Peptides protonated

It is not an exaggeration to say that electrospray has introduced a new era, not only for the analytical mass spectroscopist, but also for the more physically oriented researcher interested in physical measurements involving the above ions, which are of such great importance in condensed-phase ion chemistry. In particular, gas-phase ions produced by electrospray allow, for the first time, thermochemical measurements involving ions of biochemical significance such as protonated peptides, deprotonated nucleotides, and metal ion complexes with peptides and proteins. It is to be expected that such data will be of importance in the development of theoretical modeling of the state of these systems in the condensed phase.34,35... 

UV/Visible Photodissociation. In the case of UV/visible PD the photon energies are high enough to enable direct fragmentation. Previously, UV photodissociation was utilized mainly to study dissociation kinetics of gas-phase ions, but recently it was demonstrated that UV PD could be used for tandem MS of MALDI generated protonated peptides [18]. 

S. Ramamoorthy, W. Liu, Y. Y. Ma, T. L. Yang-Feng, V. Ganapathy, and F. H. Leibach. Proton/peptide cotransporter (PEPT 2) from human kidney functional characterization and chromosomal localization. Biochim Biophys Acta 1240 1-4 (1995). 

The relevant AGB values, calculated by using Te = 970 are listed in Table 8. According to the reported values, the heterochiral Trp/Pro and Phe/Ala complexes are more stable than the homochiral ones. The reverse is true for the Phe/ Pro and PheA al complexes. By the same token, the chiral discrimination factor, AR measured by ESl-MS for 19 amino acids was found to vary between 0.3 and 3. ° The stereochemistry associated to the CID of diastereomeric peptides has been investigated using a similar approach. The results suggest that the secondary structure of protonated peptides may play an important role in their gas-phase behavior. ... 

Dongre, A.R. Somogyi, A. Wysocki, V.H. SID an Effective Tool to Probe Structure, Energetics and Fragmentation Mecharrisrrrs of Protonated Peptides. J. Mass Spectrom. 1996, 31, 339-350. 

Scheme 1 The Expected Fragmentation Pattern of Protonated Peptide Ions and the Nomenclature of the Amino Acid Sequence Fragment Ions for Determining Amino Acid Sequences...

The protonated peptide is the leaving group. The nucleophile is fluoride ion. 

The most widely used mass spectrometric identification procedure is MALDI-Tof analysis of the entire peptide mixture. Gas-phase matrix interaction with peptide ions in MALDI-Tof results in singly charged ions, giving a mass profile that is highly characteristic of the protein from which the peptides are derived. These peptide masses (actually protonated peptide molecular ions, MH+) can be used to search databases (either protein or nucleic acid databases) to identify the proteins. The two most important factors in successfully identifying proteins by this approach are the number of matching peptide masses and the accuracy of the peptide mass determination. 

Protonated peptides fragment in ways that are now well established (Fig. 11.8). Note that the "a," "b," and "c" ions incorporate the peptide s N-terminus, while "x," "y," and z" ions incorporate the peptide s C-terminus. The numerical subscript refers to the number of residues that the ion contains, "c" and "y" ions involve rearrangements that add to the ions two more hydrogens than they would have from simple cleavage alone. Figure 11.9 shows the CID spectrum of the protonated molecular ion... 

Mass spectrum of isotopic cluster of a singly protonated peptide (C101H145N34 O44) with monoisotopic mass = 2538.015u and average mass = 2539.483 Da at a resolution of 250 (resolution typically obtained for linear TOF), 2500 (quadrupole) and 250 000 (FTICR). Redrawn (modified) from Suizdak G., Proc. 

ECD has recently been introduced as an alternative activation method to obtain fragmentation of multiply protonated peptides [57]. An example of an ECD fragmentation spectrum... 

Fragmentation paths yielding the c and z ions after activation of a multiply protonated peptide by ECD. 

Fragment ion spectrum of a protonated peptide and (top) the sequence of ions. 

Mass spectrometry is one of the major techniques in the interdisciplinary field of proteomics. It provides a rapid, sensitive and reliable means of protein identification and structural determination, allowing for development in this newly baptised but yet classical field of biochemistry and biomedicine. The use of electrospray ionisation in conjunction with a tandem mass spectrometer (MS/MS) provides essential amino acid sequence information from the m/z values of the so-called b andy ions formed from cleavage of the amide bond of a protonated peptide. This reaction requires proton catalysis, and the mechanism is of interest in the present context, since it is closely related to the processes occurring in other protonated carboxylic acid derivatives. 

The simplest model of an amide bond is found in formamide, and several features of protonated formamide are highly relevant to the cleavage of protonated peptides into b and y ions. Amides are bidentate bases, and it has been demonstrated from correlations between core electron energies and proton affinities [213] and from quantum chemical calculations [214] that the carbonyl oxygen is more basic than the amide nitrogen. As demonstrated by FT-ICR, metastable ion dissociation, and RRKM and quantum chemical model calculations [214], the unimolecular dissociation of a protonated formamide molecule depends on which site the proton is attached to ... 

Fig. 7. The mechanism for formation of b andy ions during fragmentation of protonated peptides and protein. The mass spectral pattern of b and y ions are used to determine the amino acid sequence...

Fig. 7. Dependence of the capacity factor of the protonated peptides on the concentration of D-camphor-10 sulphonate (A) and -hexyl sulfonate (B) in the mobile phase. Column /i.-Bondapak Cig flow rate 2 ml/min temperature 20°C, mobile phase 507c methanol-50% water-50 mM NaHiP04 with HjPOi added to pH 3.0, containing various concentrations of the ion-pairing reagents. The protonated peptides were as follows 1, Arg-Phe 2, Arg-Phe-Ala 3, Met-Arg-Phe 4, Met-Arg-Phe-Ala 5, Leu-Trp 6, Leu-Trp-Met-Arg 7, Leu-Trp-Met 8, Leu-Trp-Met-Arg-Phe. Reproduced from Hearn and Grego (34).

Paizs B, Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2005 24 508-548. 

Panel A The peak at 31.5 minutes ccaiespcmds to the VSV-8mer peptide, RGYVYQGL. TheicHi at m/z = 9SS.6 corre nds to the singly protonated species, while the ion at m/z = 478.3 is the doubly protonated peptide. Predicted monoisotopic mass = 955.5. 

It should be noted that ETD is a relatively inefficient process for doubly protonated peptide precursors [M + 2H]2+, which are the ions most commonly found in bottom-up proteomics experiments. This situation may be retrieved, however, by using a supplemental low-energy CID method (ETciD) to target the nondissociated electron transfer (ET) product, [M + 2H]2+. CID of the ET product then yields c- and z-type fragment ions. Swaney etal.110 have reported that in a large-scale analysis of doubly charged tryptic peptides, the use of ETciD resulted in a median sequence coverage of 89% compared to 63 and 77% for ETD and CID, respectively. 

Figure 9 Formation of b- and y-ions from singly protonated peptides.

Figure 10 Formation of b- and y-ions from doubly protonated peptides the pathway a yields singly charged b- and y-ions, and the pathway b, doubly charged y-ions.

In ECD, an ESI-produced multiply protonated peptide ion [M + H]B+ is first converted to an odd-electron [M + ion by the capture of a thermal energy electron. Subsequent transfer of H to the backbone... 

RAJ O Hair, GE Reid. Derivatization of protonated peptides via gas phase ion-molecule reactions with acetone. J Am Soc Mass Spectrom 11 244-256, 2000. 

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