High-resolution hybrid mass spectrometer with nano liquid chromatography for proteomics analyses

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In recent years, mass spectrometry-based methods have become available thatenable the proteome-wide profiling of proteins. These approaches do not only measureup- or down regulation of proteins, but also other physicochemical properties, whichchange due to posttranslational modifications, complex formation, re-localization andvarious other cellular processes. This enables a global footprint-like profiling of the entireproteome and to compare different physiological states of an organism or tissue. Aparticular focus of our research lies on the elucidation and interplay of variousposttranslational modifications of proteins, such as ac(et)ylations, phosphorylation, andglycosylations in plants. For the certain identification of a particular peptide modification,high resolution mass spectrometry, as obtained by the Orbitrap technology, is anabsolute requirement. In addition, to identify and quantify chemically modified,multiplexed, and cross-linked peptide samples, peptide fractionation via online reversedphase nano-liquid chromatography and high-field asymmetric waveform ion mobilityspectrometry is required. After electrospray ionization precursor ions have to be selectedvia a quadrupole for data acquisition in different ion traps, before and after fragmentationusing different methods such as CID, HCD, ETD, and a combination of those. Furtherfragmentation (MS3) is beneficial for accurate protein quantifications with reporter ionsfrom multiplexed samples as well as for the certain identification of dipeptides fromcrosslinked samples. A high mass range is additionally required for large peptides, intactproteins and complexome profilings.