A new method for enhancing peptide ion identification in proteomics analyses using ion mobility data is presented. Ideally, direct comparisons of experimental drift times (tD) with a standard mobility database could be used to rank candidate peptide sequence assignments. Such a database would represent only a fraction of sequences in protein databases and significant difficulties associated with the verification of data for constituent peptide ions would exist. A method that employs intrinsic amino acid size parameters to obtain ion mobility predictions that can be used to rank candidate peptide ion assignments is proposed. Intrinsic amino acid size parameters have been determined for doubly-charged peptide ions from an annotated yeast proteome. Predictions of ion mobilities using the intrinsic size parameters are more accurate than those obtained from a polynomial fit to tD versus molecular weight data. More than a two-fold improvement in prediction accuracy has been observed for a group of arginine-terminated peptide ions twelve residues in length. The use of this predictive enhancement as a means to aid peptide ion identification is discussed and a simple peptide ion scoring scheme is presented.

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Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/trans orientation of Xaa–Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.

Ubiquitin confined within nanodroplets was irradiated with a variable-power CO2 laser. Mass spectrometry analysis shows evidence for a protein "melting"-like transition within droplets prior to solvent evaporation and ion formation. Ion mobility spectrometry reveals that structures associated with early steps of denaturation are trapped because of short droplet lifetimes.

A database of 1470 collision cross sections (666 doubly- and 804 triply-charged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M(2+)) correspond to Mg(2+), Ca(2+), or Ba(2+)] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M(2+)-coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M(2+)-coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M(2+) binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition.

Isomerizations of the retinal chromophore were investigated using the IMS-IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activation voltages for isomerization for each of the reaction pathways, and by measuring the threshold activation voltage for fragmentation, the relative energies of the isomers as well as the energy barriers for isomerization were determined. The energy barrier for a single cis-trans isomerization is (0.64±0.05) eV, which is significantly lower than that observed for the reaction within opsin proteins.

Swab touch spray ionization mass spectrometry, an ambient ionization technique, has been applied to the analysis of six explosives from various surfaces including glass, metal, Teflon, plastic, human hands and three types of gloves (nitrile, vinyl and latex). A swab, attached to a metallic handle, was used to sample explosive residues and acted as the ion source. The explosives, 1,3,5-trinitro-1,3,5triazinane (RDX), 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX), and 2,2-bis[(nitrooxy)methyl]propane-1,3-diyl dinitrate (PETN) had an absolute limit of detection of 10 ng from all the surfaces except for PETN from the nitrile gloves (limit of detection 100 ng). Sodium perchlorate, 2-methyl-1,3,5-trinitrobenzene (TNT) and tetra-butylammonium perchlorate had limits of detection of 100 pg, 10 pg, and 1 pg, respectively from all surfaces. This study demonstrates the feasibility of swab touch spray ionization mass spectrometry for detection of a wide array of explosives from a variety of forensically applicable surfaces with disposable, commercial, tamperproof and individually-wrapped conductive swabs without complicated/lengthy sample preparations or extractions.

Isomerizations of the retinal chromophore were investigated using the IMS‐IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activation voltages for isomerization for each of the reaction pathways, and by measuring the threshold activation voltage for fragmentation, the relative energies of the isomers as well as the energy barriers for isomerization were determined. The energy barrier for a single cis–trans isomerization is (0.64±0.05) eV, which is significantly lower than that observed for the reaction within opsin proteins.