Dissociation Pattern of Sodiated Amide Peptides as a Tool for De Novo Sequencing

Probing Metal Ion Adduction in the ESI Charged Residue Mechanism via Gas-Phase Ion/Ion Chemistry

The final stages of the charged residue mechanism/model (CRM) for ion generation via electrospray ionization (ESI) involves the binding of excess charge onto analyte species. Ions of both polarities can bind to the analyte with an excess of ions of the same polarity as the droplet. For large biomolecule/biocomplex ions, which are commonly the species of interest in native mass spectrometry (MS), the binding of acids and salts onto the analyte can lead to extensive broadening of ion signals due to adduction. Therefore, heating step(s) to facilitate desolvation and salt adduct removal are commonplace. In this work, we describe an approach to study the final stages of CRM using gas-phase ion/ion reactions to generate analyte ion/salt clusters of well-defined composition, followed by gas-phase collision-induced dissociation (CID). While there are many variables that can be studied systematically via this approach, the work described herein is focused on salt clusters of the form [Na10X11]-, where X = acetate (Ac-), chloride (Cl-), or nitrate (NO3-), in reaction with a common charge state of ubiquitin as well as several model peptides. Experiments in which equimolar quantities of each salt (i.e., NaAc, NaCl, and NaNO3) are subjected to ESI with ubiquitin (Ubi) and gas-phase ion/ion reaction studies involving [Na10X11]- and [Ubi + 6H]6+ show similar trends, in terms of the extent of sodium ion incorporation into the protein ions. Ion/ion reaction studies using model peptides show that the acetate-containing salt transfers significantly more Na+ ions into the peptide ions. Exchange of Na+ for H+ is shown to occur at the C-terminus and at up to all of the amide linkages using [Na10X11]-, whereas only the C-terminus engages in Na+/H+ exchange with [Na10Cl11]- and [Na10(NO3)11]-. In the latter cases, an additional Na+ is taken up as the excess positive charge, presumably due to solvation of the charge by multiple sites (e.g., carbonyl oxygens and basic sites).

Origins, Technological Advancement, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.

Recent advances in mass spectrometry analysis of neuropeptides

Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.

Collision Cross-Section Measurements of Collision-Induced Dissociation Precursor and Product Ions in an FTICR-MS and an IM-MS: A Comparative Study

Sustained off-resonance irradiation-cross-sectional areas by Fourier transform ion cyclotron resonance mass spectrometry (SORI-CRAFTI) is an FTICR-MS strategy to collisionally activate precursor ions and then measure their ion-neutral collision cross sections, as well as those of selected products, at the same time. We benchmarked SORI-CRAFTI using protonated leucine-enkephalin, to excellent agreement (typically within 1-2%) with previous studies performed via collision-induced dissociation-ion mobility (CID-IMS). SORI-CRAFTI was then applied to alkali metal-cationized leucine-enkephalin and compared with CID-IMS via precursor/product cross-section ratios. Qualitative agreement between SORI-CRAFTI and CID-IMS was excellent (again, usually within 1-2%); however, neither SORI-CRAFTI nor CID-IMS could determine if metalated leucine-enkephalin was present in its canonical or zwitterionic form. When SORI-CRAFTI was used on [2.2.2]-cryptand+Cs⁺, SORI activation resulted in a 5% decrease in collision cross section, consistent with migration of the externally bound Cs⁺ into the cryptand's cavity and similar to the cross section observed when electrospraying from an isopropanol-rich solvent. Thus, SORI-CRAFTI is useful for studying gas-phase ion chemistry of small- to medium-sized molecules and host-guest systems.