Modulation of Phosphopeptide Fragmentation via Dual Spray Ion/Ion Reactions Using a Sulfonate-Incorporating Reagent

Characterization of Phosphorylated Peptides by Electron-Activated and Ultraviolet Dissociation Mass Spectrometry: A Comparative Study with Collision-Induced Dissociation

Mass-spectrometry-based methods have made significant progress in the characterization of post-translational modifications (PTMs) in peptides and proteins; however, room remains to improve fragmentation methods. Ideal MS/MS methods are expected to simultaneously provide extensive sequence information and localization of PTM sites and retain labile PTM groups. This collection of criteria is difficult to meet, and the various activation methods available today offer different capabilities. In order to examine the specific case of phosphorylation on peptides, we investigate electron transfer dissociation (ETD), electron-activated dissociation (EAD), and 193 nm ultraviolet photodissociation (UVPD) and compare all three methods with classical collision-induced dissociation (CID). EAD and UVPD show extensive backbone fragmentation, comparable in scope to that of CID. These methods provide diverse backbone fragmentation, producing a/x, b/y, and c/z ions with substantial sequence coverages. EAD displays a high retention efficiency of the phosphate modification, attributed to its electron-mediated fragmentation mechanisms, as observed in ETD. UVPD offers reasonable retention efficiency, also allowing localization of the PTM site. EAD experiments were also performed in an LC-MS/MS workflow by analyzing phosphopeptides spiked in human plasma, and spectra allow accurate identification of the modified sites and discrimination of isomers. Based on the overall performance, EAD and 193 nm UVPD offer alternative options to CID and ETD for phosphoproteomics.

Microdroplet Fusion Chemistry for Charge State Reduction of Synthetic Polymers via Bipolar Dual Spray with Anionic Reagents

Microdroplet fusion chemistry is an emerging area of analyte manipulation that utilizes the ion source region of a mass spectrometer to covalently derivatize or manipulate the charge state distribution. This technique utilizes two electrospray emitters in close proximity, where the droplets from each electrospray plume fuse and undergo the subsequent chemistry. In this study, microdroplet fusion chemistry via bipolar dual spray has demonstrated the ability to reduce the average charge state of polyethylene glycol (PEG) cations using anionic reagents. Bipolar dual spray was implemented on a commercial mass spectrometer with limited hardware modifications to the ion source. Reagents including ammonium hydroxide, formic acid, and lithium chloride showed dramatic shifts in the average charge state of PEG 3.8 K cations (e.g., 5.0+ to 2.5+) along with the emergence of newly detected charge states. An organic base, tributylamine, had no effect on the charge state distribution of PEG 3.8 K cations. These results were consistent with an ion-pairing mechanism, where reagent anions destabilized ammonium cation interactions with PEG 3.8 K upon droplet fusion from the negative and positive emitters. Additional bipolar dual spray experiments with PEG 12.6 K demonstrated the ability to transform uninterpretable mass information into distinct charge states ranging from [M+8NH₄]⁺ to [M+3NH₄]⁺. Overall, this study provides insight into the nature of dual spray chemistry and will aid future experimental design in microdroplet covalent chemistry.

Gas-phase rearrangement reaction of Schiff-base-modified peptide ions

RATIONALE

Schiff base modification of peptides has been shown to facilitate their primary structural characterization via tandem mass spectrometry. However, we have discovered a novel rearrangement reaction via ion trap collisional activation involving the imine of the Schiff base and one of several functional groups, particularly the side chains of the basic residues lysine, arginine, and histidine, in the peptide.

METHODS

Gas-phase ion/ion reactions involving an aldehyde-containing reagent were used to generate Schiff-base-modified model peptides in a hybrid triple quadrupole/linear ion trap tandem mass spectrometer. Subsequent ion trap collisional activation was used to study the rearrangement reaction.

RESULTS

Schiff-base-modified peptide ions were found to undergo a rearrangement reaction that was observed to be either a major or minor contributor to the product ion spectrum, depending upon a variety of factors that include, for example, ion polarity, identity of the nucleophile in the peptide (e.g., side chains of lysine, histidine, and arginine), and the position of the nucleophile relative to the imine.

CONCLUSIONS

Relatively low-energy rearrangement reactions can occur in Schiff-base-modified peptide ions that involve the imine of the Schiff base and a nucleophile present in the polypeptide. While this rearrangement process does not appear to compromise the structural information that can be generated via collisional activation of Schiff-base-modified peptide ions, it can siphon away signal from the structurally diagnostic processes in some instances.

Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides

Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO₃ group can be pinpointed; however, widespread SO₃ losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.