This calculation using the m/z values for any two peaks in a spectrum such as that shown in Figure 1b usually provides the mass of the protein (in this case, aerolysin k; 47,342 Da) with an error of only ±0.01%. Generating several sets of peaks, repeating the calculation, and averaging the results generally provides an even more accurate value for M. Computer algorithms can transform the m/z spectrum into a single peak that

FIGURE 2 Obtaining protein sequence information with tandem

MS. (a) After proteolytic hydrolysis, a protein solution is injected into a mass spectrometer (MS-1). The different peptides are sorted so that only one type is selected for further analysis. The selected peptide is further fragmented in a chamber between the two mass spectrometers, and m/z for each fragment is measured in the second mass spectrometer (MS-2). Many of the ions generated during this second fragmentation result from breakage of the peptide bond, as shown. These are called b-type or y-type ions, depending on whether the charge is retained on the amino- or carboxyl-terminal side, respectively. (b) A typical spectrum with peaks representing the peptide fragments generated from a sample of one small peptide (10 residues). The labeled peaks are y-type ions. The large peak next to y5" is a doubly charged ion and is not part of the y set. The successive peaks differ by the mass of a particular amino acid in the original peptide. In this case, the deduced sequence was Phe-Pro-Gly-Gln-(Ile/Leu)-Asn-Ala-Asp-(Ile/Leu)-Arg. Note the ambiguity about Ile and Leu residues, because they have the same molecular mass. In this example, the set of peaks derived from y-type ions predominates, and the spectrum is greatly simplified as a result. This is because an Arg residue occurs at the carboxyl terminus of the peptide, and most of the positive charges are retained on this residue.

also provides a very accurate mass measurement (Fig. 1b, inset).

Mass spectrometry can also be used to sequence short stretches of polypeptide, an application that has emerged as an invaluable tool for quickly identifying unknown proteins. Sequence information is extracted using a technique called tandem MS, or MS/MS. A solution containing the protein under investigation is first treated with a protease or chemical reagent to hydrolyze it to a mixture of shorter peptides. The mixture is then injected into a device that is essentially two mass spectrometers in tandem (Fig. 2a, top). In the first, the peptide mixture is sorted and the ionized fragments are manipulated so that only one of the several types of peptides produced by cleavage emerges at the other end. The sample of the selected

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Collision cell

MS-2 Detector

Collision cell


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