Transfer of Structural Elements from Compact to Extended States in Unsolvated Ubiquitin

This instrument combines the capabilities of ion/ion reactions with ion mobility (IM) and time-of-flight (TOF) measurements for conformation studies and top-down analysis of large biomolecules. Ubiquitin ions from either of two electrospray ionization (ESI) sources are stored in a three dimensional (3D) ion trap (IT) and reacted with negative ions from atmospheric sampling glow discharge ionization (ASGDI). The proton transfer reaction products are then separated by IM and analyzed via a TOF mass analyzer. In this way, ubiquitin ϩ7 ions are converted to lower charge states down to ϩ1; the ions in lower charge states tend to be in compact conformations with cross sections down to ϳ880 Å 2 . The duration and magnitude of the ion ejection pulse on the IT exit and the entrance voltage on the IM drift tube can affect the measured distribution of conformers for ubiquitin ϩ7 and ϩ6. Alternatively, protein ions are fragmented by collision-induced dissociation (CID) in the IT, followed by ion/ion reactions to reduce the charge states of the CID product ions, thus simplifying assignment of charge states and fragments using the mobility-resolved tandem mass spectrum. Instrument characteristics and the use of a new ion trap controller and software modifications to control the entire instrument are described. Ion mobility (IM) [4,5] has become a very useful technique for analysis of biological ions in the gas phase [6]. IM provides information about ion size and structure [7], as it rapidly separates ions based on collision cross-section, rather than just m/z ratio. The use of IM to disperse a mixture of ions in time before analysis via a time-of-flight (TOF) MS, i.e., nested drift (flight) time measurements, is an important recent advance. These experiments were pioneered by Clemmer and coworkers in the mid-1990s [8], and have now been used by several other groups [9 -13]. The recent Synapt ESI-IMS-MS by Waters Corp. provides a commercially available instrument for gas-phase ion conformation studies by IM using a novel traveling wave approach [9].In a series of instrumental designs, the Clemmer group has made various modifications to the initial ESI-IM-TOF, including the insertion of a collision cell between the IM drift tube and the TOF for mobility labeling experiments [14,15], and the addition of an IT before the mobility drift tube to improve the duty cycle from the continuous ESI source [16,17]. One publication demonstrated MS/MS capabilities with an ion trap before IM-TOF [18], but the entire instrument was not under computer control. Therefore, only relatively simple experiments were possible.IM has been used to analyze the products of ionmolecule reactions [19], including proton transfer [20,21], H/D exchange [22], and solvation [23][24][25][26]. In these studies, the desired reactions take place either in the atmospheric pressure ion source interface region or in the drift tube itself. Thus, only short reaction times and certain reagent ions can be used. In addition, performing reactions in the IM cell can make spe...

Section: Cross-section Measurementsmentioning

confidence: 61%

“…Initial experiments and instrument characteristics are described, including use of a new ion trap controller and software to control the entire instrument. Ubiquitin is used as a test compound to compare the new results with the extensive previous studies of this protein [21,[47][48][49][50][51][52].…”

mentioning

confidence: 99%

An ion trap-ion mobility-time of flight mass spectrometer with three ion sources for ion/ion reactions

Zhao

Soyk

Schieffer

et al. 2009

“…The development of a 3-D trap-IM-time of flight (TOF) instrument allows time-dependent studies of gas-phase protein ions, including folding, unfolding and structural transitions [20 -23]. A multi-stage IMS-MS instrument [24,25] provides two important new functions. First, a protein ion with a specific structure can be selected by IMS, then activated and separated in the next drift region.…”

mentioning

confidence: 99%

Effects of ion/ion proton transfer reactions on conformation of gas-phase cytochrome c ions

Zhao

Schieffer

Soyk

et al. 2010

Positive ions from cytochrome c are studied in a 3-D ion trap/ion mobility (IM)/quadrupoletime-of-flight (TOF) instrument with three independent ion sources. The IM separation allows measurement of the cross section of the ions. Ion/ion reactions in the 3-D ion trap that remove protons cause the cytochrome c ions to refold gently without other degradation of protein structure, i.e., fragmentation or loss of heme group or metal ion. The conformation(s) of the product ions generated by ion/ion reactions in a given charge state are similar regardless of whether the cytochrome c ions are originally in ϩ8 or ϩ9 charge states. In the lower charge states (ϩ1 to ϩ5) cytochrome c ions made by the ion/ion reaction yield a single IM peak with cross section of ϳ1110 to 1180 Å 2 , even if the original ϩ8 ion started with multiple conformations. The conformation expands slightly when the charge state is reduced from ϩ5 to ϩ1. For product ions in the ϩ6 to ϩ8 charge states, ions created from higher charge states (ϩ9 to ϩ16) by ion/ion reaction produce more compact conformation(s) in somewhat higher abundances compared with those produced directly by the electrospray ionization ( [5][6][7][8][9], and native electron capture dissociation (NECD) [10,11]. Of these methods, IM provides a direct way to examine the gas-phase conformation of the ions by probing the average cross-section of the protein ions via collisions with buffer gas [3,4]. Early IM research on protein folding and unfolding was done with an IMquadrupole instrument [1]. To study ions in lower charge states than those made directly from the electrospray ionization (ESI) source, a basic collision gas (e.g., acetophenone or 7-methyl-1,3,5-triazabicyclo 4,4,0] dec-5-ene, MTBD) [12] was introduced into the source region. The neutral gas extracted protons from the protein ion and created lower charge state ions through proton transfer reactions in the source. In these studies, the reactions took place only in the atmospheric pressure ion source interface region. Thus, control and variation of the reaction time and extent of reaction were difficult, and only certain reagent species were available.Gas-phase ion/ion reactions provide another dimension for gas-phase bioanalysis by MS. To date, these reactions have been mainly used to simplify complex MS/MS spectra [13,14] or generate fragments for structural assignment [15,16] by methods like electrontransfer dissociation (ETD) [17][18][19].Recent instrumentation improvements have greatly extended the type of structural information and number of possible experiments available in this area. The development of a 3-D trap-IM-time of flight (TOF) instrument allows time-dependent studies of gas-phase protein ions, including folding, unfolding and structural transitions [20 -23]. A multi-stage IMS-MS instrument [24,25] provides two important new functions. First, a protein ion with a specific structure can be selected by IMS, then activated and separated in the next drift region. Second, "state-to-state" structural

“…Ion mobility-mass spectrometry studies suggest an unfolding from compact structures to unfolded conformations when intramolecular Coulomb repulsion exceeds the attractive, structure-defining interactions in gas-phase peptide and protein ions [6,7,9,20,21]. Further increase in charge leads to a gradual increase in collision cross-section of already extended conformations, which was earlier recognized to be an indicator for an unzipping of remaining secondary structural elements [6,9].…”

Section: Discussionmentioning

confidence: 99%

“…The different structures that ubiquitin ions can adopt in the gas phase have been investigated previously using ion mobility-mass spectrometry (IM-MS) and related techniques [7,9,20,21]. Such experiments typically yield arrival time distributions (ATDs) from which the overall size of the ions by means of an angular-averaged collision crosssection (CCS) can be deduced.…”

Section: Ubiquitin -From Compact To Stringmentioning

confidence: 99%

From Compact to String—The Role of Secondary and Tertiary Structure in Charge-Induced Unzipping of Gas-Phase Proteins

Warnke

Hoffmann

Seo

et al. 2016

In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS) based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues.In the gas-phase environment of a mass spectrometer, proteins can adopt a broad range of distinct structures. When electrosprayed from native, buffered solutions especially large proteins and protein complexes are known to retain features of their condensed-phase conformation -a fact that found broad application in the field of native mass spec-