Tandem mass spectra

Eng, J. K. McCormack, A. L. Yates, J. R. An approach to correlate tandem mass spectra data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994,5, 976-989. 

Bred, L. A. Tabb, D. L. Yates, J. R. Wysocki, V. H. Cleavage Y-terminal to proline Analysis of a database of peptide tandem mass spectra. Anal. Chem. 2003, 75,1963-1971. 

Sadygov, R.G., Cociorva, D., Yates, J.R., 3rd (2004). Large-scale database searching using tandem mass spectra looking up the answer in the back of the book. Nat. Methods 1, 195-202. 

Figure 3.9 Conceptual view of tandem mass spectrometry with a tandem-inspace triple quadrupole mass analyzer." The first mass analyzer (Ql) selects the precursor ion of interest by allowing only it to pass, while discriminating against all others. The precursor ion is then fragmented, usually by energetic collisions, in the second quadrupole (q2) that is operated in transmissive mode allowing all fragment ions to be collimated and passed into the third quadrupole (Q3). Q3 performs mass analysis on the product ions that compose the tandem mass spectra and are rationalized to a structure.

Complete sequencing of this peptide requires acquisition of additional tandem mass spectra, preferably MS3 fragmentation, of one of the low-mass y-ions. Because the peptide of interest is derived from a biological source, yet another possibility might be the use of sequence databases, similarly to the previous example. Actually, this approach works very well in this case, allowing identification of the peptide of interest as H-LGEYGFQNALIVR-OH, the 421-433 fragment of bovine serum albumin. 

The straightforward approach to de novo sequencing sometimes fails, for example, due to the low quality tandem mass spectra. Often it is not caused by the equipment settings or operator s capabilities, but just by unfavorable fragmentation pattern of a given peptide. Among possible approaches to solve such issues is chemical derivatization of peptides. 

R. Craig and R. C. Beavis. TANDEM Matching Proteins with Tandem Mass Spectra. Bioinformatics, 20, no. 9 (2004) 1466-1467. 

Figure 14.1. Tandem mass spectra of amino acids. Top left panel shows the product ion spectra of the buylester of phenylalanine. Fragmentation that explains the neutral loss of 102 Da is shown in the top left panel of the figure. The bottom panel is a neutral loss scan from m/z 125 to 270 which includes many common amino acids. The profile is obtained by an analysis of a blood spot from a patient with PKU.

Fig. 11.17. Simulated mass chromatograms resulting from precursor ion and constant neutral loss tandem mass spectra (middle and bottom traces), illustrating the selectivity that those MS/MS scan modes can bring to chromatographic analyses. The top trace in the figure represents a total ion chromatogram obtained using a conventional single stage of mass analysis.

Papayannopoulos I.A. (1995), The interpretation of collision-induced dissociation tandem mass spectra of peptides, Mass Spectrom. Rev. 14, 49-73. 

FIGURE 18.2 Ion chromatogram and the corresponding tandem mass spectra of tetracycline and chlortetra-cycline obtained for a sample of an agricnltnral soil amended with mannre, (Reprinted from Lopez de Alda, M,J, and Barcelo, D, J. Chromatogr. A, 1000, 503, 2003, Copyright 2003, With permission from Elsevier,)... 

For example, the ion of [M-69]+, which is observed in the tandem mass spectra of lycopene, neurosporene, and y-carotene but not a-carotene, p-carotene, lutein, or zeaxanthin, indicates the presence of a terminal acyclic isoprene unit. Elimination of a hydroxyl group or a molecule of water, [M-17]+ or [MH-18]+, from carotenoids such as astaxanthin or zeaxanthin is characteristic of the presence of a hydroxyl group. Also, tandem mass spectrometry can be used to distinguish between isomeric carotenoids such as a-carotene and p-carotene, or lutein and zeaxanthin. For example, the ring of a-carotene containing the double bond that i s not conj ugated to the rest of the polyene chain shows unique retro-Diels-Alder fragmentation to form the ion of [M-56]+. In a similar manner, isomeric lutein and zeaxanthin differ by the... 

The fragmentation patterns and characteristic fragment ions for the carotenoids observed in FAB-MS and LSIMS tandem mass spectra are also observed in the tandem mass spectra obtained following ESI (see Basic Protocol 4), APCI (see Basic Protocol 5), and other methods. A detailed account of structure determination of carotenoids using FAB ionization with CID and MS/MS is presented in van Bree-men el al. (1995). Finally, another advantage of MS/MS is that matrix ions formed during FAB-MS or LSIMS, and any other contaminating ions, are eliminated, which simplifies interpretation of the mass spectrum. 

Contains the most complete set of tandem mass spectra of carotenoids and their interpretation. Fragmentation patterns and characteristicfragment ions described here are common to all CID tandem mass spectra of carotenoids. 

Static FAB/LSIMS provides a continuous signal for chlorophylls and their derivatives so that exact mass measurements may be carried out to determine elemental compositions, or tandem mass spectra following CID may be recorded. 

The most complete reference of tandem mass spectra for chlorophylls and chlorophyll derivatives including pheophytins, chlotophyllides, pheophorbides, and pyropheophytins. 

The most common types of MS/MS instruments available to researchers in food chemistry include triple quadrupole mass spectrometers and ion traps. Less common but commercially produced tandem mass spectrometers include magnetic sector instruments, Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, and quadrupole time-of-flight (QTOF) hybrid instruments (Table A.3A.1). Beginning in 2001, TOF-TOF tandem mass spectrometers became available from instrument manufacturers. These instruments have the potential to deliver high-resolution tandem mass spectra with high speed and should be compatible with the chip-based chromatography systems now under development. 

Inherent low-mass cutoff limits Information rich tandem mass spectra... 

JR Yates III, JK Eng, AL McCormack. Mining genomes correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem 67 3202-3210, 1995. 

Wilkins MR, Williams KL, Appel RD, Hochstrasser DF (1997) Proteome research new frontiers in functional genomics. Springer Verlag, Berlin Heidelberg Yates JR, Speicher S, Griffin PR, Hunkapiller T (1993) Peptide mass maps A highly informative approach to protein identification. Anal Biochem 214 397—408 Yates JR, Eng JK, McCormack AL, Schieltz D (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Analytical Chemistry 67 1426-1436. 

An algorithm has been developed for the interpretation of tandem mass spectra of oligonucleotides. [201] This greatly facilitates the interpretation of mass spectra of oligonucleotides and is based on the general fragmentation scheme of these molecules. 

The low-energy tandem mass spectra of the deprotonated molecular ions of acylglycerol contain a type of ion whose formal mass-based composition corresponds to a ketone obtained by the combination of two fatty acid chains with a carbonyl group, minus a proton. The ketone contains mainly the chains of the central fatty acid combined with one of the two external fatty acids, even if the ketone containing the two external fatty acids is present with a much weaker intensity. The formation of these ions may be explained by an internal Claisen condensation followed by a fragmentation induced by a nucleophile substitution and then by a decarboxylation, as shown in Figure 8.64. 

This experimental observation is illustrated in Figure 8.66 by the tandem mass spectra of two bile acids of the A4-3-oxo class the taurine conjugates oI 7a-hydroxy-3-oxochol-4-cn-24-oic acid and 7a, 12a-dihydro-3-oxochol-4-en-24-oic acid. [311] Similar spectra were obtained for the A4-3-hydroxy derivatives. The general fragmentation diagram deduced from these spectra is shown in Figure 8.67. 

DBT, 2-DBT (2-methyldibenzo[3]thiophene), and 4,6-DBT (4,6-dimethyldibenzo[3]thiophene) in ESI tandem mass spectra have a a consistent 32 Da neutral loss, which is believed to be sulfur. Based on the tandem mass spectrum of the PASH compounds, the mechanism of fragmentation is considered to be a charge site-initiated reaction followed by a radical site-initiated fragmentation. Taking the example of DBT, Scheme 4 shows a possible mechanism. 

Ethier M, Saba JA, Ens W, Standing KG, Perreault H. Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra. Rapid Commun. Mass Spectrom. 2002 16 1743-1754. 

J.R. Yates, III, J.K. Eng, A.L. McConnack, D. Schielti, Methods to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem.,67(1995) 1426. 

Fig. 2 ESI LC/MS/MS analysis of penicillins fortified at a concentration of 0.05 mg/kg in bovine liver, (a) Mass chromatograms monitored at [M-H-141] (b) tandem mass spectra of penicillins recorded at the top of each peak on the mass chromatograms (a).

When [M-H] serves as a precursor ion for MS/ MS, [M-H-CO2] and [M-H-141] were generated as product ions (listed in Table 2), and they are very useful for the confirmation of penicillins. After a series of detailed examinations, the other MS/MS conditions including the compound-specific parameters were selected. To provide the applicability of the present method, the fortified bovine tissues, at a concentration of 0.05 mg/kg of each six penicillins, were analyzed. As shown in Fig. 2 left, all six penicillins from the liver sample appeared as separate peaks on the mass chromatograms monitored at [M-H-141] under ESI LC/MS/MS conditions. Fig. 2 right shows the tandem mass spectra of the penicillins recorded at the top of each peak on the mass chromatograms shown in Fig. 2 left. All of these mass chromatograms and tandem mass spectra of fortified samples were almost the same as for the respective standards. Based on the results of the analyses of the fortified samples at 0.02 mg/kg, the lower limit of confirmation of the present method for muscle sample was estimated to be 0.02 mg/kg for all six penicillins, and those for kidney and liver were between 0.02 and 0.03 mg/kg. 

Hart, K. J., Palmer, P. T., Diedrich, D. L. and Enke, C. G. Generation of substructure identification rules using feature-combinations from tandem mass spectra. ]. Am. Soc. Mass Spectrom. 3 159-168, 1992. 

---