Combined Use of Post-Ion Mobility/Collision-Induced Dissociation and Chemometrics for b Fragment Ion Analysis

Although structural isomers may yield indistinguishable ion mobility (IM) arrival times and similar fragment ions in tandem mass spectrometry (MS), it is demonstrated that post-IM/collision-induced dissociation MS (post-IM/CID MS) combined with chemometrics can enable independent study of the IM-overlapped isomers. The new approach allowed us to investigate the propensity of selected b type fragment ions from AlaAlaAlaHisAlaAlaAla-NH₂ (AAA(His)AAA) heptapeptide to form different isomers. Principle component analysis (PCA) of the unresolved post-IM/CID profiles indicated the presence of two different isomer types for b₄ ⁺, b₅ ⁺, and b₆ ⁺ and a single isomer type for b₇ ⁺ fragments of AAA(His)AAA. We employed a simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) to calculate the total IM profiles and CID mass spectra of b fragment isomers. The deconvoluted CID mass spectra showed discernible fragmentation patterns for the two isomers of b₄ ⁺, b₅ ⁺, and b₆ ⁺ fragments. Under our experimental conditions, calculated percentages of the “cyclic” isomers (at the 95 % confidence level for n = 3) for b₄ ⁺, b₅ ⁺, and b₆ ⁺ were 61 (± 5) %, 36 (± 5) %, and 48 (± 2) %, respectively. Results from the SIMPLISMA deconvolution of b₅ ⁺ species resembled the CID MS patterns of fully resolved IM profiles for the two b₅ ⁺ isomers. The “cyclic” isomers for each of the two-component b fragment ions were less susceptible to ion fragmentation than their “linear” counterparts.

Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b₁₀ ²⁺ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b₁₀ ²⁺ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b₁₀. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b₁₀ ²⁺, suggesting that b₁₀ ²⁺ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b₁₀ ²⁺; over 30 % of the observed SORI-CID fragment ions from substance P b₁₀ ²⁺ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b₁₀ ²⁺, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b₁₀ ²⁺.