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Deamidation is a major fragmentation channel upon activation by collision induced dissociation (CID) for protonated peptides containing glutamine (Gln) and asparagine (Asn) residues. Here, we investigate these NH3-loss reactions for four Asn- and Gln-containing protonated peptides in terms of the resulting product ion structures using infrared ion spectroscopy with the free electron laser FELIX. The influence of the side chain length (Asn versus Gln) and of the amino acid sequence on the deamidation reaction has been examined. Molecular structures for the product ions are determined by comparison of experimental IR spectra with spectra predicted by density functional theory (DFT). The reaction mechanisms identified for the four dipeptides AlaAsn, AsnAla, AlaGln, and GlnAla are not the same. For all four dipeptides, primary deamidation takes place from the amide side chain (and not from the N-terminus) and, in most cases, resembles the mechanisms previously identified for the protonated amino acids asparagine and glutamine. Secondary fragmentation reactions of the deamidation products have also been characterized and provide further insight in – and confirmation of – the identified mechanisms. Overall, this study provides a comprehensive molecular structure map of the deamidation chemistry of this series of dipeptides. Graphical Abstractᅟ Electronic supplementary material The online version of this article (doi:10.1007/s13361-016-1462-5) contains supplementary material, which is available to authorized users.

Agrochemicals frequently undergo various chemical and metabolic transformation reactions in the environment that often result in a wide range of derivates that must be comprehensively characterized to understand their toxicity profiles and their persistence and outcome in the environment. In the development phase, this typically involves a major effort in qualitatively identifying the correct chemical isomer(s) of these derivatives from the many isomers that could potentially be formed. Liquid chromatography-mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy are often used in attempts to characterize such environment transformation products. However, challenges in confidently correlating chemical structures to detected compounds in mass spectrometry data and sensitivity/selectivity limitations of NMR frequently lead to bottlenecks in identification. In this study, we use an alternative approach, infrared ion spectroscopy, to demonstrate the identification of hydroxylated derivatives of two plant protection compounds (azoxystrobin and benzovindiflupyr) contained at low levels in tomato and spinach matrices. Infrared ion spectroscopy is an orthogonal tandem mass spectrometry technique that combines the sensitivity and selectivity of mass spectrometry with structural information obtained by infrared spectroscopy. Furthermore, IR spectra can be computationally predicted for candidate molecular structures, enabling the tentative identification of agrochemical derivatives and other unknowns in the environment without using physical reference standards.

The mid-infrared emission spectra of a large variety of astronomical objects are dominated by the aromatic infrared bands (AIBs), which are now widely accepted to originate from gaseous polycyclic aromatic hydrocarbons (PAHs). It is believed that the astrophysically most relevant molecules are at least 40–50 carbon atoms in size. Still, the large majority of laboratory experiments have been performed on smaller PAHs, mainly for reasons of experimental limitations and availability. Here, we show that combination of atmospheric pressure chemical ionization (APCI) with a direct insertion probe (DIP) inlet gives efficient access to larger, ionic PAHs for action spectroscopy studies. We present the gaseous IR spectra of two astrophysically relevant large PAHs, hexa-peri-hexabenzocoronene ( C 42 H 19 + ) and dicoronylene ( C 48 H 21 + ) in their protonated form. Compared to their radical cation analogs, the protonated species have a lower dissociation threshold as they can expel a neutral hydrogen radical leaving behind the resonance-stabilized radical cation; provided that the mass spectrometer can resolve precursor and product ions at one amu difference, this generates good quality spectra under multiple-photon dissociation conditions. Quantum-chemical computations at the density functional level are used to support experiments. Despite the apparent similarity of different protonation isomers, their IR spectra are predicted to be remarkably distinct. This facilitates a straightforward identification of the isomers formed experimentally. For both species studied, protonation occurs on the peripheral CH moiety in the ’bay region’ of the molecules. We compare the spectra of the protonated species with those of their radical cation analogs reported previously and briefly discuss the astrophysical relevance.

Supplemental Material for Isotope labeling and infrared multiple-photon photodissociation investigation of product ions generated by dissociation of [ZnNO3(CH3OH)2]+: Conversion of methanol to formaldehyde by Evan Perez, Theodore A Corcovilos, John K Gibson, Jonathan Martens, Giel Berden, Jos Oomens and Michael J Van Stipdonk in European Journal of Mass Spectrometry