Ion mobility–mass spectrometry analysis of large protein complexes

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.

[1]  Brandon T Ruotolo,et al.  Peak capacity of ion mobility mass spectrometry: the utility of varying drift gas polarizability for the separation of tryptic peptides. , 2004, Journal of mass spectrometry : JMS.

[2]  M. Jarrold,et al.  Helices and Sheets in vacuo. , 2007, Physical chemistry chemical physics : PCCP.

[3]  C. Robinson,et al.  Structural Insight into the Mechanism of Activation of the Toll Receptor by the Dimeric Ligand Spätzle* , 2008, Journal of Biological Chemistry.

[4]  M. Jarrold,et al.  High-resolution ion mobility measurements , 1997 .

[5]  Min Zhao,et al.  Application of direct current electric fields to cells and tissues in vitro and modulation of wound electric field in vivo , 2006, Nature Protocols.

[6]  B. Ruotolo,et al.  Ion mobility-mass spectrometry applied to cyclic peptide analysis: Conformational preferences of gramicidin S and linear analogs in the gas phase , 2004, Journal of the American Society for Mass Spectrometry.

[7]  A. Shvartsburg,et al.  An exact hard-spheres scattering model for the mobilities of polyatomic ions , 1996 .

[8]  David van der Spoel,et al.  Protein structures under electrospray conditions. , 2007, Biochemistry.

[9]  C. Robinson,et al.  Aspects of native proteins are retained in vacuum. , 2006, Current opinion in chemical biology.

[10]  B. Chait,et al.  Determining the architectures of macromolecular assemblies , 2007, Nature.

[11]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[12]  S. Kaufman,et al.  Analysis of a 3.6-MDa hexagonal bilayer hemoglobin from Lumbricus terrestris using a gas-phase electrophoretic mobility molecular analyzer. , 1998, Analytical biochemistry.

[13]  B. Ruotolo,et al.  Surface-induced dissociation on a MALDI-ion mobility-orthogonal time-of-flight mass spectrometer: sequencing peptides from an "in-solution" protein digest. , 2001, Analytical chemistry.

[14]  D. Clemmer,et al.  Structural Transitions of Electrosprayed Ubiquitin Ions Stored in an Ion Trap over 10 ms to 30 s , 2002 .

[15]  J P Reilly,et al.  Gas-phase separations of protease digests , 1998, Journal of the American Society for Mass Spectrometry.

[16]  C. Robinson,et al.  Mass measurements of increased accuracy resolve heterogeneous populations of intact ribosomes. , 2006, Journal of the American Chemical Society.

[17]  M. Bowers,et al.  Structures and energies of small carbon clusters: what experiment and theory have to say about C+8, C+9 and C+10 , 1994 .

[18]  C. Robinson,et al.  Thermal dissociation of multimeric protein complexes by using nanoelectrospray mass spectrometry. , 2003, Analytical chemistry.

[19]  R. Bateman,et al.  Applications of a travelling wave-based radio-frequency-only stacked ring ion guide. , 2004, Rapid communications in mass spectrometry : RCM.

[20]  Christine Slingsby,et al.  Crystal structure and assembly of a eukaryotic small heat shock protein , 2001, Nature Structural Biology.

[21]  John A. McLean,et al.  Ion mobility–mass spectrometry: a new paradigm for proteomics , 2005 .

[22]  T. Wyttenbach,et al.  Conformation of Macromolecules in the Gas Phase: Use of Matrix-Assisted Laser Desorption Methods in Ion Chromatography , 1995, Science.

[23]  A. Heck,et al.  Optimizing macromolecular tandem mass spectrometry of large non-covalent complexes using heavy collision gases , 2007 .

[24]  T. Earnest,et al.  From words to literature in structural proteomics , 2003, Nature.

[25]  V. Kickhoefer,et al.  Sizing large proteins and protein complexes by electrospray ionization mass spectrometry and ion mobility , 2007, Journal of the American Society for Mass Spectrometry.

[26]  George C. Schatz,et al.  Structural Information from Ion Mobility Measurements: Effects of the Long-Range Potential , 1996 .

[27]  A. Sali,et al.  The molecular sociology of the cell , 2007, Nature.

[28]  M. Ratner,et al.  Application of evolutionary algorithm methods to polypeptide folding: comparison with experimental results for unsolvated Ac-(Ala-Gly-Gly)5-LysH+. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Carol V. Robinson,et al.  Characterising electrosprayed biomolecules using tandem-MS—the noncovalent GroEL chaperonin assembly , 2004 .

[30]  M. Bowers,et al.  Gas-Phase Conformations of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling , 2003 .

[31]  C. Robinson,et al.  Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry , 2007, Nature Protocols.

[32]  C. Robinson,et al.  Mass spectrometry of macromolecular assemblies: preservation and dissociation. , 2006, Current opinion in structural biology.

[33]  Martin F. Jarrold,et al.  Structural Information from Ion Mobility Measurements: Effects of the Long-Range Potential , 1996 .

[34]  C. Robinson,et al.  Tandem mass spectrometry defines the stoichiometry and quaternary structural arrangement of tryptophan molecules in the multiprotein complex TRAP. , 2004, Journal of the American Chemical Society.

[35]  M. Ratner,et al.  THERMAL UNFOLDING OF UNSOLVATED CYTOCHROME C : EXPERIMENT AND MOLECULAR DYNAMICS SIMULATIONS , 1999 .

[36]  The initial steps in the hydration of unsolvated peptides: water molecule adsorption on alanine-based helices and globules. , 2002, Journal of the American Chemical Society.

[37]  B. Ruotolo,et al.  Gas-Phase Conformations of Proteolytically Derived Protein Fragments: Influence of Solvent on Peptide Conformation , 2004 .

[38]  A. Heck,et al.  The effect of the source pressure on the abundance of ions of noncovalent protein assemblies in an electrospray ionization orthogonal time-of-flight instrument. , 2001, Rapid communications in mass spectrometry : RCM.

[39]  Edward A. Mason,et al.  Transport Properties of Ions in Gases: MASON:TRANSPORT PROPERTIES O-BK , 2005 .

[40]  C. Robinson,et al.  Protein complexes in the gas phase: technology for structural genomics and proteomics. , 2007, Chemical reviews.

[41]  A. Heck,et al.  Native protein mass spectrometry: from intact oligomers to functional machineries. , 2004, Current opinion in chemical biology.

[42]  Michael T Bowers,et al.  Intermolecular interactions in biomolecular systems examined by mass spectrometry. , 2007, Annual review of physical chemistry.

[43]  C. Robinson,et al.  Drug binding revealed by tandem mass spectrometry of a protein-micelle complex. , 2004, Journal of the American Chemical Society.

[44]  M. Bowers.  Cluster ions: carbon, met-cars, and .sigma.-bond activation , 1994 .

[45]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[46]  M. Jarrold,et al.  The energy landscape of unsolvated peptides: helix formation and cold denaturation in Ac-A4G7A4 + H+. , 2002, Journal of the American Chemical Society.

[47]  S. Kaufman,et al.  Electrospray ionization mass spectrometry and ion mobility analysis of the 20S proteasome complex , 2005, Journal of the American Society for Mass Spectrometry.

[48]  S. Valentine,et al.  H/D Exchange Levels of Shape-Resolved Cytochrome c Conformers in the Gas Phase , 1997 .

[49]  C. Robinson,et al.  Subunit Exchange of Multimeric Protein Complexes , 2002, The Journal of Biological Chemistry.

[50]  E. W. McDaniel,et al.  Transport Properties of Ions in Gases , 1988 .

[51]  David H. Russell,et al.  Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry , 2002 .

[52]  J P Reilly,et al.  Three-dimensional ion mobility/TOFMS analysis of electrosprayed biomolecules. , 1998, Analytical chemistry.

[53]  D. Clemmer,et al.  Mobility labeling for parallel CID of ion mixtures. , 2000, Analytical chemistry.

[54]  D. Clemmer,et al.  Gas-phase separations of electrosprayed peptide libraries. , 1999, Analytical chemistry.

[55]  D. Clemmer,et al.  Evidence for unfolding and refolding of gas-phase cytochrome c ions in a Paul trap , 2005, Journal of the American Society for Mass Spectrometry.

[56]  D. Clemmer,et al.  Monitoring Structural Changes of Proteins in an Ion Trap over ∼10−200 ms: Unfolding Transitions in Cytochrome c Ions , 2001 .

[57]  C. Robinson,et al.  Evidence for Macromolecular Protein Rings in the Absence of Bulk Water , 2005, Science.

[58]  M. Bowers,et al.  The structures of small iron-carbon cluster anions. Linear to planar to three-dimensional , 1994 .

[59]  Albert J R Heck,et al.  Investigation of intact protein complexes by mass spectrometry. , 2004, Mass spectrometry reviews.

[60]  Michael T. Bowers,et al.  ON THE QUESTION OF SALT BRIDGES OF CATIONIZED AMINO ACIDS IN THE GAS PHASE: GLYCINE AND ARGININE , 1999 .

[61]  P Zöllner,et al.  Charge-reduced nano electrospray ionization combined with differential mobility analysis of peptides, proteins, glycoproteins, noncovalent protein complexes and viruses. , 2001, Journal of mass spectrometry : JMS.

[62]  C. Robinson,et al.  Ion mobility-mass spectrometry reveals long-lived, unfolded intermediates in the dissociation of protein complexes. , 2007, Angewandte Chemie.

[63]  B. Ruotolo,et al.  Peak capacity of ion mobility mass spectrometry: separation of peptides in helium buffer gas. , 2002, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[64]  Jonathan P. Williams,et al.  Coupling desorption electrospray ionisation and neutral desorption/extractive electrospray ionisation with a travelling-wave based ion mobility mass spectrometer for the analysis of drugs. , 2008, Rapid communications in mass spectrometry : RCM.

[65]  C. Robinson,et al.  A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. , 2002, Analytical chemistry.

[66]  Michal Sharon,et al.  Subunit architecture of intact protein complexes from mass spectrometry and homology modeling. , 2008, Accounts of chemical research.

[67]  K. Thalassinos,et al.  An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument , 2007 .

[68]  M. Jarrold,et al.  Peptides and proteins in the vapor phase. , 2000, Annual review of physical chemistry.

[69]  D. Clemmer,et al.  Anhydrous protein ions. , 1999, Chemical reviews.