Residues, mass differences

The vertical distance of each calibration point from the curve is calculated. This distance represents the remaining (or residual) mass difference after calibration. 

FIGURE 11.9 Percentage residual mass differences between resin-flame-retardant clay and respective resin-flame-retardant TGA responses to show the effect of Cloisite 25A clay on the thermal degradation of a vinyl ester resin containing the flame retardants ammonium polyphosphate (APP), melamine phosphate (NH), melamine phosphate and dipentaerythritol (NW), and alumina trihydrate (ATH). (From Ref. 13, with permission from the Royal Society of Chemistry.)... 

MS and MS/MS are particularly useful for identifying and locating heavy isotopes. For example. Figure 3 shows a portion of the MS/MS spectrum of three versions of a 14-residue peptide prepared for an NMR study, two of which contain labels at a carbonyl and an a-carbon in two alanine residues. Mass differences between successive a and b ions allow the positions of these residues to be determined... 

When extracting sequence information from mass spectra, not only is the m/z value at which the ions occur of importance since these provide an indication of the amino acid composition of the peptide giving rise to the ion, but so is the mass difference between adjacent ions. This indicates the particular amino acid residue that has been lost and thus provides the sequence information required. The mass differences arising from each of the amino acids are shown in Table 5.6. 

In this example, we will use the third approach—as one ion series is already available, finding the reverse ion series should be easy. Indeed, starting from the peak at 300.1 Th (which comes from the cleavage of the same bond as the 1080.8 peak) we see the mass differences of 163.2 and 56.9 Th, corresponding to tyrosine and glycine. Using the same procedure, the entire previously assigned sequence can be proven correct, but also—extend the already revealed sequence by one more residue—the mass shift between 1206.6 and 1305.8 equal to 99.2 Th corresponds to valine. 

Gros M, Petrovic M, Barcelo D (2009) Tracing pharmaceutical residues of different therapeutic classes in environmental waters by using liquid chromatography/quadmpole-linear ion trap mass spectrometry and automated library searching. Anal Chem 81 898-912... 

Great care has to be taken in the analytical characterization of synthetic cyclic peptides.[73] The major side reactions during cyclization are epimerization of the C-terminal amino acid residue and cyclodimerization. Cyclodimers can be detected by mass spectrometry, although the analysis is not trivial, because artifacts do occur in some ionization techniques such as ES-MS as a result of aggregation.1 1 Ll 121 Real dimers can be detected as double-charged particles with mlz values identical to the cyclic monomers, but with a mass difference of 0.5 amu in the resolved isotope signals. The mass difference of the corresponding monomer is 1 amu. The cyclodimerization has received some attention as a direct method for the synthesis of C2-symmetrical cyclic peptides.[62 67 94113 115]... 

Determine the number of cysteine residues by dividing the mass difference calculated for the acrylamide sample by 72.08 and 58.05 g/mol for the iodoacetamide sample (e.g., the mass shift of 432.49 g/mol for acylamide and 348.07 g/mol for iodoacetamide correspond to six cysteine residues in both cases, i.e., three disulfide bonds in the original sample). 

The mass difference between consecutive ions within a series allows the identity of the consecutive amino acids to be determined (see Table 8.2) and thus deduction of the peptide sequence. Indeed, the 20 common amino acid residues have distinctive elemental compositions and consequently distinctive masses. There is one exception with Leu and He, which are isomers. However, a low-accuracy measurement may be incapable of discriminating between Gin and Lys, which differ by 0.036 u. In addition, there are combinations of amino acid residues that yield the same nominal mass or even the same elemental composition. 

A point mutation within a protein leads to the molecular mass variation of this protein. This variation is equal to the difference in mass between the wild type and mutant residues. Indeed,18 of the 20 natural amino acid residues have distinctive molecular masses. There is one exception with Leu and He, which are isomers. For the others, the mass differences among amino acid substitutions range from 0.0364 Da for Gln/Lys to 129.0578 Da for... 

Table 8.6 Monoisotopic mass differences (Da) observed between various amino acids. The residue in the column corresponds to the expected amino acid whereas the residue in the row corresponds to the mutant amino acid. 

Trypsin digests of both wild type HRV virus and the mutant were analyzed using MALDI-TOF and MALDI Fourier transform mass spectrometry (FTMS). For HRV, the mass spectra for both wild-type and mutant were identical except for one peptide occurring at mlz 4700. This corresponds to residues 187-227 in the wild type sequence. The corresponding peak in the mutant mass spectrum occurs at 4783.5 (Fig. 4, inset). This mass difference of 83 Da corresponds exactly to a mutation of a Cys to Trp residue and there are no other possible mutations that would be separated by 83 Da. Since there is only one Cys in the peptide 187-227 at position 199, the mutant can be localized as HRV14-Cysl99Trp, which contains a Trp at position 199 instead of Cys in the wild type. 

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