Electron transfer dissociation mass spectrometry in proteomics

Mass spectrometry has rapidly evolved to become the platform of choice for proteomic analysis. While CID remains the major fragmentation method for peptide sequencing, electron transfer dissociation (ETD) is emerging as a complementary method for the characterization of peptides and post-translational modifications (PTMs). Here, we review the evolution of ETD and some of its newer applications including characterization of PTMs, non-tryptic peptides and intact proteins. We will also discuss some of the unique features of ETD such as its complementarity with CID and the use of alternating CID/ETD along with issues pertaining to analysis of ETD data. The potential of ETD for applications such as multiple reaction monitoring and proteogenomics in the future will also be discussed.     

Electron transfer dissociation of peptides generated by microwave D-cleavage digestion of proteins

The nonenzymatic digestion of proteins by microwave D-cleavage is an effective technique for site-specific cleavage at aspartic acid (D). This specific cleavage C-terminal to D residues leads to inherently large peptides (15-25 amino acids) that are usually relatively highly charged (above +3) when ionized by electrospray ionization (ESI) due to the presence of several basic amino acids within their sequences. It is well-documented that highly charged peptide ions generated by ESI are well-suited for electron transfer dissociation (ETD), which produces c- and z-type fragment ions via gas-phase ion/ion reactions. In this paper, we describe the sequence analysis by ETD tandem mass spectrometry (MS/MS) of multiply charged peptides generated by microwave D-cleavage of several standard proteins. Results from ETD measurements are directly compared to CID MS/MS of the same multiply charged precursor ions. Our results demonstrate that the nonenzymatic microwave D-cleavage technique is a rapid (<6 min) and specific alternative to enzymatic cleavage with Lys-C or Asp-N to produce highly charged peptides that are amenable to informative ETD.     

Hybridization of pulsed-Q dissociation and collision-activated dissociation in linear ion trap mass spectrometer for iTRAQ quantitation

Coupling of multiplex isobaric tags for relative and absolute quantitation (iTRAQ) to a sensitive linear ion trap (LTQ) mass spectrometer (MS) is a challenging, but highly promising approach for quantitative high-throughput proteomic profiling. Integration of the advantages of pulsed-Q dissociation (PQD) and collision-activated dissociation (CAD) fragmentation methods into a PQD-CAD hybrid mode, together with PQD optimization and data manipulation with a bioinformatics algorithm, resulted in a robust, sensitive and accurate iTRAQ quantitative proteomic workflow. The workflow was superior to the default PQD setting when profiling the proteome of a gastric cancer cell line, SNU5. Taken together, we established an optimized PQD-CAD hybrid workflow in LTQ-MS for iTRAQ quantitative proteomic profiling that may have wide applications in biological and biomedical research.     

Improved proteome coverage by using iTRAQ labelling and peptide OFFGEL fractionation

Background  

The development of mass spectrometric techniques and fractionation methods now allows the investigation of very complex protein mixtures ranging from subcellular structures to tissues. Nevertheless, this work is particularly difficult due to the wide dynamic range of protein concentration in eukaryotic tissues. In this paper, we present a shotgun method whereby the peptides are fractionated using OFFGEL electrophoresis after iTRAQ labelling.     

Electron microscopic studies of viruses labeled with magnetite

We were able to develop a method with which to successfully and specifically detect virus particles under the electron microscope by using magnetite. This method was devised on the principle that magnetite-labeled antibody or magnetite coupled with protein A selectively bind virus or antibody-treated virus particles on the electron microscope grid by the action of an electromagnet. Another advantage characterizing the technique is the possibility of detection of a small number of virus particles. This is done through a process of concentration and purification of the reaction complexes trapped rigidly by magnetic force.     

Electron transfer in quinoproteins

Soluble quinoprotein dehydrogenases oxidize a wide range of sugar, alcohol, amine, and aldehyde substrates. The physiological electron acceptors for these enzymes are not pyridine nucleotides but are other soluble redox proteins. This makes these enzymes and their electron acceptors excellent systems with which to study mechanisms of long-range interprotein electron transfer reactions. The tryptophan tryptophylquinone (TTQ)-dependent methylamine dehydrogenase (MADH) transfers electrons to a blue copper protein, amicyanin. It has been possible to alter the rate of electron transfer by using different redox forms of MADH, varying reaction conditions, and performing site-directed mutagenesis on these proteins. From kinetic and thermodynamic analyses of the reaction rates, it was possible to determine whether a change in rate is due a change in Delta G(0), electronic coupling, reorganization energy or kinetic mechanism. Examples of each of these cases are discussed in the context of the known crystal structures of the electron transfer protein complexes. The pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase transfers electrons to a c-type cytochrome. Kinetic and thermodynamic analyses of this reaction indicated that this electron transfer reaction was conformationally coupled. Quinohemoproteins possess a quinone cofactor as well as one or more c-type hemes within the same protein. The structures of a PQQ-dependent quinohemoprotein alcohol dehydrogenase and a TTQ-dependent quinohemoprotein amine dehydrogenase are described with respect to their roles in intramolecular and intermolecular protein electron transfer reactions.     

Electron transfer in biology

Table VII presents a list of the topics I have discussed. Underlying biological electron transfer which employs metal ions overwhelmingly is the intimacy of the interaction between metal ion properties and protein properties. Attacking the problems is attacking a cornerstone of life - bioenergetics. It is appropriate that this is the Heyrovsky Memorial Lecture since he devised the polarograph which is a device for coupling electrolytes (protons) in solution with electrons in metal atoms.     

Electron transfer mechanisms in electron transfer chains

Mechanisms responsible for the transfer of electrons through mitochondrial and photosynthetic electron transport chains are considered. Mechanisms considered include diffusion, ligand-mediated transfer, tunneling and semiconduction. Perturbations which create satisfactory conditions for electron transfer are also considered. There is a brief discussion of the electron transport chain environment and constituents. Sponsored in part by a grant from the Department of Health, Education, and Welfare (Public Health Service Grant Number 5 R01 RL00480)     

Discovery- and target-based protein quantification using iTRAQ and pulsed Q collision induced dissociation (PQD)

Pulsed Q collision-induced dissociation (PQD) was developed in part to facilitate detection of low-mass reporter ions using labeling reagents (e.g. iTRAQ) on LTQ platforms. It has generally been recognized that the scan speed and sensitivity of an LTQ are superior than those of an Orbitrap using the higher-energy collisional dissociation (HCD). However, the use of PQD in quantitative proteomics is limited, primarily due to the meager reproducibility of reporter ion ratios. Optimizations of PQD for iTRAQ quantification using LTQ have been reported, but a universally applicable strategy for quantifying the less abundant proteins has not been fully established. Adjustments of the AGC target, μscan, or scan speed offer only incremental improvements in reproducibility. From our experience, however, satisfactory coefficients of variation (CVs) of reporter ion ratios were difficult to achieve using the discovery-based approach. As an alternative, we implemented a target-based approach that obviates data dependency to allow repetitive data acquisitions across chromatographic peaks. Such a strategy generates enough data points for more reliable quantification. Using cAMP treatment in S49 cell lysates and this target-based approach, we were able to validate differentially expressed proteins, which were initially identified as potential candidates using the discovery-based PQD. The target-based strategy also yielded results comparable to those obtained from HCD in an Orbitrap. Our findings should aid LTQ users who desire to explore iTRAQ quantitative proteomics but have limited access to the more costly Orbitrap or other instruments.     

Higher-energy C-trap dissociation for peptide modification analysis

Peptide sequencing is the basis of mass spectrometry-driven proteomics. Here we show that in the linear ion trap-orbitrap mass spectrometer (LTQ Orbitrap) peptide ions can be efficiently fragmented by high-accuracy and full-mass-range tandem mass spectrometry (MS/MS) via higher-energy C-trap dissociation (HCD). Immonium ions generated via HCD pinpoint modifications such as phosphotyrosine with very high confidence. Additionally we show that an added octopole collision cell facilitates de novo sequencing.     

Electron capture dissociation in the analysis of protein phosphorylation

Protein phosphorylation is a widespread and important post-translational modification. Despite recent advances in phosphoproteomic methods, phosphopeptide identification and site localization remain challenging. Electron capture dissociation has inherent advantages for phosphorylation analysis. The use of electron capture dissociation in this area to date is reviewed and future prospects are outlined.     

Electron microscopic localization of cytoplasmic myosin with ferritin- labeled antibodies

We localized myosin in vertebrate nonmuscle cells by electron microscopy using purified antibodies coupled with ferritin. Native and formaldehyde-fixed filaments of purified platelet myosin filaments each consisting of approximately 30 myosin molecules bound an equivalent number of ferritin-antimyosin conjugates. In preparations of crude platelet actomyosin, the ferritin-antimyosin bound exclusively to similar short, 10-15 nm wide filaments. In both cases, binding of the ferritin-antimyosin to the myosin filaments was blocked by preincubation with unlabeled antimyosin. With indirect fluorescent antibody staining at the light microscope level, we found that the ferritin-antimyosin and unlabeled antimyosin stained HeLa cells identically, with the antibodies concentrated in 0.5-microns spots along stress fibers. By electron microscopy, we found that the concentration of ferritin-antimyosin in the dense regions of stress fibers was five to six times that in the intervening less dense regions, 20 times that in the cytoplasmic matrix, and 100 times that in the nucleus. These concentration differences may account for the light microscope antibody staining pattern of spread interphase cells. Some, but certainly not all, of the ferritin-antimyosin was associated with 10-15-nm filaments. In mouse intestinal epithelial cells, ferritin- antimyosin was located almost exclusively in the terminal web. In isolated brush borders exposed to 5 mM MgCl2, ferritin-antimyosin was also concentrated in the terminal web associated with 10-15-nm filaments.     

Electron transfer in ruthenium-modified proteins

Photochemical techniques have been used to measure the kinetics of intramolecular electron transfer in Ru(bpy)₂(im)(His)²⁺-modified (bpy = 2,2-bipyridine; im = imidazole) cytochromec and azurin. A driving-force study with the His33 derivatives of cytochromec indicates that the reorganization energy () for Fe²⁺Ru³⁺ ET reactions is 0.8 eV. Reductions of the ferriheme by either an excited complex,^*Ru²⁺, or a reduced complex, Ru⁺, are anomalously fast and may involve formation of an electronically excited ferroheme. The distance dependence of Fe²⁺Ru³⁺ and Cu⁺Ru³⁺ electron transfer in 12 different Ru-modified cytochromes and azurins has been analyzed using a tunneling-pathway model. The ET rates in 10 of the 12 systems exhibit an exponential dependence on metal-metal separation (decay constant of 1.06 å^–1) that is consistent with predictions of the pathway model.     

Electron transfer reactions in methanogens

Abstract Methanogenic bacteria comprise a specialized group of obligately anaerobic microorganisms able to reduce a limited number of substrates to CH₄. The intermediates involved in this reduction process remain bound to a series of typical C₁-carriers. Reducing equivalents are either obtained from the oxidation of H₂ or from oxidation of carbon substrates to CO₂. Electron transfer reactions thus constitute the very essence of the process of methanogenesis.
In recent years much progress has been made in the elucidation of the special metabolic pathways and the nature of the C₁-carriers involved in methanogenic bacteria. The energy generated at the oxidoreduction reactions, notably at the methylreductase step, is conserved by ATP synthesis. The energy is used for cell carbon synthesis and, in catalytic amounts, for the reductive activation of some methanogenic enzymes. Before the condensing reaction resulting in the formation of acetyl-CoA takes place, 2 C₁-units are reduced or oxidized depending on the substrate to a carbonyl and a -CH₃ group. Formation of the latter proceeds via the methanogenic route. Intermediary cell carbon synthesis starting from acetyl-CoA involves reductive carboxylations and oxidoreductions by the participation of the enzymes of the tricarboxylic acid cycle.     

Electron transfer by diflavin reductases

Diflavin reductases are enzymes which emerged as a gene fusion of ferredoxin (flavodoxin) reductase and flavodoxin. The enzymes of this family tightly bind two flavin cofactors, FAD and FMN, and catalyze transfer of the reducing equivalents from the two-electron donor NADPH to a variety of one-electron acceptors. Cytochrome P450 reductase (P450R), a flavoprotein subunit of sulfite reductase (SiR), and flavoprotein domains of naturally occurring flavocytochrome fusion enzymes like nitric oxide synthases (NOS) and the fatty acid hydroxylase from Bacillus megaterium are some of the enzymes of this family. In this review the results of the last decade of research are summarized, and some earlier results are reevaluated as well. The kinetic mechanism of cytochrome c reduction is analyzed in light of other results on flavoprotein interactions with nucleotides and cytochromes. The roles of the binding sites of the isoalloxazine rings of the flavin cofactors and conformational changes of the protein in electron transfer are discussed. It is proposed that minor conformational changes during catalysis can potentiate properties of the redox centers during the catalytic turnover. A function of the aromatic residue that shields the isoalloxazine ring of the FAD is also proposed.     

Electron transfer in photosystem II

The picture presently emerging from studies on the mechanism of photosystem II electron transport is discussed. The reactions involved in excitation trapping, charge separation and stabilization of the charge pair in the reaction center, followed by the reactions with the substrates, plastoquinone reduction and water oxidation, are described successively. Finally, a brief discussion on photosystem II heterogeneity is presented.     

Electron transfer in nitrogenase catalysis

Nitrogenase is a two-component enzyme that catalyzes the nucleotide-dependent reduction of N2 to 2NH3. This process involves three redox-active metal-containing cofactors including a [4Fe-4S] cluster, an eight-iron P cluster and a seven-iron plus molybdenum FeMo-cofactor, the site of substrate reduction. A deficit-spending model for electron transfer has recently been proposed that incorporates protein conformational gating that favors uni-directional electron transfer among the metalloclusters for the activation of the substrate-binding site. Also reviewed is a proposal that each of the metal clusters cycles through only two redox states of the metal-sulfur core as the system accumulates the multiple electrons required for substrate binding and reduction. In particular, it was suggested that as FeMo-cofactor acquires the four electrons necessary for optimal binding of N2, each successive pair of electrons is stored as an Fe-H--Fe bridging hydride, with the FeMo-cofactor metal-ion core retaining its resting redox state. We here broaden the discussion of stable intermediates that might form when FeMo-cofactor receives an odd number of electrons.     

Electron transfer proteins/enzymes

The crystal structures of eight electron-carrier proteins, three electron-transfer enzymes and three intermolecular complexes, analyzed during the period of this review, are described. These studies have established the structures of two new metal redox clusters, helped to define the interactions between electron-transfer proteins, and illustrated possible paths for electron flow in these biological systems.