Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry

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

doi:10.1016/s1387-3806(01)00583-8

Cited by 41 publications

(44 citation statements)

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“…IM-MS data are inherently three-dimensional, consisting of mass, drift time and intensity (relative abundance) data for all the ions observed [23][24][25][26] . A typical data set is illustrated in Figure 2, which shows a mass spectrum (a), an IM-MS contour plot (b) and a total integrated IM spectrum (c) for a series of ions corresponding to the small heat shock protein from wheat, TaHSP16.9.…”

Section: Introductionmentioning

confidence: 99%

“…The numbers indicated correspond to the IM resolution necessary to resolve ring and collapsed structures along the corresponding trend. Above these lines the structures are also resolved at the indicated value of R. Generally, plots of drift time versus m/z, as shown in Figure 2b, reveal trends in the data that can be indicative of either the charge state or molecular class of the ions observed [23][24][25][26] . 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 .…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ion mobility–mass spectrometry analysis of large protein complexes

et al. 2008

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“…[27][28][29][30][31][32][33][34][35] Recent works dealing with the use of the technique to the identification and structural analysis of various compounds can be mentioned. [36][37][38][39][40][41][42][43][44][45][46][47][48] Coupling of MALDI with liquid chromatography, capillary electrophoresis (CE) and gel chromatography is a way to extend its applicability. 32,[49][50][51][52][53][54][55][56][57][58] The possibility to attain the sensitivity of physical limits (a few atoms or molecules) by laser-assisted reflectron TOF-MS has been stated.…”

Section: An Overview Of Analytical Applications Of Tof-ms Analyzersmentioning

confidence: 99%

An Overview of Analytical Applications of Time of Flight-Mass Spectrometric (TOF-MS) Analyzers and an Inductively Coupled Plasma-TOF-MS Technique

Balcerzak

2003

ANAL. SCI.

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“…ncorporation of post-ionization, gas-phase separations with matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) represents a significant advance in bioanalytical research, especially studies of proteomics [1,2] and imaging mass spectrometry [3,4]. Ion mobility-mass spectrometry (IM-MS) offers several advantages over traditional MS, including increased dynamic range [5], discrimination against chemical noise [5,6], the ability to separate geometric isomers [7], and separation of ions based on composition and charge state [1,8]. The cumulative result is highly sensitive, information-rich datasets that are unique to IM-MS techniques.…”

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confidence: 99%

“…Ion mobility-mass spectrometry (IM-MS) offers several advantages over traditional MS, including increased dynamic range [5], discrimination against chemical noise [5,6], the ability to separate geometric isomers [7], and separation of ions based on composition and charge state [1,8]. The cumulative result is highly sensitive, information-rich datasets that are unique to IM-MS techniques.…”

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A novel approach to collision-induced dissociation (CID) for ion mobility-mass spectrometry experiments

Becker

Fernandez-Lima

Gillig

et al. 2009

J. Am. Soc. Mass Spectrom.

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Collision induced dissociation (CID) combined with matrix assisted laser desorption ionizationion mobility-mass spectrometry (MALDI-IM-MS) is described. In this approach, peptide ions are separated on the basis of mobility in a 15 cm drift cell. Following mobility separation, the ions exit the drift cell and enter a 5 cm vacuum interface with a high field region (up to 1000 V/cm) to undergo collisional activation. Ion transmission and ion kinetic energies in the interface are theoretically evaluated accounting for the pressure gradient, interface dimensions, and electric fields. Using this CID technique, we have successfully fragmented and sequenced a number of model peptide ions as well as peptide ions obtained by a tryptic digest. This instrument configuration allows for the simultaneous determination of peptide mass, peptide-ion sequence, and collision-cross section of MALDI-generated ions, providing information critical to the identification of unknown components in complex proteomic samples. ncorporation of post-ionization, gas-phase separations with matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) represents a significant advance in bioanalytical research, especially studies of proteomics [1,2] and imaging mass spectrometry [3,4]. Ion mobility-mass spectrometry (IM-MS) offers several advantages over traditional MS, including increased dynamic range [5], discrimination against chemical noise [5,6], the ability to separate geometric isomers [7], and separation of ions based on composition and charge state [1,8]. The cumulative result is highly sensitive, information-rich datasets that are unique to IM-MS techniques. For example, a single IM-MS separation can provide peptide molecular weights (peptide mass-fingerprint), ion-neutral collision cross-sections, and residue specific identification of post-translational modifications (PTMs) [1,2].When coupled to fragment ion analysis for determination of primary structure, IM-MS adds a "per sample" throughput advantage over traditional MALDI-MS/MS techniques. That is, the ion mobility spectrometry (IMS) separation provides a temporal correlation between the precursor and product ions, circumventing the need to pre-select each precursor mass of interest [1,9,10]. A number of fragmentation techniques have been previously developed with IM-MS; including photodissociation [11], surface-induced dissociation (SID) [12,13], and collision-induced dissociation (CID) [10,14]. Among the available fragmentation techniques, CID is the most widely used owing to the robust nature of the experiment and the high level of sequence coverage obtained. CID is also readily adapted to IMS experiments owing to the presence of a buffer gas at elevated pressures in the IMS cell. Clemmer and coworkers have demonstrated two approaches to CID fragmentation of ions as they exit the mobility cell: (1) by applying a high electric field between the drift tube and mass analyzer [10], and (2) a split-field drift cell design [14]. Additionally, Waters Corpora...

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Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry

Cited by 41 publications

References 30 publications

Ion mobility–mass spectrometry analysis of large protein complexes

Ion mobility–mass spectrometry analysis of large protein complexes

An Overview of Analytical Applications of Time of Flight-Mass Spectrometric (TOF-MS) Analyzers and an Inductively Coupled Plasma-TOF-MS Technique

A novel approach to collision-induced dissociation (CID) for ion mobility-mass spectrometry experiments

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