Peptides, mass spectra

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. 

The importance of linked scanning of metastable ions or of ions formed by induced decomposition is discussed in this chapter and in Chapter 34. Briefly, linked scanning provides information on which ions give which others in a normal mass spectrum. With this sort of information, it becomes possible to examine a complex mixture of substances without prior separation of its components. It is possible to look highly specifically for trace components in mixtures under circumstances in which other techniques could not succeed. Finally, it is possible to gain information on the molecular structures of unknown compounds, as in peptide and protein sequencing (see Chapter 40). 

Different samples exhibit different levels of response to FAB, and, with a mixture of components, it is feasible that not all will be detected. In some cases, the minor components of a sample appear more prominently in the mass spectrum than the major ones. Despite these limitations, FAB is in widespread use and is an excellent technique for determining the molecular masses of peptides up to 10,000 Daltons, with an accuracy of 0.5 Da. 

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. 

However, interpretation of, or even obtaining, the mass spectrum of a peptide can be difficult, and many techniques have been introduced to overcome such difficulties. These techniques include modifying the side chains in the peptide and protecting the N- and C-terminals by special groups. Despite many advances made by these approaches, it is not always easy to read the sequence from the mass spectrum because some amide bond cleavages are less easy than others and give little information. To overcome this problem, tandem mass spectrometry has been applied to this dry approach to peptide sequencing with considerable success. Further, electrospray ionization has been used to determine the molecular masses of proteins and peptides with unprecedented accuracy. 

Palmitic acid, structure of, 1062 Palmitoleic acid, structure of, 1062 PAM resin, solid-phase peptide synthesis and, 1037 Para (m), 519 Paraffin, 91 Parallel synthesis, 586 Parent peak (mass spectrum), 410 Partial charge, 36 Pasteur, Louis, 297, 307... 

Figure 5.19 MALDI-ToF mass spectrum, providing a molecular-weight profile of the tryptic peptides derived from spot 22 (see Figure 5.18) of the silver-stained two-dimensional gel of the proteins extracted from the yeast S. cerevisiae. From Poutanen, M., Salusjarvi, L., Ruohonen, L., Penttila, M. and KaUddnen, N., Rapid Commun. Mass Spectrom., 15, 1685-1692, copyright 2001. John Wiley Sons Limited. Reproduced with permission.

Figure 5.23 Electrospray mass spectrum of the tryptic peptide with a retention time of 41.81 min from intact CMY-2 -lactamase. Reprinted from Biochim. Biophys. Acta, 1547, Bonomo, R. A., Liu, J., Chen, Y., Ng, L., Hujer, A. M. and Anderson, V. E., Inactivation of CMY-2 0-lactamase by tazobactam initial mass spectroscopic characterization , 196-205, Copyright (2001), with permission from Elsevier Science.

Then the mass spectrum of the mentioned peptide mixture is measured. The set of molecular mass values (peak list) corresponding to individual peptides is characteristic for the protein and can be considered as its fingerprint. 

Proteins and peptides are most often seen in the mass spectra as pseudomolecular ions, that is, molecules with attached charge-carrying protons (in the negative-ion mode, proteins and peptides lose protons and thus acquire a negative net charge). This additional proton has to be taken into consideration in order to predict correctly the m/z value at which the peptide of interest will be seen in a mass spectrum. For example, a peptide whose molecular weight (MW) (or molar mass) is equal to 2000 Da, when singly ionized, will be detected at 2001 m/z (for simplification, we assume the mass of proton as equal to 1) ... 

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.

R. Craig, et al., Using Annotated Peptide Mass Spectrum Libraries for Protein Identification. J. Proteome Res., 5, no. 8 (2006) 1843-1849. 

Example Peptides often contain sulfur from cysteine. Provided there are at least two cysteines in the peptide molecule, the sulfur can be incorporated as thiol group (SH, reduced) or sulfur bridge (S-S, oxidized). Often, both forms are contained in the same sample. At ultrahigh-resolution, the contributions of these compositions to the same nominal m/z can be distinguished. The ultrahigh-resolution matrix-assisted laser desorption/ionization (MALDI) FT-ICR mass spectrum of native and reduced [D-Pen jenkephalin gives an example of such a separation (Fig. 3.25). [39] The left expanded view shows fully resolved peaks due to and C2 isotopomers of the native and the all- C peak of the reduced compound at m/z 648. The right expansion reveals the peak of the native plus the... 

Fig. 9.2. Comparison of the efficiency of xenon, argon and neon FAB gas for the FAB mass spectrum of Met-enkephahn, a small peptide. The intensities are in scale. Reproduced from Ref. [34] by permission. Elsevier Science, 1983.

Example The Cf-PD mass spectrum of bovine insulin exhibits the [M+H]" quasimolecular ion as well as the doubly charged [M+2H] and triply charged [M+3H] ion (Fig. 9.20). [156] Fragment ions corresponding to the A and B chain as well as some a-type peptide fragments ions are observed in addition. 

In tandem MS mode, because the product ions are recorded with the same TOF mass analyzers as in full scan mode, the same high resolution and mass accuracy is obtained. Isolation of the precursor ion can be performed either at unit mass resolution or at 2-3 m/z units for multiply charged ions. Accurate mass measurements of the elemental composition of product ions greatly facilitate spectra interpretation and the main applications are peptide analysis and metabolite identification using electrospray iomzation [68]. In TOF mass analyzers accurate mass determination can be affected by various parameters such as (i) ion intensities, (ii) room temperature or (iii) detector dead time. Interestingly, the mass spectrum can be recalibrated post-acquisition using the mass of a known ion (lock mass). The lock mass can be a cluster ion in full scan mode or the residual precursor ion in the product ion mode. For LC-MS analysis a dual spray (LockSpray) source has been described, which allows the continuous introduction of a reference analyte into the mass spectrometer for improved accurate mass measurements [69]. The versatile precursor ion scan, another specific feature of the triple quadrupole, is maintained in the QqTOF instrument. However, in pre-... 

Figure 2 The Mass Spectrum of a Peptide Obtained via Protonation...

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