Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides

Abstract

Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging.

Vibrational and electronic spectra of protonated vanillin: exploring protonation sites and isomerisation

“…), although the use of the cryogenic conditions (implemented in this work for UVPD) is not yet widely extended. [29][30][31]75 We highlight that these techniques would ideally be combined in the form of IR/UV double resonance experiments to obtain more precise information. For a more indepth analysis of the conformer ratios generated in the sources and the parameters influencing this ratio, the coupling of action spectroscopies with other techniques sensitive and selective to conformation, such as ion mobility spectroscopy, can also be envisaged.…”

“…[25][26][27][28] However, the combined utilisation of IRMPD and UVPD is less commonly found in the literature, although very interesting works have been published. 11,[29][30][31] To the best of our knowledge, none of these works take advantage of the use of cryogenic temperatures. 25 Vanillin (3-methoxy-4-hydroxybenzaldehyde, Fig.…”

Instrumentation at the Leading Edge of Proteomics

“…Outside of the Orbitrap systems, the other main commercial option for FTMS is Bruker’s solariX platform, which offers 7, 12, and 15 T magnet options that provide >10 M resolving power and 0.6, 0.3, and 0.25 ppm mass accuracy, respectively. These instruments are Qq-FTICR instruments with the rf-only collision cell ( q ) having trapping capabilities for ETD fragmentation (including negative ETD), in addition to ion–electron activation (e.g., ECD, EDD, and niECD) in the ICR cell. − The solariX platform has also been modified for SID as well as UVPD and IRMPD activation, although these are not commercial options. ,− The performance of these instruments has been enhanced in recent years by introduction of the ParaCell ICR cell on the solariX XR and 2xR platforms, which ultimately improves resolving power for a given magnetic field and thus offers increased performance metrics even when magnetic field strength limitations cannot be overcome. , Additionally, a collaboration with government labs and several instrument companies (namely, Thermo and Bruker) has resulted in two world-record 21 T FTICR instruments that are accessible through collaboration programs. , Even though FTICR instruments have become increasingly less prevalent in proteomics research, they remain highly advantageous for intact protein and top-down analyses in addition to petroleomics, metabolomics, and other analyses that benefit from fine isotope structure determination. , …”

Instrumentation at the leading edge of proteomics

“…[370][371][372][373][374][375] The solariX platform has also been modified for SID as well as UVPD and IRMPD activation, although these are not commercial options. 285,[376][377][378][379][380][381] The performance of these instruments has been enhanced in recent years by introduction of the ParaCell ICR cell on the solariX XR and 2xR platforms, which ultimately improves resolving power for a given magnetic field and thus offers increased performance metrics even when magnetic field strength limitations cannot be overcome. 382,383 Additionally, a collaboration with government labs and several instrument companies (namely, Thermo and Bruker) have resulted in two world-record 21T FTICR instruments that are accessible through collaboration programs.…”