2014).
pubmed: 24473158 doi: 10.1039/c3cp54825b
Jeon, A. et al. Guanidination of lysine residue improves the sensitivity and facilitates the interpretation of free radical initiated peptide sequencing (FRIPS) mass spectrometry results. Int. J. Mass Spectrom. 390, 110–117 (2015).
doi: 10.1016/j.ijms.2015.06.019
Thomas, D. A., Sohn, C. H., Gao, J. & Beauchamp, J. L. Hydrogen bonding constrains free radical reaction dynamics at serine and threonine residues in peptides. J. Phys. Chem. A 118, 8380–8392 (2014).
pubmed: 24605822 doi: 10.1021/jp501367w
Falvo, F., Fiebig, L. & Schäfer, M. Presentation of a homobifunctional azo-reagent for protein structure analysis by collision-induced dissociative chemical cross-linking: Proof-of-principle. Int. J. Mass Spectrom. 26, 354–355 (2013).
Hage, C., Ihling, C. H., Götze, M., Schäfer, M. & Sinz, A. Dissociation behavior of a TEMPO-active ester cross-linker for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) in negative ESI-MS. J. Am. Soc. Mass Spectrom. 28, 56–68 (2017).
pubmed: 27418170 doi: 10.1007/s13361-016-1426-9
Lacobucci, C., Schäfer, M. & Sinz, A. Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis. Mass Spectrom. Rev. 38, 187–201 (2019).
doi: 10.1002/mas.21568
Lee, M., Kang, M., Moon, B. & Oh, H. B. Gas-phase peptide sequencing by TEMPO-mediated radical generation. Analyst 134, 1706–1712 (2009).
pubmed: 20448941 doi: 10.1039/b904115j
Zhang, X. & Julian, R. R. Exploring radical migration pathways in peptides with positional isomers, deuterium labeling, and molecular dynamics simulations. J. Am. Soc. Mass Spectrom. 24, 524–533 (2013).
pubmed: 23361370 doi: 10.1007/s13361-012-0540-6
Sun, Q., Nelson, H., Ly, T., Stoltz, B. M. & Julian, R. R. Side chain chemistry mediates backbone fragmentation in hydrogen deficient peptide radicals. J. Proteome Res. 8, 958–966 (2009).
pubmed: 19113886 doi: 10.1021/pr800592t
DeGraan-Weber, N., Zhang, J. & Reilly, J. P. Distinguishing aspartic and isoaspartic acids in peptides by several mass spectrometric fragmentation methods. J. Am. Soc. Mass Spectrom. 27, 2041–2053 (2016).
pubmed: 27613306 pmcid: 5748252 doi: 10.1007/s13361-016-1487-9
Lee, C. S., Jang, I., Hwangbo, S., Moon, B. & Oh, H. B. Side chain cleavage in TEMPO-assisted free radical initiated peptide sequencing (FRIPS): Amino acid composition information. Bull. Korean Chem. Soc. 36, 810–814 (2015).
Lee, M. et al. Disulfide bond cleavage in TEMPO-free radical initiated peptide sequencing mass spectrometry. J. Mass Spectrom. 46, 830–839 (2011).
pubmed: 21834022 doi: 10.1002/jms.1955
Jang, I. et al. Free radical-initiated peptide sequencing mass spectrometry for phosphopeptide post-translational modification analysis. J. Am. Soc. Mass Spectrom. 30, 538–547 (2019).
pubmed: 30414067 doi: 10.1007/s13361-018-2100-1
Götze, M. et al. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. J. Am. Soc. Mass Spectrom. 26, 83–97 (2015).
pubmed: 25261217 doi: 10.1007/s13361-014-1001-1
Lacobucci, C. et al. A cross-linking/mass spectrometry workflow based on MS-cleavable cross-liners and the MeroX software for studying protein structures and protein-protein interactions. Nat. Protoc. 13, 2864–2889 (2018).
doi: 10.1038/s41596-018-0068-8
Hage, C., Lacobucci, C., Rehkamp, A., Arlt, C. & Sinz, A. The first zero-length mass spectrometry-cleavable cross-linker for protein structure analysis. Angew. Chem. Int. Ed. Engl. 56, 14551–14555 (2017).
pubmed: 28876504 doi: 10.1002/anie.201708273
Lee, J.-U. et al. TEMPO-assisted free-radical-initiated peptide seqeuncing mass spectrometry for ubiquitin ions: An insight on the gas-phase conformations. J. Am. Soc. Mass Spectrom. 33, 471–481 (2022).
pubmed: 35099967 doi: 10.1021/jasms.1c00313
Gasper, K., Fabijanczuk, K., Otegui, T., Acosta, J. & Gao, J. Development of novel free radical initiated peptide sequencing reagent: Application to identification and characterization of peptides by mass spectrometry. J. Am. Soc. Mass Spectrom. 30, 548–556 (2019).
doi: 10.1007/s13361-018-2114-8
Jang, I. et al. TEMPO-assisted free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) in Q-TOF and orbitrap mass spectrometers: Single-step peptide backbone dissociations in positive ion mode. J. Am. Soc. Mass. Spectrom. 28, 154–163 (2017).
pubmed: 27686973 doi: 10.1007/s13361-016-1508-8
Lee, J. et al. One-step peptide backbone dissociations in negative-ion free radical initiated peptide sequencing mass spectrometry. Anal. Chem. 85, 7044–7051 (2013).
pubmed: 23802150 doi: 10.1021/ac303517h
Wu, Z. et al. MASH Explorer: A universal software environment for top-down proteomics. J. Proteome Res. 19, 3867–3876 (2020).
pubmed: 32786689 pmcid: 7728713 doi: 10.1021/acs.jproteome.0c00469
Cooper, H. J., Hudgins, R. R., Håkansson, K. & Marshall, A. G. Characterization of amino acid side chain losses in electron capture dissociation. J. Am. Soc. Mass Spectrom. 13, 241–249 (2002).
pubmed: 11908804 doi: 10.1016/S1044-0305(01)00357-9
Wee, S., O’Hair, R. A. & McFadyen, W. D. Side-chain radical losses from radical cations allows distinction of leucine and isoleucine residues in the isomeric peptides Gly-XXX-Arg. Rapid Commun. Mass Spectrom. 16, 884–890 (2002).
pubmed: 11948821 doi: 10.1002/rcm.658
Yin, H., Chacon, A., Porter, N. A. & Masterson, D. S. Free radical-induced site-specific peptide cleavage in the gas phase: low-energy collision induced dissociation in ESI- and MALDI mass spectrometry. J. Am. Soc. Mass Spectrom. 18, 807–816 (2007).
pubmed: 17307363 doi: 10.1016/j.jasms.2007.01.004
Ly, T. & Julian, R. R. Residue-specific radical-directed dissociation of whole proteins in the gas phase. J. Am. Chem. Soc. 130, 351–358 (2008).
pubmed: 18078340 doi: 10.1021/ja076535a
Lee, J.-U., Kim, Y. J., Kim, W. Y. & Oh, H. B. Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide. Phys. Chem. Chem. Phys. 22, 5057–5069 (2020).
pubmed: 32073000 doi: 10.1039/C9CP05433B
Chu, I. K., Rodriquez, C. F., Lau, T.-C., Hopkinson, A. C. & Siu, K. W. M. Molecular radical cations of oligopeptides. J. Phys. Chem. B. 104, 3393–3397 (2000).
doi: 10.1021/jp994487d
Wee, S., O’Hair, R. A. J. & McFadyen, W. D. Comparing the gas-phase fragmentation reactions of protonated and radical cations of the tripeptides GXR. Int. J. Mass Spectrom. 234, 101–122 (2004).
doi: 10.1016/j.ijms.2004.02.018
Laskin, J., Yang, Z., Lam, C. & Chu, I. K. Charge-remote fragmentation of odd-electron peptide ions. Anal. Chem. 79, 6607–6614 (2007).
pubmed: 17676923 doi: 10.1021/ac070777b
Chu, I. K., Radriguez, C. F., Hopkinson, A. C., Siu, K. W. M. & Lau, T. C. Formation of molecular radical cations of enkephalin derivatives via collisional-induced dissociation of electrospray-generated copper (II) complex ions of amines and peptides. J. Am. Soc. Mass Spectrom. 12, 1114–1119 (2001).
pubmed: 11605973 doi: 10.1016/S1044-0305(01)00297-5
Boersema, P. J., Mohammed, S. & Heck, A. J. R. Phosphopeptide fragmentation and analysis by mass spectrometry. J. Mass Spectrom. 44, 861–878 (2009).
pubmed: 19504542 doi: 10.1002/jms.1599

Auteurs

Sang Tak Lee (ST)

Department of Chemistry, Sogang University, Seoul, 04107, Korea.

Hyemi Park (H)

Department of Chemistry, Sogang University, Seoul, 04107, Korea.

Inae Jang (I)

Department of Chemistry, Sogang University, Seoul, 04107, Korea.

Choong Sik Lee (CS)

Department of Chemistry, Sogang University, Seoul, 04107, Korea.
Department of Toxicology and Chemistry, Scientific Investigation Laboratory, Criminal Investigation Command, Ministry of National Defense, Seoul, 04351, Korea.

Bongjin Moon (B)

Department of Chemistry, Sogang University, Seoul, 04107, Korea. bjmoon@sogang.ac.kr.

Han Bin Oh (HB)

Department of Chemistry, Sogang University, Seoul, 04107, Korea. hanbinoh@sogang.ac.kr.

Articles similaires

Cicer Germination Proteolysis Seeds Plant Proteins
Humans Pisum sativum Breast Neoplasms Tandem Mass Spectrometry Plant Extracts
Hyperaldosteronism Humans Renin Aldosterone Middle Aged
Humans Biomarkers Machine Learning Cardiovascular Diseases Male

Classifications MeSH