Neutral Fragment Mass Spectra via Ambient Thermal Dissociation of Peptide and Protein Ions

2007 ◽  
Vol 129 (18) ◽  
pp. 5880-5886 ◽  
Author(s):  
Hao Chen ◽  
Livia S. Eberlin ◽  
R. Graham Cooks
Keyword(s):  
Mass Spectra ◽  
Thermal Dissociation ◽  
Neutral Fragment ◽  
Fragment Mass ◽  
Protein Ions

Mass spectra of 4,4-dimethyl-A-homocholestane-3,5- and 3,4a diols and their derivatives

1982 ◽  
Vol 47 (12) ◽  
pp. 3328-3338
Author(s):  
Antonín Trka ◽  
Helena Velgová
Keyword(s):  
Mass Spectrum ◽  
Electron Impact ◽  
Mass Spectra ◽  
Neutral Fragment ◽  
Molecular Ion ◽  
Impact Fragmentation ◽  
Fragmentation Processes

Partial mass spectra of the following 4,4-dimethyl-A-homocholestane derivatives are given: 3,5-epoxides I and II, 3,5-diols III-VI, 3-methoxy-5-ols VII-IX, 3-acetoxy-5-ol X, 3,4a-diols XI-XIV, 3-acetoxy-4a-ols XV-XVIII and 4,4-[2H6]-dimethyl-3,4a-diol XIX, and their electron impact fragmentation investigated. The mass spectra of epoxides I and II, diols III-VI and acetate X are very similar. Considerable differences in mass spectra of methoxy derivatives VII-IX are explained by two mechanisms of elimination of CH3OH from M+. The same similarity of the fragmentation processes and the mass spectra is also observed in diols XI-XIV and acetates XV-XVIII. For the formation of the characteristic ion m/z 288 a fragmentation scheme containing an usual cleavage of the rings A, B, and C is proposed. On the basis of comparison with the mass spectrum of the 4,4-[2H6]dimethyl analogue XIX it was shown that the ion m/z 361 in the mass spectra of diols XI-XIV is formed by elimination of the neutral fragment C6H13 from A-ring of the molecular ion, the last process being accompanied by the 3-hydroxyl transfer from A-ring to the rest of the molecular ion.

scholarly journals Characterization of fullerene derivatives by maldi fragment mass spectra

2013 ◽  
Vol 17 (2) ◽  
pp. 177-183
Author(s):  
B. L. Milman ◽  
L. B. Piotrovsky ◽  
D. N. Nikolaev ◽  
M. A. Dumpis ◽  
E. V. Litasova ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Fullerene Derivatives ◽  
Fragment Mass

scholarly journals A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 26
Author(s):  
Matthias Fahrner ◽  
Lucas Kook ◽  
Klemens Fröhlich ◽  
Martin L. Biniossek ◽  
Oliver Schilling
Keyword(s):  
Open Source ◽  
Cell Lines ◽  
Search Engines ◽  
Mass Spectra ◽  
Proteolytic Processing ◽  
Systematic Evaluation ◽  
Fragment Mass ◽  
The Impact ◽  
Spectrum Matching ◽  
Specific Peptide

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventional settings, such as fully specific enzymatic constraints. Here we evaluated the impact of the fragment mass tolerance in combination with the enzymatic constraints on the performance of three search engines. Three open-source search engines (Myrimatch, X! Tandem, and MSGF+) were evaluated concerning the suitability in semi- and unspecific searches as well as the importance of accurate fragment mass spectra in non-specific peptide searches. We then performed a semispecific reanalysis of the published NCI-60 deep proteome data applying the most suited parameters. Semi- and unspecific LC-MS/MS data analyses particularly benefit from accurate fragment mass spectra while this effect is less pronounced for conventional, fully specific peptide-spectrum matching. Search speed differed notably between the three search engines for semi- and non-specific peptide-spectrum matching. Semispecific reanalysis of NCI-60 proteome data revealed hundreds of previously undescribed N-terminal peptides, including cases of proteolytic processing or likely alternative translation start sites, some of which were ubiquitously present in all cell lines of the reanalyzed panel. Highly accurate MS2 fragment data in combination with modern open-source search algorithms enable the confident identification of semispecific peptides from large proteomic datasets. The identification of previously undescribed N-terminal peptides in published studies highlights the potential of future reanalysis and data mining in proteomic datasets.

scholarly journals Multiplexed Single Ion Mass Spectrometry Improves Measurement of Proteoforms and Their Complexes

2019 ◽  
Author(s):  
Jared O. Kafader ◽  
Rafael D. Melani ◽  
Kenneth R. Durbin ◽  
Bon Ikwuagwu ◽  
Bryan P. Early ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Analysis Procedure ◽  
Modes Of Operation ◽  
Charge Detection ◽  
Individual Protein ◽  
Protein Ions ◽  
True Mass ◽  
Ion Analysis

AbstractA new Orbitrap-based single ion analysis procedure is shown to be possible by determining the direct charge on numerous measurements of individual protein ions to generate true mass spectra. The deployment of an Orbitrap system for charge detection enables the characterization of highly complicated mixtures of proteoforms and their complexes in both denatured and native modes of operation, revealing information not obtainable by traditional measurement of an ensemble of ions.

Mass spectrometric studies. IX. Benzylidenemalonic esters and related compounds

1971 ◽  
Vol 24 (4) ◽  
pp. 823 ◽  
Author(s):  
QN Porter ◽  
CR Ramsay
Keyword(s):  
Mass Spectra ◽  
Alkoxy Group ◽  
Mass Spectrometric ◽  
Neutral Fragment ◽  
Carbonium Ion ◽  
Skeletal Rearrangements ◽  
Related Compounds

Skeletal rearrangements resulting from alkoxy-group migrations are prominent in the mass spectra of some benzylidenemalonic esters, and involve elimination of C3O2 as a neutral fragment. Similar rearrangements of a chloride atom dominate the mass spectra of benzylidenemalonyl chloride, but migrations of alkyl and aryl groups are unimportant in the mass spectra of structurally related benzylidene β-diketones. The rearrangements observed have been rationalized as the result of a four-centre migration to a carbonium ion centre.

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