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Collisional Energy Dependence of Peptide Ion Fragmentation



Pedatsur Neta, Y Simon-Manso, Xiaoyu Yang, Stephen Stein


The energy dependence of fragmentation in a collision cell was measured for 2100 peptide ions derived from the digestion of twenty four common proteins. Most proteins were digested by trypsin and derived peptides were divided into several classes, depending on the mobility (basicity) of the least tightly bound proton and in some cases on charge. The collision voltage at which the sum of the fragment ion abundances was equal to the remaining parent ion (V1/2) was the principal measure of fragmentation. Each class was characterized by a linear relation between V1/2 and m/z whose slope depended on the peptide class and with little adjustment intersected the origin. The slope provides a measure of resistance to dissociation. Peptide ions where the number of protons is no greater than as the number of arginine residues have the greatest slope, V1/2 /(m/z) = 0.0482 (all slopes in units of V Da-1 e) with a correlation coefficient of R2 = 0.983. For peptides where the number of protons is greater than the number of arginine residues, but not greater than the total number of basic residues (no mobile protons), the slope decreases to 0.0416 (R2 = 0.978) for singly-charged ions, 0.0382 (R2 = 0.952) for doubly-charged ions, 0.0361 (R2 = 0.958) for triply-charged ions, and 0.0305 (R2 = 0.848) for more highly charged ions. With one mobile proton, the slope is about 0.029 for singly- and doubly-charged ions and slightly lower for more highly charged ions. With 2 or more mobile protons the slope drops to 0.0204 (R2 = 0.917). By removing m/z dependence, the deviation of a V1/2 value from the line provides a relative measure of the ease of fragmentation of an ion in each class. A few peptides with certain structures do not fit these correlations and are discussed separately. This information can guide the selection of optimal conditions for MS/MS studies in collision cells for selected peptide ions as well as aid in comparing the reactivity of ions differing in m/z and charge state.
Journal of the American Society for Mass Spectrometry


Mass Spectrometry, Proteomics, Proteins, Peptides, Collision Induced Dissociation, Electrospray


Neta, P. , Simon-Manso, Y. , Yang, X. and Stein, S. (2009), Collisional Energy Dependence of Peptide Ion Fragmentation, Journal of the American Society for Mass Spectrometry (Accessed June 12, 2024)


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Created February 28, 2009, Updated October 12, 2021