Fragments spectrum

The size distribution of the clusters produced in the cluster source is quite smooth, containing no information about the clusters except their composition. To obtain information about, for example, the relative stability of clusters, it is often useful to heat the clusters. Hot clusters will evaporate atoms and molecules, preferably until a more stable cluster composition is reached that resists further evaporation. This causes an increase in abundance of the particularly stable species (i.e., enhancing the corresponding peak in the mass spectrum, then commonly termed fragmentation spectrum ). Using sufficiently high laser fluences (=50 /iJ/mm ), the clusters can be heated and ionized simultaneously with one laser pulse. 

Figure 14. Standard molecular fragmentation spectrum of adamantane (136m/z).

Figure 4 IRMPD fragmentation spectrum of the species a) SisO20H7" at m/z 550.8 and b) Si2o047Hi22 at m/z 661.7...

A tandem-in-space mass spectrometer consists of an ion source, a precursor ion activation device, and at least two nontrapping mass analyzers. The first mass analyzer is used to select precursor ions within a narrow m/z range. Isolated precursor ions are allowed to enter the ion activation device, for example, a gas-filled collision cell, where they dissociate. Created fragments continue on to the second mass analyzer for analysis. The second mass analyzer can either acquire a full mass fragment spectrum or be set to monitor a selected, narrow, m/z range. In principle the second mass analyzer could be followed by more ion activation devices and mass analyzers for MSn experiments. However, due to rapidly decreasing transmission and increasing experimental... 

Figure 6.3. Real-life example of a tandem MS experiment in an electrospray ion trap instrument. Top panel a complex peptide mixture. Middle panel ion at 1318.9 m/z was isolated from other sample components. Note the lack of any other peaks and a very low background. Bottom panel fragmentation spectrum of the selected parent ion (1318.9 m/z), note the different scale of the m/z axis. All peaks seen in this mass spectrum are product ions that were formed due to the controlled fragmentation of the parent ion. The main peak at 1300.8 m/z corresponds to the loss of water molecule, a lower intensity parent ion at 1318.9 m/z is also seen.

Figure 6.4. Fragmentation spectrum of a tryptic peptide obtained from bovine serum albumin. Peptide sequence LGEYGFQNALIVR, monoisotopic [M + H]+ = 1479.796, monoisotopic [M+2H]2+ =740.402. Upper panel full scan MS spectrum. Lower panel MS/MS spectrum of a doubly-charged ion at 740.7 m/z with a ladder of y ions, the distances between which correspond to amino acid residues (upper row of letters). A shorter series of b ions is also seen (lower row of letters). See Fig. 6.5 for description of nomenclature. Note the often observed phenomenon where multiply-charged ions lose the charge during fragmentation process and, therefore, have higher m/z values than the original parent ion.

Figure 6.14. Example 2 fragmentation spectrum of singly charged peptide, precursor mass of 1098.6.

Figure 6.19. Fragmentation spectrum of doubly charged peptide precursor at 741.0Th, used in Example 3.

The second example contained two basic amino acids in the middle of the sequence, but closer to the C-terminus. The fragmentation spectrum contained a huge number of both C- and N-terminal peaks, with a high number of doubly charged ions, including both basic amino acids. The presence of basic residues caused a more balanced number of b- and y-ions but also made it very difficult to obtain fragments with bond cleavage near basic residues. 

Fig. 2. Schematics of an electrospray triple quadrupole mass spectrometer. A mass spectrum is acquired by scanning the first quadrupole Qi over the desired mass range. For a fragment spectrum the first quadrupole is fixed at a given m/z value transmitting only ions of this m/z value into the gas-filled collision zone. The fragments are extracted and their mass determined by the scanning third quadrupole Q3. For a precursor ion scan the third quadrupole is fixed at the mass of a specific fragment ion (e.g., a phosphate ion) and the second is scanning over the mass range.

Fig. 2.57. Identification of a flavonoid diglycoside from unhydrolized chokeberry sample, (a) Positive total ion chromatogram, (b) ion source collision-induced dissociation chromatogram for the ion m/z 303 (quercetin), (c) full scan MS spectrum of the peak at 14.1min, (d) full scan MS-MS spectrum of the [M+H] ion, (e) fragmentation spectrum (MS3) of the m/z 303.3 ion. Reprinted with permission from S. Hakkinen et al. [161].

Every type of molecule produces a certain, constant mass spectrum or fragment spectrum which is characteristic for this type of molecule (fingerprint, cracking pattern). 

Figure 16.1—Bar (fragmentation) spectrum and mass spectrum presented in graphical and tabular form. a) Bar spectrum of methanol b) non-conventional representation of the same spectrum in the form of a circular diagram for each 321 ions formed, there are statistically 100 ions of mass 31 u (Da), 72 of mass 29 u, etc. The various ions constitute different populations c) part of a high-resolution recording of compound M with two ions with very close m/z ratios (one due to loss of CO and the other due to loss of C2H4).

Quantitative evaluation of molecular similarity. The fragment spectrum obtained in the above can be described as a kind of multidimensional pattern vector. Consequently, using this pattern representation of a spectrum it is possible to apply diverse quantitative methods for the evaluation of similarity. 

A common drawback of these two instruments is the impossibility to observe any metastable fragmentation which occurs in the first mass analyser between the source and the first reflectron. Because these fragment ions penetrate in the first reflectron, they do not arrive at the deflection gate and collision cell at the same time as their precursors. Thus, they do not contribute to the detected fragment ions and are not recorded in the fragmentation spectrum of the selected ion. Since such metastable fragmentations are generally not minor processes, this reduces the efficiency of these mass spectrometers. 

ECD has recently been introduced as an alternative activation method to obtain fragmentation of multiply protonated peptides [57]. An example of an ECD fragmentation spectrum... 

Interpretation of the spectra is based on the mechanisms and the fragmentation pathways described above, as shown by the following example. A CID MS/MS fragment spectrum of a peptide with sequence Gly-Ile-Pro-Thr-Leu-Leu-Leu-Phe-Lys measured at high energy is shown in Figure 8.13. This spectrum contains the complete series of b ions, thus allowing one to deduce the peptide sequence from the N-terminal acid to the C-terminal acid, whereas the series of y ions allows identification of the sequence in the reverse direction. In fact, the mass difference of 97 Da between peak b2 and b3 indicates that the amino acid in position 3 corresponds to a proline (see Table 8.2). Similarly, the 147 Da difference between peaks yi and y2 indicates that, the amino acid in the next-to-last position is a phenylalanine. The m/z values of ions W3, W4, W5 and wg imply that the amino acid in... 

The ESI/MS/MS fragmentation spectrum of permethylated LNF-II is displayed in Figure 8.48. [243] This spectrum is somewhat more complicated than the one from the per-acetylated derivative, but allows additional structural information to be obtained. As for the peracetylated derivative, this spectrum contains the ions characteristic of the sequence observed at m/z 638 (B2, trisaccharidic Hex-[Fuc]-GlcNAc-Me 8) and 842 (B3, Hex-[Fuc]-GlcNAc-Hex-Me 11), which allow the branched structure and the sequence on the reducing side to be established. 

This differentiation is based mainly on the ratios of the intensities of the two couples of ions at m/z 187 and 190 and m/z 111 and 114, respectively. The monosaccharides substituted on the 2 and 6 positions display the same spectrum. They can, however, be distinguished clearly by the fragmentation spectrum of the (oxonium-MeOH) ions. A systematic study has shown that the MS/MS spectra are predictable and largely independent of the nature of the monosaccharide. 

---