Surface-Induced Dissociation on a MALDI-Ion Mobility-Orthogonal Time-of-Flight Mass Spectrometer:  Sequencing Peptides from an “In-Solution” Protein Digest

Stone, Earle G.; Gillig, Kent J.; Ruotolo, Brandon T.; Führer, Katrin; Gonin, Marc; Schultz, and Albert; Russell, David H.

doi:10.1021/ac001430a

Cited by 83 publications

(57 citation statements)

References 34 publications

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“…Russell's group has shown SID to be a simple, yet effective method of activating ions in ion mobility-orthogonal time-of-flight instruments [82][83][84]. The advantage of these instruments is that complex proteomic samples can be separated in the gas phase by ion mobility followed by comparatively faster MS and tandem MS analyses as species exit the mobility drift cell.…”

Section: The Role Of Sid In Developing the Mobile Proton Model And Elmentioning

confidence: 99%

Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes

Wysocki

Joyce

Jones

et al. 2008

J. Am. Soc. Mass Spectrom.

130

138

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This article provides a perspective on collisions of ions with surfaces, including surfaceinduced dissociation (SID) and reactive ion scattering spectrometry (RISS). The content is organized into sections on surface-induced dissociation of small ions, surface characterization of organic thin films by collision of well-characterized ions into surfaces, the use of SID to probe peptide fragmentation, and the dissociation of large non-covalent complexes by SID. Examples are given from the literature with a focus on experiments from the authors' laboratory. The article is not a comprehensive review but is designed to provide the reader with an overview of the types of results possible by collisions of ions into surfaces. (J Am Soc Mass Spectrom 2008, 19, 190 -208) © 2008 American Society for Mass Spectrometry T andem mass spectrometry (MS/MS) is an essential tool for elucidating ion structure. The MS/MS experiment involves mass selection of a precursor ion followed by ion activation and subsequent dissociation. The ion activation step is commonly accomplished via collision-induced dissociation (CID) in which the initial kinetic energy of a projectile ion is converted into internal energy through inelastic collisions with a neutral gas. Several alternative activation methods have been used in tandem mass spectrometry, one of which is surfaceinduced dissociation (SID). SID is analogous to CID, except that a surface replaces the neutral gas as the collision target. A typical ion-surface collision event is illustrated in Figure 1.The incorporation of a surface into a mass spectrometer for ion activation was pioneered in the laboratory of R. Graham Cooks in the mid-1970s and early 1980s [1][2][3]. Since that time, collisions of lowenergy (eV) organic ions with surfaces within the tandem mass spectrometer have been valuable for analyzing surface composition, characterizing reactions between organic projectile ions and surface adsorbates, chemically modifying surfaces, and determining projectile ion structure. A major motivation for development of SID is that energy transfer to ionic projectiles can be improved by increasing the mass of the collision target. The total available energy for transfer into the internal modes of the projectile ion is defined by the center-of-mass energy (E COM ) described by eq 1:where E LAB is the laboratory collision energy and M ION and M N are the masses of the projectile ion and neutral, respectively. Energy transfer in CID is limited by the mass of the collision partner, typically inert gases such as helium, argon, or xenon. In SID, if one assumes that the surface is an infinitely large collision partner, E COM becomes independent of mass and approaches the laboratory collision energy. The assumption that the entire surface can be viewed as the collision partner is not always valid, however, and there are instances where the mass of the terminal groups on the surface influence the amount of energy transfer [4,5]. Nonetheless, the use of a massive surface target should, in theory, provide ...

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Section: The Role Of Sid In Developing the Mobile Proton Model And Elmentioning

confidence: 99%

Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes

Wysocki

Joyce

Jones

et al. 2008

J. Am. Soc. Mass Spectrom.

130

138

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“…The mass spectrometer was externally calibrated using two-point calibration on C 60 (M r ϭ 720) and C 70 (M r ϭ 840) radical cations (Sigma) [5]. The measurements of collision cross sections were externally calibrated with [M ϩ H] ϩ ions of bradykinin (⍀ meas ϭ 245 Å 2 and substance P (⍀ meas ϭ 292 Å 2 [28]. The 2D IM-MS data were acquired and processed by using custom software (Ionwerks, Inc., Houston, TX, USA).…”

Section: Maldi-im-tofmsmentioning

confidence: 99%

The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Tao

Dahl

Pérez

et al. 2009

J. Am. Soc. Mass Spectrom.

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Molecular dynamics (MD) is an essential tool for correlating collision cross-section data determined by ion mobility spectrometry (IMS) with candidate (calculated) structures. Conventional methods used for ion structure determination rely on comparing the measured cross-sections with the calculated collision cross-section for the lowest energy structure(s) taken from a large pool of candidate structures generated through multiple tiers of simulated annealing. We are developing methods to evaluate candidate structures from an ensemble of many conformations rather than the lowest energy structure. Here, we describe computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH 2 -Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI, and compare the structures of MIFAGIK derivatives to test the 'sensitivity' of the cluster analysis method. Cluster analysis suggests that [MIFAGIK ϩ H] ϩ ions formed by MALDI have a predominantly turn structure even though the low-energy ions prefer partial helical conformers. T he emphasis of mass spectrometry based biological chemistry is shifting from compound identification to structural studies of large biomolecules and biomolecule complexes [1][2][3][4][5][6][7], including membrane proteins [8]. The next phase of 'omics' related research must be aimed at obtaining and predicting additional dimensions of information, such as secondary, tertiary, and quaternary structures and linkage-specific information for glycans. Although sophisticated structural characterization tools, such as NMR and XRD, provide the most information, high throughput analysis of complex biological mixtures obtained by using these techniques is an underdeveloped technology. On the other hand, IMS is much more than a separation device, the structural information derived from 2D conformation space afforded by IM-MS is potentially well-suited to both high throughput applications and complex biological samples.A number of laboratories have focused their research on developing IM-MS for biophysical studies of peptides and proteins [9 -14]. In previous work, we showed that a large proportion of singly charged peptide ions (formed by MALDI) appear on a single trendline in 2D mobility-m/z plots, i.e., plots of arrival-time distribution (ATD) or ion-neutral collision cross-section (⍀) versus m/z [15]; however, a few ion signals deviate (Ͼ3% to ϳ20%) from the expected trendline and nonpeptidic ion signals appear on separate, compound class specific trendlines [14,15]. Ruotolo et al. showed that gas-phase [M ϩ H] ϩ ions of LLGNVLVVVLAR (derived from bovine hemoglobin) prefer extended (helical) structure(s) resulting in a larger collision cross-section than random coil structures having the same or similar m/z values [12,13], while some post-translationally modified (PTM) peptide ions (phosphopeptides) tend to pack more tightly than the unmodified protonated peptide ions owing to intra-molecular charge-solvation and/or formation of salt-...

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“…For most protein complex ions, we have observed that the signals for a charge state series corresponding to a monodisperse protein assembly display a good correlation (R 2 4 0.99) to a linear relationship between drift time and m/z allowing for polydisperse samples to be identified readily 30 . In addition, plotting data in a format similar to Figure 2b often highlights the presence of post-mobility cell fragmentation 31,32 . If protein complexes are separated by ion mobility as intact assemblies and are activated before mass measurement, any fragmentation products generated will appear at the same drift time as the original parent ion.…”

Section: Introductionmentioning

confidence: 99%

Ion mobility–mass spectrometry analysis of large protein complexes

et al. 2008

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Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry. INTRODUCTIONLarge-scale interaction maps suggest a complex interplay of proteins within a myriad of functional assemblies 1,2 . A critical step in assigning functions to these assemblies is to determine their structure 3 . This goal is challenging, as many of these assemblies exist in low-copy numbers within cells, are frequently heterogeneous and may interact only transiently. Consequently, structural information for many protein complexes is not readily accessible by using the classical tools of structural biology (e.g., X-ray crystallography, nuclear magnetic resonance spectroscopy). New approaches are being developed that involve integrating data from a number of lower-resolution experimental methods and by combining distance and interaction restraints from these methods with homology modeling, architectural or even atomic models are being generated 4 . These restraints can be derived from a variety of experimental measurements including MS of intact complexes, chemical cross-linking, fluorescence resonance energy transfer, small angle X-ray scattering, and analytical ultracentrifugation 5,6 . One very recent addition to this series of biophysical tools is ion mobility separation coupled to mass spectrometry (IM-MS). IM is an established technique for studying shape and conformation in small molecules and individual proteins in the gas phase 7-10 but has only recently been applied to intact protein complexes 11,12 . When IM is coupled with MS, mass and consequently subunit composition can be determined simultaneously with the overall topology of protein complexes 10,12,13 .IM-MS analysis is performed by first ionizing the protein complex of interest. In our experiments, nano-electrospray ionization is used, typically requiring careful preparation procedures for most protein complexes. These procedures, as well as general practical aspects of sample preparation, are detailed in a protocol by Hernández and Robinson 14 . Although they are not discussed in detail here, knowledge of the materials and protocol steps described in that work are critical to the success of the protocol described below.After ionization, ions are injected into a region containing neutral gas at a controlled pressure (e.g., 0.5 mBar of nitrogen gas). Under the influence of a relatively weak electric field, injected ions undergo IM separation [7]...

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Surface-Induced Dissociation on a MALDI-Ion Mobility-Orthogonal Time-of-Flight Mass Spectrometer: Sequencing Peptides from an “In-Solution” Protein Digest

Cited by 83 publications

References 34 publications

Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes

Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes

The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Ion mobility–mass spectrometry analysis of large protein complexes

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