Mass spectra amino acids

Fifty-three peptide samples were submitted by 48 laboratories. Previous studies by this committee have demonstrated the need for multiple analytical methods for the assessment of purity. Therefore the peptides in this study were analyzed by AAA, HPLC, ESI-MS and MALDI-MS to determine purity (Table I). Only two peptide samples had less than 50% of the desired product, and three other samples had less than 70% of the desired product, as judged by their mass spectra, amino acid composition and HPLC retention time. Overall, the peptides were of excellent quality. 

Extend the y-ion series toward lower m/z. Extend the y-ion series backwards (toward lower m/z) liom the y 2-ion via working with the residue masses of amino acids (Table 5.3). As a y-ion is identified, calculate the m/z of the corresponding b-ion and identify that ion in the spectrum. Work toward extending the y-ion series from the y -2-ion to the yi-ion. 

The amino add analysis of all peptide chains on the resins indicated a ratio of Pro Val 6.6 6.0 (calcd. 6 6). The peptides were then cleaved from the resin with 30% HBr in acetic acid and chromatogra phed on sephadex LH-20 in 0.001 M HCl. 335 mg dodecapeptide was isolated. Hydrolysis followed by quantitative amino acid analysis gave a ratio of Pro Val - 6.0 5.6 (calcd. 6 6). Cycll2ation in DMF with Woodward s reagent K (see scheme below) yielded after purification 138 mg of needles of the desired cyc-lododecapeptide with one equiv of acetic add. The compound yielded a yellow adduct with potassium picrate, and here an analytically more acceptable ratio Pro Val of 1.03 1.00 (calcd. 1 1) was found. The mass spectrum contained a molecular ion peak. No other spectral measurements (lack of ORD, NMR) have been reported. For a thirty-six step synthesis in which each step may cause side-reaaions the characterization of the final product should, of course, be more elaborate. 

An alternative approach to peptide sequencing uses a dry method in which the whole sequence is obtained from a mass spectrum, thereby obviating the need for multiple reactions. Mass spec-trometrically, a chain of amino acids breaks down predominantly through cleavage of the amide bonds, similar to the result of chemical hydrolysis. From the mass spectrum, identification of the molecular ion, which gives the total molecular mass, followed by examination of the spectrum for characteristic fragment ions representing successive amino acid residues allows the sequence to be read off in the most favorable cases. 

E. Sample Mass Spectrum TBDMS Derivatized Amino Acids... 

Figure 5.20 shows an MS-MS spectrum produced from a peptide of molecular weight 1782.96 Da. The mass losses observed and corresponding amino acid assignments are shown in Table 5.11. 

Figure 2.3. A. Mass spectrometer consisting of an ionization source, a mass analyzer and an ion detector. The mass analyzer shown is a time-of -flight (TOF) mass spectrometer. Mass-to-charge (m/z) ratios are determined hy measuring the amount of time it takes an ion to reach the detector. B. Tandem mass spectrometer consisting of an ion source, a first mass analyzer, a collision cell, a second mass analyzer and a detector. The first mass analyzer is used to choose a particular peptide ion to send to the collision cell where the peptide is fragmented. The mass of the spectrum of fragments is determined in the second mass analyzer and is diagnostic of the amino acid sequence of the peptide. Figure adapted from Yates III (2000).

Figure 2.5. Tandem mass spectrometry. A. A peptide mixture is electrosprayed into the mass spectrometer. Individual peptides from the mixture are isolated (circled peptide) and fragmented. B. The fragments from the peptide are mass analyzed to obtain sequence information. The fragments obtained are derived from the N or C terminus of the peptide and are designated "b" or "y" ions, respectively. The spectrum shown indicates peptides that differ in size by the amino acids shown.

As noted with the chemotaxonomic studies, the limited resolving power and mass accuracy of MALDI-TOF complicates identification of unknown proteins. If the greatly improved resolving power and accuracy of MALDI-FTMS can be used to monitor overexpressed proteins, it could have significant advantages. Figure 13.12 is a MALDI-FTMS spectrum of E. coli whole cells that have been genetically altered to produce the soluble core domain mammalian cytochrome b5 protein, which consists of 98 amino acids. 

A systematic investigation of the free amino acids of the Leguminosae led to the isolation of a novel ninhydrin-positive compound from the leaves of Derris elliptica Benth. (Papilionidae) (93). This substance was analyzed as C6H,3N04 (microanalysis and high resolution mass spectrometry) and was shown to be an amino alcohol. The absence of a carbonyl in the 1R, the loss of 31 mass units in the mass spectrum, and a positive periodate cleavage reaction were best embodied into a dihydroxydihydroxymethylpyrrolidine structure. The relative simplicity of the NMR spectra (three peaks in the 13C spectrum four spin-system in the H spectrum) pointed out a symmetrical structure. Inasmuch as the material was optically active ([a]D 56.4, c = 7, H20), meso structures were ruled out, and the 2R, 3R, 4R, 5R relative configuration was retained (93). This structure (53) was further confirmed by an X-ray determination (94). 

The example spectrum is shown in Fig. 6.19. The precursor m/z is 741.0 Th and the charge is 2+. Brief examination of the spectrum shows that there are almost no abundant doubly charged ions. Also, the spectmm does not cover the mass range near the precursor m/z region. Therefore, we cannot begin with the same procedure as previously described. On the other hand, there are a number of very intense peaks with mass differences specific for particular amino acids. 

Figure 6.20. Annotated spectrum used in Example 3. The 17 Th mass difference corresponds to ammonia loss from the amide amino acids side-chains. Such peaks being non-sequence-specific themselves, can be very useful during sequencing.

Fig. 7.5. Comparison of (a) 70 eV El spectrum and (b) methane reagent gas Cl spectrum of the amino acid methionine. Fragmentation is strongly reduced in the d mass spectrum.

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