Formation of (bn−1 + H2O) ions by collisional activation of maldi-formed peptide [M + H]+ ions in a QqTOF mass spectrometer

She, Yi‐Min; Krokhin, Oleg V.; Spicer, Victor; Лобода, А. В.; Garland, Gideon; Ens, Werner; Standing, Kenneth G.; Westmore, John B.

doi:10.1016/j.jasms.2007.02.008

Cited by 21 publications

(27 citation statements)

References 56 publications

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“…Our proposed mechanism can also explain the previous different and sometimes even contradictory reports on positions of Arg residue that enhance the formation of b + H 2 O ions [40,[42][43][44][45]. These positions include the (n -1) position [42], at or near C- [44,45], or N-terminus [44], or alternatively, a combination of one at the C-terminus and the other somewhere in the peptide backbone [40].…”

Section: ) P -supporting

confidence: 63%

“…Interestingly, no such product ions were observed in the pseudo MS 3 spectrum of the ion of the same peptide but with a different charge state-(y 10 -SH) + (Figure 4b). Different mechanisms [42][43][44][45][46] have been proposed for the formation of b n-1 + H 2 O ions from dissociation of peptide ions; however, none of these mechanisms can explain why the b n-1 + H 2 O (i.e., (b 9 + H 2 O) 2+ ion) and related ions were present in the pseudo MS 3 spectrum of (y 10 -SH) 2+ ion but absent in that of (y 10 -SH) + (Figure 4). A mechanism instead is proposed here for the formation of these ions (Scheme 4), where a mobile proton present in (y 10 -SH) 2+ along with salt bridge formation is involved.…”

Section: ) P -mentioning

confidence: 99%

“…Such features include the stabilization of deprotonated C-terminal carboxyl group by a salt-bridge [42], the weakening of the (n -1) th amide bond by a hydrogen bond between protonated Arg and the amide oxygen [43,45], the nucleophilic attacking of the amide carbon center by the negatively charged oxygen of the Cterminal carboxyl group [25,42,46] (which is supported by the disappearance of the b n-1 + H 2 O ion from dissociation of precursor ion of peptide RYGGFL upon C-terminal methylation [26]), and the stabilization of the transition ion and product ion by a salt-bridge [42]. Our proposed mechanism is very similar to the one proposed by Gonzalez et al [42], however, with one important difference, i.e., the weakening of the amide bond.…”

Section: ) P -mentioning

confidence: 99%

“…Our proposed mechanism is very similar to the one proposed by Gonzalez et al [42], however, with one important difference, i.e., the weakening of the amide bond. Gonzalez et al [42] proposed "the cationized guanidine group involved in a salt bridge could interact more efficiently with its own carbonyl group via the [ 43] also proposed that the (n -1) th amide bond was weakened by a hydrogen bond between protonated Arg and the amide oxygen. In contrast, based on the absence of b n-1 + H 2 O ion in the pseudo MS 3 spectrum of (y 10 -SH) + , we propose it is the hydrogen bond formed between the protonated N-terminus amine group and the (n -1) th amide oxygen that weakens the amide bond; the reason is likely that the protonated N-terminus amine group is more flexible and probably undergoes less energy strain and steric hindrance for the hydrogen bond formation compared with the protonated Arg residue.…”

Section: ) P -mentioning

confidence: 99%

“…These positions include the (n -1) position [42], at or near C- [44,45], or N-terminus [44], or alternatively, a combination of one at the C-terminus and the other somewhere in the peptide backbone [40]. When one Arg residue was at the C-terminus, two of the reports on b n-1 + H 2 O ions are contradictory: absent in one work [42], while significantly present in another [44], with the former report partially supported by a systematic study on the formation of b n-1 + H 2 O ions, where a non-C-terminal basic residue was a proposed requirement [43]. These different observations can be rationalized based on Scheme 4.…”

Section: ) P -mentioning

confidence: 99%

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A Pseudo MS³Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

Chen

Shiyanov

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et al. 2011

J. Am. Soc. Mass Spectrom.

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It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS 3 approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole timeof-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c i-1 ions (the i th residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS 3 spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS 3 approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs.

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Section: ) P -supporting

confidence: 63%

Section: ) P -mentioning

confidence: 99%

Section: ) P -mentioning

confidence: 99%

Section: ) P -mentioning

confidence: 99%

Section: ) P -mentioning

confidence: 99%

See 3 more Smart Citations

A Pseudo MS³Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

Chen

Shiyanov

Schlager

et al. 2011

J. Am. Soc. Mass Spectrom.

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MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini

et al. 2022

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N‐terminal derivatization of proteins with permanently positive charged reagent constitutes a viable mass spectrometry bottom‐up strategy for systematic confident identification of protein N‐termini. Although shotgun nanoLC‐ESI‐MS/MS approaches are commonly applied in that context by dissociating multiply charged molecular ions upon low energy collision‐induced dissociations (CID), we were keen to investigate an alternative sequencing method reckoning on more comprehensive high energy charge remote fragmentations (CRF) available with a MALDI‐Tof/Tof instrument. Hence, two tunable activation methods, i. e. metastable laser‐induced dissociations (LID) and high energy CID, were applied to several synthetic N‐terminal tris(trimethoxyphenyl)phosphonium (TMPP) acetyl peptides and their MS/MS behaviors were compared with low energy CID MS/MS data (LC‐ESI‐QqTof equipment). The amino acid composition was found to play a significant role in the peptide backbone dissociation pathways of these fixed singly charged ions. Proline, arginine, aspartic acid, glutamic acid, but also surprisingly aliphatic residues were impacting the expected sequence fragmentation pattern.

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P, Sanz L. Snake venomics. Strategy and applications. J Mass Spectrom 2007; 42: 1405. He MY, Chen H. Current mass spectrometry of synthetic polymer. Curr Org Chem 2007; 11: 909. Helmke SM, Duncan MW. Measurement of the NO metabolites, nitrite and nitrate, in human biological fluids by GC-MS. J Chromatogr B 2007; 851: 83. Herrmann AM, Ritz K, Nunan N, Clode PL, Pett-Ridge J, Kilburn MR, Murphy DV, O'Donnell AG, Stockdale EA. Nano-scale secondary ion mass spectrometry -A new analytical tool in biogeochemistry and soil ecology: A review article. Soil Biol Biochem 2007; 39: 1835. Luque-Garcia JL, Neubert TA. Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry. J Chromatogr A 2007; 1153: 259. Nelson BC. The expanding role of mass spectrometry in folate research. Curr Anal Chem 2007; 3: 219. Portier S, Bremier S, Walker CT. Secondary ion mass spectrometry of irradiated nuclear fuel and cladding: An overview. Int J Mass Spectrom 2007; 263: 113. Vogl J. Characterization of reference materials by isotope dilution mass spectrometry. J Anal Atom Spectrom 2007; 22: 475. Wiechert W, Schweissgut O, Takanaga H, Frommer WB. Fluxomics: Mass spectrometry versus quantitative imaging. Curr Opin Plant Biol 2007; 10: 323. Williamson LN, Bartlett MG. Quantitative liquid chromatography/time-offlight mass spectrometry. Biomed Chromatogr 2007; 21: 567. Wyttenbach T, Bowers MT. Intermolecular interactions in biomolecular systems examined by mass spectrometry. Annu Rev Phys Chem 2007; 58: 511. 2 INSTRUMENTAL TECHNIQUES & METHODS Alvarez PA, Ramaswamy HS, Ismail AA. Effect of high-pressure treatment on the electrospray ionization mass spectrometry (ESI-MS) profiles of whey proteins. Int Dairy J 2007; 17: 881. Andreev VP, Li LY, Cao L, Gu Y, Rejtar T, Wu SL, Karger BL. A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS. J Proteome Res 2007; 6: 2186. Bereman MS, Muddiman DC. Detection of attomole amounts of analyte by desorption electrospray ionization mass spectrometry (DESI-MS) determined using fluorescence spectroscopy. J Am Soc Mass Spectrom 2007; 18: 1093. Borges CR. Concept for facilitating analyst-mediated interpretation of qualitative chromatographic-mass spectral data: An alternative to manual examination of extracted ion chromatograms. Anal Chem 2007; 79: 4805. Carreira RJ, Cordeiro FM, Moro AJ, Rivas MG, Rial-Otero R, Gaspar EM, Moura I, Capelo JL. New findings for in-gel digestion accelerated by high-intensity focused ultrasound for protein identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Chromatogr A 2007; 1153: 291. Chambers E, Wagrowski-Diehl DM, Lu ZL, Mazzeo JR. Systematic and comprehensive strategy for reducing matrix effects in LC/MS/MS analyses. J Chromatogr B 2007; 852: 22. Charvat A, Abel B. How to make big molecules fly out of liquid water: Applications, features and physics of laser assisted liquid phase dispersion mass spectrometry. Phys Chem Chem Phys 2007; 9: 3335. Codrea MC, Jimenez CR, Heri...

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Formation of (b_n−1 + H₂O) ions by collisional activation of maldi-formed peptide [M + H]⁺ ions in a QqTOF mass spectrometer

Cited by 21 publications

References 56 publications

A Pseudo MS³Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

A Pseudo MS³Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini

Current literature in mass spectrometry

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Formation of (bn−1 + H2O) ions by collisional activation of maldi-formed peptide [M + H]+ ions in a QqTOF mass spectrometer

Cited by 21 publications

References 56 publications

A Pseudo MS3Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

A Pseudo MS3Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini

Current literature in mass spectrometry

Contact Info

Product

Resources

About

Formation of (b_n−1 + H₂O) ions by collisional activation of maldi-formed peptide [M + H]⁺ ions in a QqTOF mass spectrometer

A Pseudo MS³Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search

A Pseudo MS³Approach for Identification of Disulfide-Bonded Proteins: Uncommon Product Ions and Database Search