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MASS SPECTROMETRY OF BIOMOLECULES
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TABLE 15.8. Data Used to Search for a Peptide Sequence Using the Tag Approacha Match Criteria Enzyme speci city Measured peptide molecular mass Run of sequence ions Type of ion series Partial sequence Mass of region 1 (m1) Mass of region 3 (m3) Search string Trypsin 2111 0.4 977.4, 1074.5, 1161.5 b series (see Fig. 15.13) PS 977.4 949.5 (977.4)PS(949.5)
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a The masses are monoisotopic and in daltons. The mass difference between the 997.4 and 1074.5 peaks corresponds to the mass of a proline residue.
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15.6. PROTEIN PEPTIDE SEQUENCING There are several instrumental MS methods that can be used to obtain sequence information from proteins and peptides. ESI-triple-quadrupole is frequently used; this con guration produces a reasonable number of fragments, the resolution is usually suf cient and the equipment is relatively inexpensive. With this MS/MS con guration, peptides up to 2500 Da can be analyzed. A MALDI with a TOF re ectron and Fourier transform ion cyclotron resonance mass analyzers are also beginning to be used.21 A typical procedure for protein sequencing begins by digestion with a protease such as trypsin in order to obtain a collection of tryptic peptides. Other enzymes and their cleavage sites are described elsewhere.22 This peptide collection can be ionized using ESI, separated by the rst quadrupole according to m/z ratios, and then fragmented (CID), with the resulting fragments analyzed in the third quadrupole. The mass spectrum can be analyzed to establish the peptide sequence, or compared directly with a peptide database. Figure 15.12 depicts this typical protocol. The CID procedure causes more or less random peptide bond cleavage. Therefore, a number of fragments are obtained that differ by a single amino acid residue. Several types of fragments are produced, and their nomenclature is shown in Figure 15.13. Two main classes of ions are formed by CID, those that contain the C terminus plus one or more additional residues (ions of types xn , yn, and zn ) and those that contain the N-terminus and one or more additional residues (ions of types an , bn , and cn ). Ions of types yn and bn are formed by the rupture of amide bonds, and the mass differences between these fragments are limited to the masses of the naturally occurring 19 different amino acid residues (Table 15.9). Isoleucine and leucine,
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Figure 15.12. Typical procedure used to obtain protein sequence information.
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which are structural isomers and therefore have the same molecular weight, cannot be distinguished with MS. Moreover, lysine and glutamine can only be differentiated if resolution is high, since their mass difference is only 0.0432 Da. The sequencing process consists of the simultaneous measurement of a peptide collection, as shown in Figure 15.14. The sequence is obtained by observation of
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Figure 15.13. Nomenclature used for the more common fragments produced by CID peptide fragmentation. The b and y fragment families , that occur when the peptide bond is broken, are normally produced at higher concentration.
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MASS SPECTROMETRY OF BIOMOLECULES
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TABLE 15.9. Average Masses of Amino Acids in Their Free and Residue Statesa Codes 3-Letter Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Mr 1-Letter Residue Free A R N D C Q E G H I L K M F P S T W Y V 71.0786 156.1870 114.1036 115.0884 103.1386 128.1304 129.1152 57.0518 137.1408 113.1590 113.1590 128.1736 131.1922 147.1762 97.1164 87.0780 101.1048 186.2128 163.1756 99.1322 89.0938 174.2022 132.1188 133.1036 121.1538 146.1456 147.1304 75.0670 155.1560 131.1742 131.1742 146.1888 149.2074 165.1914 115.1316 105.0932 119.1200 204.2280 181.1908 117.1474
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Amino Acid Alanine Arginine Asparagine Aspartic acid Cysteine Glutamine Glutamic acid Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine
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a One letter codes are customary in the MS area. Reprinted, with permission, from M. Mann and M. Wilm, Anal. Chem. 66 (No 24), 1994, 4390-4399. Error Tolerant Identi cation of Peptides in Sequence Databases by Peptide Sequence Tags . Copyright # 1994 American Chemical Society.
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the mass differences within one family of ions; the y family is fully represented in this example. The obtained sequence was then matched to an E. coli membrane protein.23 With this instrumentation, it is possible to analyze peptides with MW up to 2500 Da, although some limitations apply; if only a limited peptide collection is obtained, only limited sequence information can be produced. Sequence information can also be obtained using Edman degradation to remove amino-terminal residues from a peptide, to produce a collection of peptides. MALDI TOF can then be used to obtain the peptides masses, and the sequence determined by mass difference between consecutive peptides. This methodology is called protein ladder sequencing, and allows information to be obtained for up to 30 residues. This method is useful for the identi cation of posttranslational modi cations, such as phosphorylated amino acid residues.24 Once a peptide family has been sequenced, the next step is to overlap the available sequence information, in order to obtain the protein sequence. However, peptide sequences are more frequently used to identify proteins by searching the peptide sequences in databases. Several databases are available, and their utility
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