Selected reaction monitoring | EPFL Graph Search

Selected reaction monitoring (SRM), also called Multiple reaction monitoring, (MRM), is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion product of a fragmentation reaction of the precursor ions is selected in the second mass spectrometer stage for detection. Variants A general case of SRM can be represented by :ABCD^+ \to AB + CD^+ where the precursor ion ABCD+ is selected by the first stage of mass spectrometry (MS1), dissociates into molecule AB and product ion CD+, and the latter is selected by the second stage of mass spectrometry (MS2) and detected. The precursor and product ion pair is called a SRM "transition." Consecutive reaction monitoring (CRM) is the serial application of three or more stages of mass spectrometry to SRM, represented in a simple case by :ABCD^+ \to AB + CD^+ \to C + D^+ where ABCD+ is selected by MS1, dissociates

Acid-base-induced fac → mer isomerization of luminescent iridium(iii) complexes

Farzaneh Fadaei Tirani, Anastasia Gitlina, Carolina Luciana Plaice, Albert Ruggi, Kay Severin

Luminescent Ir(C^N)3 complexes (C^N = cyclometalated arylpyridine ligand) exist in the form of two stable isomers with distinct photophysical and electrochemical properties: fac and mer. Herein, we show that fac-Ir(C^N)3 complexes can be converted into the thermodynamically less stable mer forms by a consecutive reaction with first acid and then base. The chemically induced isomerization is fast, quantitative, and stereoselective, and it can be inversed by light. The new isomerization process opens the possibility to use highly luminescent Ir(C^N)3 complexes as molecular switches.

2022

Electronic and vibrational spectroscopy of cold protonated amino acids in the gas phase

Sébastien Mercier

In this thesis report, we describe a novel home-built instrument designed to study the spectroscopy of biomolecular ions in the gas phase and at low temperature, and we present the first experimental results obtained on protonated aromatic amino acids. The apparatus consists in a tandem mass spectrometer equipped with a nanospray ion source and a cryocooled 22-pole ion trap. The charged species produced by the source traverse a first quadrupole mass filter and mass-selected ions are then accumulated and thermalized in the ion trap, where their vibrational temperature can be lowered to ~ 10 K. Two setups allow us to generate ultraviolet and infrared laser light to spectroscopically probe the trapped ions by photodissociation. The resulting fragment ions are finally released from the trap and mass analyzed by a second quadrupole spectrometer. Photodissociation electronic spectra have been measured for the protonated amino acids tryptophan (TrpH+) and tyrosine (TyrH+), as well as for hydrated complexes of the former. The spectrum of TyrH+ exhibits sharp, fully resolved vibronic transitions, which attests to the low temperature of the ions. In contrast, that of tryptophan shows a broad absorption band that covers several hundreds of wavenumbers. This has been attributed to lifetime broadening related to an ultrafast (< ~ 100 fs) deactivation mechanism of the TrpH+ S1(ππ*) excited state. This phenomenon is caused by a strong coupling between this ππ* state and a nearby dissociative state of πσ* character mainly localized on the charged ammonium group. Solvation of TrpH+ by only two water molecules is sufficient to significantly destabilize the σ* orbitals and reduce that coupling, which results in a longer excited-state lifetime and a fully resolved electronic spectrum. These interpretations are supported by ab initio and density functional theory (DFT) calculations. Infrared-ultraviolet double resonance spectroscopic techniques have been successfully implemented to identify the different conformers of TyrH+ and doubly hydrated protonated tryptophan (TrpH+·W2) by measuring conformer-specific vibrational and electronic spectra for each of them. By comparison with the results of DFT geometry and harmonic frequency calculations, we could confidently determine the structures of the TyrH+ conformers and suggest possible assignments for those of TrpH+·W2. Two important stabilizing interactions could be inferred from these results: (i) the attraction between the charged ammonium group and the π-electron cloud of the aromatic ring; (ii) the hydrogen-bonding interaction of a donor water molecule to the acceptor indole ring of TrpH+·W2.

EPFL2008

On the utility of predictive chromatography to complement mass spectrometry based intact protein identification

Hisham Ben Hamidane, Yury Tsybin

The amino acid sequence determines the individual protein three-dimensional structure and its functioning in an organism. Therefore, "reading" a protein sequence and determining its changes due to mutations or post-translational modifications is one of the objectives of proteomic experiments. The commonly utilized approach is gradient high-performance liquid chromatography (HPLC) in combination with tandem mass spectrometry. While serving as a way to simplify the protein mixture, the liquid chromatography may be an additional analytical tool providing complementary information about the protein structure. Previous attempts to develop "predictive" HPLC for large biomacromolecules were limited by empirically derived equations based purely on the adsorption mechanisms of the retention and applicable to relatively small polypeptide molecules. A mechanism of the large biomacromolecule retention in reversed-phase gradient HPLC was described recently in thermodynamics terms by the analytical model of liquid chromatography at critical conditions (BioLCCC). In this work, we applied the BioLCCC model to predict retention of the intact proteins as well as their large proteolytic peptides separated under different HPLC conditions. The specific aim of these proof-of-principle studies was to demonstrate the feasibility of using "predictive" HPLC as a complementary tool to support the analysis of identified intact proteins in top-down, middle-down, and/or targeted selected reaction monitoring (SRM)-based proteomic experiments.

Springer-Verlag2012

Electronic and vibrational spectroscopy of cold protonated amino acids in the gas phase

Sébastien Mercier

EPFL2008