Protein fragmentation via liquid chromatography–quadrupole time-of-flight mass spectrometry: The use of limited sequence information in structural characterization

Johnson, Robert W.; Ahmed, Tanveer; Miesbauer, Laura J.; Edalji, Rohinton; Smith, Richard; Harlan, John E.; Dorwin, Sarah A.; Walter, Karl A.; Holzman, Tom

doi:10.1016/j.ab.2005.03.009

Cited by 10 publications

(9 citation statements)

References 50 publications

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“…in 200414 and Johnson et al . in 200515 proposed two methods for TD analysis of proteins with CID. In both cases structural information was nevertheless generated in a pseudo‐MS 3 approach, exploiting a preliminary ‘in‐source’ fragmentation of the protein followed by a MS/MS analysis of a fragment ion.…”

Section: Discussionmentioning

confidence: 99%

Alternative Reaction Pathways in Domino Reactions of Hydrazinediidozirconium Complexes with Alkynes

Gehrmann¹,

Scholl²,

Lloret‐Fillol³

et al. 2012

Chemistry A European J

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Reaction of [Zr{(NAr)(2)N(py)}(NMe(2))(2)] (Ar=3,5-xylyl: 2 a, mesityl: 2 b) with one or two molar equivalents of 1,1-diphenylhydrazine gave the mixed amido/hydrazido(1-) complex [Zr{(NMes)(2)N(py)}(HNNPh(2))(NMe(2))] (3), the bis-hydrazido complex [Zr{(NMes)(2)N(py)}(HNNPh(2))(2)] (4), and, in the presence of excess 4-dimethylaminopyridine (DMAP), hexacoordinate hydrazinediidozirconium complexes [Zr{(NXyl)(2)N(py)}(=NN(Me)Ph)(dmap)(2)] (5) and [Zr{(NXyl)(2)N(py)}(=NNPh(2))(dmap)(2)] (6). The reaction of one equivalent of the zirconium-hydrazinediide [Zr{(NTBS)(2)N(py)}(NNPh(2))(py)] (1) with disubstituted alkynes at RT for 16 h led to the formation of seven-membered diazazirconacycles 7 a-7 e in high yields. Similar reactivity was observed by reacting bis-amido complex 2 b with one molar equivalent of the corresponding alkyne and diphenylhydrazine. The formation of the seven-membered zirconacycles implied a key coupling step that involved the alkyne and one of the aryl rings of the diphenylhydrazinediido ligand. In some cases, such as the reaction with 2-butyne, the corresponding metallacycle was only obtained in modest yields (45 % for the reaction with 2-butyne) and a second major product, vinylimido complex 9, was formed in almost equal amounts (42 %) by 1,2-amination (formal insertion of the alkyne). The formation of compounds 7 a and 9 followed in part the same sequence of reaction steps and a key intermediate, an azirinido complex, represented a "bifurcation point" in the reaction network. Reaction of 1.2 equivalents of several diarylhydrazines and various substituted alkynes (1 equiv) at ambient temperature (or at 80 °C) in the presence of 10 mol % [Zr{(NXyl)(2)N(py)}(NMe(2))(2)] (2 a) gave the corresponding indole derivatives. On the other hand, the replacement of 1,1-diarylhydrazines by 1-methyl-1-phenyl hydrazine led to head-to-head cis-1,3-enynes in good yields.

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Section: Discussionmentioning

confidence: 99%

Alternative Reaction Pathways in Domino Reactions of Hydrazinediidozirconium Complexes with Alkynes

Gehrmann¹,

Scholl²,

Lloret‐Fillol³

et al. 2012

Chemistry A European J

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“…Many thousands of proteins have been analyzed without fragmentation in the same instruments with the same operating parameters. However, it is known from collision-induced dissociation of peptides and from experiments, where the cone voltage is used to induce fragmentation, that bonds involving proline rupture most readily (32)(33)(34).…”

Section: Resultsmentioning

confidence: 99%

Bovine Complex I Is a Complex of 45 Different Subunits

Carroll

Fearnley

Skehel³

et al. 2006

Journal of Biological Chemistry

438

313

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Mammalian mitochondrial complex I is a multisubunit membrane-bound assembly with a molecular mass approaching 1 MDa. By comprehensive analyses of the bovine complex and its constituent subcomplexes, 45 different subunits have been characterized previously. The presence of a 46th subunit was suspected from the consistent detection of a molecular mass of 10,566 by electrospray ionization mass spectrometry of subunits fractionated by reverse-phase high pressure liquid chromatography. The component was found associated with both the intact complex and subcomplex I␤, which represents most of the membrane arm of the complex, and it could not be resolved chromatographically from subunit SGDH (the subunit of bovine complex I with the N-terminal sequence Ser-Gly-Asp-His). It has now been characterized by tandem mass spectrometry of intact protein ions and shown to be a C-terminal fragment of subunit SGDH arising from a specific peptide bond cleavage between Ile-55 and Pro-56 during the electrospray ionization process. Thus, the subunit composition of bovine complex I has been established. It is a complex of 45 different proteins plus non-covalently bound FMN and eight iron-sulfur clusters.

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“…Several studies have reported on the top-down analysis of proteins by Q-TOF-type instruments. [33][34][35] Not only model proteins but also unknown proteins have successfully been characterized by Q-TOF analysis. As discussed by NemethCawley and Rouse, product ions are often buried in chemical noise, resulting in multiple choices from which to predict the next amino acid.…”

Section: Fragmentation Of Intact Protein With Mchip-ce/msmentioning

confidence: 99%

Top‐down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry

Akashi

Suzuki

Arai

et al. 2006

Rapid Comm Mass Spectrometry

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A system of microchip capillary electrophoresis/electrospray ionization mass spectrometry (microchip-CE/ESI-MS) for rapid characterization of proteins has been developed. Capillary electrophoresis (CE) enables rapid analysis of a sample present in very small quantity, such as at femtomole levels, at high resolution. Faster CE/MS analysis is expected by downsizing the normal capillary to the microchip (microchip) capillary. Although rapidity and high resolution are advantages of CE separation, electroosmotic flow (EOF) instability caused by the interaction between proteins and the microchannel surface results in low reproducibility in the analysis of basic proteins under neutral pH conditions. By coating the microchannel surface with a basic polymer, polyE-323, basic proteins, which have pI values of over 7.5, could be separated and detected by microchip-CE/MS on quadrupole (Q) and time-of-flight (TOF) hybrid instruments. By increasing the cone and collision voltages during the analysis by microchip-CE/ESI-MS of a small protein, some product ions, which contain the sequence information, could also be obtained, i.e., 'top-down' analysis of the protein could be accomplished with this microchip-CE/MS system. To our knowledge, this is the first report of 'top-down' analysis of a protein by microchip-CE/MS. Since it requires a much shorter time and a smaller sample amount for analysis than the conventional liquid chromatography (LC)/ESI-MS method, microchip-CE/MS promises to be suitable for the high-throughput characterization of proteins.

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Protein fragmentation via liquid chromatography–quadrupole time-of-flight mass spectrometry: The use of limited sequence information in structural characterization

Cited by 10 publications

References 50 publications

Alternative Reaction Pathways in Domino Reactions of Hydrazinediidozirconium Complexes with Alkynes

Alternative Reaction Pathways in Domino Reactions of Hydrazinediidozirconium Complexes with Alkynes

Bovine Complex I Is a Complex of 45 Different Subunits

Top‐down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry

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