Peptide high-performance instrumentation

Tandem mass spectrometry (MS/MS) is very useful for the amino acid sequencing of peptides, and has been used widely in both protein biochemistry and pro-teomics to identify proteins, to deduce the sequence of a peptide, and to detect and locate post-translational modifications. Until around a decade ago, the concept of amino acid sequencing by MS-technologjes was synonymous with ESI-MS/MS, but today MALDI-MS/MS techniques are implemented in high-performance instruments such that the quality of MALDI tandem mass spectra is comparable with that of ESI-MS/MS spectra. Currently, MALDI tandem mass spectrometers exist in a number of geometries, including TOF-TOF, Q-TOF, ion trap and orbitrap analyzers that each provide unique analytical features for the sequencing of peptides and proteins by MS/MS (details of the instrumentation for different types of MS/MS are provided in Chapter 2). 

High performance capillary electrophoresis was introduced originally as an analytical tool. Now that instruments are equipped with automated fraction collection, however, capillary electrophoresis can be used for micropreparative collection of individual peaks separated from a mixture. Using the fraction collection feature, nanomolar amounts of solute such as proteins, peptides, oligonucleotides can be collected in amounts sufficient for microsequencing. An intersample washing procedure and use of well-formed capillaries aid in the prevention of artifacts.44... 

High performance liquid chromatography (HPLC) and capillary electrophoresis (CE) are two instrumental separation techniques that are applicable to the separation of proteins and peptides. The advantage of HPLC and CE techniques is that they afford the analyst the freedom to resolve a complex mixture by different routes employing different... 

A few years ago, we began a research program to develop methods of analysis which would involve the use of FAB and a high performance tandem mass spectrometer. The tandem instrument was the first triple sector mass spectrometer to be designed and built by a commercial instrument company (Kratos of Manchester, U.K.). The first mass spectrometer of the combination is a double focussing Kratos MS-50 which is coupled to a low resolution electrostatic analyzer, which serves as the second mass spectrometer U). This FAB MS-MS combination has been used to verify the structures of an unknown cyclic peptide (2), a new amino acid modified by diphtheria toxin (3), and an ornithine-containing lipid (4). A number of methods have also been worked out which rely on this instrumentation. They Include the structural determination of cyclic peptides (5), nucleosides and nucleotides (6), and unsaturated fatty acids (7) and the analysis of mixtures of both anionic (8) and cationic surfactants (9). 

The IMER approach does not require that the enzyme be placed in close proximity to the detector if the transducer signal is generated by a soluble product or cosubstrate of the enzymatic reaction. In the latter case, a variety of flow systems and postreactor detectors can be utilized to produce simultaneous determinations of the concentrations of several analytes. For example, an IMER can be combined with a high-performance liquid chromatography (HPLC) instrument (perhaps also in combination with mass spectroscopy) for purposes of both qualitative and quantitative analysis. The chemo-, stereo-, and regio-selectivities of enzymes facilitate separation and/or identification of analytes that may be present as different isomers (e.g., in peptide analysis based on use of peptidase IMERs in combination with these techniques to obtain structural information about the sequence of amino acids in peptides). 

A single capillary scale reverse phase high-performance liquid chromatography system coupled online to automated electrospray ion trap tandem mass spectrometry (ID-LCMS) is usually performed to characterize the protein fractions. The following protocol is an example of the implementation of the method to identify the peptide components of tryptic digests of the yeast HPLC fractions analysis using the ion trap tandem mass spectrometer instrument described in Section 13.2.2.5, and typical results are shown in Figure 13.2-3. 

There are several ways to increase the fidelity of protein identification. Chief among them are to use better performing instrumentation [12] (nowadays a typical high-performance mass spectrometer can achieve —5-10 ppm mass accuracy) and to identily more peptides. Improving the mass accuracy to 50 ppm for the same set of miz values does not increase the coverage, but it reduces the number of hits from 114 to a single one, human hemoglobin a subunit. 

The m/z values of peptide ions are mathematically derived from the sine wave profile by the performance of a fast Fourier transform operation. Thus, the detection of ions by FTICR is distinct from results from other MS approaches because the peptide ions are detected by their oscillation near the detection plate rather than by collision with a detector. Consequently, masses are resolved only by cyclotron frequency and not in space (sector instruments) or time (TOF analyzers). The magnetic field strength measured in Tesla correlates with the performance properties of FTICR. The instruments are very powerful and provide exquisitely high mass accuracy, mass resolution, and sensitivity—desirable properties in the analysis of complex protein mixtures. FTICR instruments are especially compatible with ESI29 but may also be used with MALDI as an ionization source.30 FTICR requires sophisticated expertise. Nevertheless, this technique is increasingly employed successfully in proteomics studies. 

The quadrupole ion trap still suffers from mass accuracy problems (in comparison with the high resolution attainable) but <30 ppm has been obtained for peptides [240]. This reference nicely addresses performance features of the linear QIT in particular, but mentions other instrument types as well. As with the resolution, to obtain better mass accuracy, sensitivity and speed have to be reduced. 

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-... 

Some laboratories do not have access to mass spectrometric analysis, but the number is fewer as the cost for this type of instrumentation is decreasing. It is suggested that these laboratories utilize amino acid analysis due to reduced cost and rapid turnaround. Peptide composition and stoichiometry can be determined, the technique is highly reproducible, and can be used to monitor cycle-to-cycle coupling efficiency. However, not all amino acids are recovered quantitatively. Cys and Trp are totally destroyed and must be quantitated using distinctly different hydrolysis procedures. Ser and Thr can be partially destroyed. Some laboratories perform amino acid analysis in addition to mass spectrometric analysis in order to assure peptide composition, stoichiometry, and quantity (see also Sections 7.3, 7.3.1 and 7.3.2). 

---