Fragmentation ion structures

For the confirmatory procedure, it is recommended that the sponsor develop spectral data based on at least three structurally specific ions that completely define the marker residue molecule. These ions may or may not include the molecular ion. The use of water loss and isotopic ions is usually unacceptable and CVM concurrence should be sought when water loss ions or isotopic ions are selected for the confirmatory analysis. The proposed fragment ion structures should be consistent with the fragmentation pattern, and justification for specificity of selected ions or scan range should be included. All confirmation criteria should be specified in the standard operating procedure. 

Proposed fragment ion structures, consistent with fragmentation pattern. 

The best guess at present is that both of these q values represent rearrangement barriers on the way to the low-energy tropylium (benzotropylium) fragment ion structures. 

Their proposed fragment ion structures were supported by accurate mass measurements, as shown in Figure 19-18. Clearly, microwave-assisted Akabori reaction can lead to rapid identification of C-terminus amino acid in a polypeptide including its amino acid sequence information at both C-terminus and the N-terminus. It was also found that microwave-assisted hydrazinolysis of N-terminal substituted polypeptides followed the same... 

If structure candidates are given, the calculation of match values can be improved using knowledge on MS fragmentation reactions to generate possible fragment ions. Structure comparison values are used for ranking and selection of structure candidates (Subsection 8.4.2). 

Somogyi, A. Probing Peptide Fragment Ion Structures by Combining Sustained Off-Resonance Collision-Induced Dissociation and Gas-Phase H/D Exchange (SORI-HDX) in Fourier Transform Ion-Cyclotron Resonance (FT-ICR) Instruments. J. Am. Soc. Mass Spectrom. 2008, 19, 1771-1775. 

The high intensity quasi-molecular ion is the ideal precursor for MS/MS. The product ion spectrum with the fragment ion structures predicted by Mass Frontier software for the protonated molecular ion is given with Figure 4.155. The mechanism for confirmation of the m/z 116 ion by Mass Frontier is shown as a fragmentation pathway in Figure 4.156. In conclusion, the generation of the... 

A single instrument — a hybrid of a quadrupole and a TOF analyzer — can measure a full mass spectrum of ions produced in an ion source. If these are molecular ions, their relative molecular mass is obtained. Alternatively, precursor ions can be selected for MS/MS to give a fragment-ion spectrum characteristic of the precursor ions chosen, which gives structural information about the original molecule. 

Some mild methods of ionization (e.g., chemical ionization. Cl fast-atom bombardment, FAB electrospray, ES) provide molecular or quasi-molecular ions with so little excess of energy that little or no fragmentation takes place. Thus, there are few, if any, normal fragment ions, and metastable ions are virtually nonexistent. Although these mild ionization techniques are ideal for yielding molecular mass information, they are almost useless for providing details of molecular structure, a decided disadvantage. 

Metastable and collisionally induced fragment ions can be detected efficiently by a triple quadrupole instmment. By linking the scanning regions of the first and third quadrupoles, important information about molecular structure is easily obtained. 

Ionization Method Type of Molecular Ion Formed Good Molecular Mass Information Abundant Fragment Ions MS/MS Needed for Structural Information Accurate Values for Isotope Ratios... 

Typical MS/MS configuration. Ions produced from a source (e.g., dynamic FAB) are analyzed by MS(1). Molecular ions (M or [M + H]+ or [M - H]", etc.) are selected in MS(1) and passed through a collision cell (CC), where they are activated by collision with a neutral gas. The activation causes some of the molecular ions to break up, and the resulting fragment ions provide evidence of the original molecular structure. The spectrum of fragment ions is mass analyzed in the second mass spectrometer, MS(2). 

Metastable ions are useful for determining the paths by which molecular ions of an unknown substance have decomposed to give fragment ions. By retracing these fragmentation routes, it is often possible to deduce some or all of the molecular structure of the unknown. 

The fragment ions are characteristic of any given substance in that the way a compound fragments can be regarded as a fingerprint. For the fragment ions to be useful, it is necessary to know how they relate to each other. In other words, it is necessary to understand which fragment should be connected to which others in the overall chemical structure. 

Nitrogen-containing fulvalenes have not been systematically studied by mass spectroscopy. Only isolated data for several examples of compounds have been reported. Most of the data consist of electron impact (El) mass spectra recorded for analytical purposes. Only a minor fraction dealt with the characterization of ion structures or focused on the effects of substituents, the ring size of fulvalenes, or the number and arrangement of nitrogen atoms and the fragmentation pathways. 

Because mass-spectral fragmentation patterns are usually complex, it s often difficult to assign structures to fragment ions. Most hydrocarbons fragment in many ways, as the mass spectrum of hexane shown in Figure 12.4 demonstrates. The hexane spectrum shows a moderately abundant molecular ion at m/z = 86... 

Methylpentane (C.6H]4) has the mass spectrum shown. WTiich peak represents M+ Which is the base peak Propose structures for fragment ions of m z = 71, 57, 43, and 29. Why does the base peak have the mass it does ... 

Select Structural Type Characteristic Fragment Ions... 

Assign possible structures to all abundant fragment ions from the tabulated ions listed in the structurally significant tables of Part III. Two or more ions together may define the type of compound. For example, the presence of the following ions suggest specific compounds ... 

GC/MS was used to distinguish between the two structures. The mass spectrum showed a molecular ion at m/z 260. The fragment ions occurred at m/z 245, 241, 231, and 205. This is a good example of nitrogen atom-influenced fragmentation therefore, structure I was highly favored. 

Examine fragment ions to determine the mass of the neutral fragments that were lost from the molecular ion, even though these high-mass peaks may be of low abundances. Compare the neutral loss from the molecular ion with the neutral losses tabulated in Part III to see if these losses agree with the suspected structural type. 

The first step in the application of mass spectra is obviously to obtain a list of fragment ions formed by electron bombardment of the molecule under study and their relative amounts by appropriate techniques. The goal from this point will necessarily be to relate the positive ions to the molecular structure whether it be an unknown structure to be identified, or a known structure of which a knowledge of fragmentation is desired. The fragment ions observed indicate the pieces of which the molecule is composed... 

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