Tandem mass spectrometry of peptides using hybrid and four-sector instruments: A comparative study

Abstract

Product-ion spectra produced by high- and low-energy collisionally activated dissociation (CAD) of [M + H]+ ions of a series of peptides (Mr 550-2500) have been compared on four-sector and hybrid tandem mass spectrometers, respectively. The fast atom bombardment product-ion spectra obtained for the smallest peptide analyzed (methionine-enkephalin) were remarkably similar, but substantial differences in fragmentation were observed for the heavier analytes. For peptides with Mr greater than 1000, more complete sequence information was obtained from high-energy CAD on the four-sector instrument. Nevertheless, low-energy CAD on the hybrid mass spectrometer was able to produce partial sequence information even for the largest of the peptides compared. Limits of analysis, defined as the least quantities of analyte for which product-ion spectra of essentially uncompromised quality could be obtained, were similar (ca. 15 pmol) for small peptides, but lower limits were achieved for larger peptides (Mr greater than 1000) with the four-sector instrument. High-energy CAD spectra were found to be highly reproducible, with qualitatively similar spectra obtained over a wide range of operating conditions. In contrast, it was necessary to carefully control collision gas pressures and collision energies in order to obtain good reproducible data for low-energy CAD. Experimental procedures for obtaining reproducible spectra with good sensitivity for peptides on the hybrid instrument are presented.

Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes

“…Since that time, improvements in sequencing have been spurred by the development of protein-identification algorithms as well as a better understanding of peptide dissociation in the gas phase. The latter advancement has been achieved by exploring the effects of peptide size, sequence, gasphase basicity, charge state, and secondary structure on fragmentation [62][63][64][65][66][67][68][69][70]. Surface-induced dissociation was influential in helping to develop a general framework for peptide fragmentation through the energyresolved study of systematically varied model peptides.…”

“…As the number of tandem MS peptide studies increased, several researchers began to notice enhanced fragmentation at particular amino acid residues that prevented complete backbone cleavage, and resulted in incomplete sequencing information [59,62,64,68,70,[75][76][77][78]. Protein-identification algorithms may benefit from the incorporation of selective cleavage rules if residuespecific influences are more completely understood.…”

Stability of Asp-Pro bond under high and low energy collision induced dissociation conditions in the immunodominant epitope region of Herpes simplex virion glycoprotein D

“…This process is known to be less favoured. 19 For compounds 2 to 7, fission of the DP amide bond is one of the most abundant processes compared to other amide bond cleavages in these peptides. The facile cleavage of the DP bond does not seem to depend on the length of the peptide chain.…”

A mixed‐integer optimization framework for de novo peptide identification

“…26 Although it has been reported that the energy of fragmentation in low-energy CID might be insufficient to break the bond between the a-carbon and the carbonyl, 57 x-ions are included in the C-terminal ion series of the theoretical MS/MS. Also included in the peaks of this spectra are what are known as internal fragment ions 56,[59][60][61] …”