Sequential Collision-induced Dissociation Research Articles

Imaging and Structural Characterization of Phosphatidylcholine Isomers from Rat Brain Tissue Using Sequential Collision-Induced Dissociation/Electron-Induced Dissociation.

The chemical complexity of biological tissues creates challenges in the analysis of lipids via imaging mass spectrometry. The presence of isobaric and isomeric compounds introduces chemical noise that makes it difficult to unambiguously identify and accurately map the spatial distributions of these compounds. Electron-induced dissociation (EID) has previously been shown to profile phosphatidylcholine (PCs) sn-isomers directly from rat brain tissue in matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry. However, the acquisition of true pixel-by-pixel images, as opposed to regional profiling measurements, using EID is difficult due to low fragmentation efficiency and precursor ion signal dilution into multiple fragment ion channels, resulting in low sensitivity. In this work, we have developed a sequential collision-induced dissociation (CID)/EID method to visualize the distribution of sn-isomers in MALDI imaging mass spectrometry experiments. Briefly, CID is performed on sodium-adducted PCs, which results in facile loss of the phosphocholine headgroup. This ion is then subjected to an EID analysis. Since the lipid headgroup is removed prior to EID, a major fragmentation pathway common to EID ion activation is eliminated, resulting in a more sensitive analysis. This sequential CID/EID workflow generates sn-specific fragment ions allowing for the assignment of the sn-positions. Carbon-carbon double-bond (C═C) positions are also localized along the fatty acyl tails by the presence of a 2 Da shift pattern in the fragment ions arising from carbon-carbon bond cleavages. Moreover, the integration of the CID/EID method into MALDI imaging mass spectrometry enables the mapping of the absolute and relative distribution of sn-isomers at every pixel. The localized relative abundances of sn-isomers vary throughout brain substructures and likely reflect different biological functions and metabolism.

Gas‐Phase Models for the Nickel‐ and Palladium‐Catalyzed Deoxygenation of Fatty Acids

AbstractUsing fatty acids as renewable sources of biofuels requires deoxygenation. While a number of promising catalysts have been developed to achieve this, their operating mechanisms are poorly understood. Here, model molecular systems are studied in the gas phase using mass spectrometry experiments and DFT calculations. The coordinated metal complexes [(phen)M(O2CR)]+ (where phen=1,10‐phenanthroline; M=Ni or Pd; R=CnH2n+1, n≥2) are formed via electrospray ionization. Their collision‐induced dissociation (CID) initiates deoxygenation via loss of CO2 and [C,H2,O2]. The CID spectrum of the stearate complexes (R=C17H35) also shows a series of cations [(phen)M(R’)]+ (where R’ < C17) separated by 14 Da (CH2) corresponding to losses of C2H4‐C16H32 (cracking products). Sequential CID of [(phen)M(R’)]+ ultimately leads to [(phen)M(H)]+ and [(phen)M(CH3)]+, both of which react with volatile carboxylic acids, RCO2H, (acetic, propionic, and butyric) to reform the coordinated carboxylate complexes [(phen)M(O2CR)]+. In contrast, cracking products with longer carbon chains, [(phen)M(R)]+ (R>C2), were unreactive towards these carboxylic acids. DFT calculations are consistent with these results and reveal that the approach of the carboxylic acid to the “free” coordination site is blocked by agostic interactions for R > CH3.

Fullerene Radiolysis in Astrophysical Ice Analogs: A Mass Spectrometric Study of the Products.

The γ-radiolysis of fullerenes (C60 and C70) was performed to investigate the role of fullerenes as a carbon source in building organic molecules in astrophysical ice analog media. Mass spectrometric analyses and the sequential collision-induced dissociation processes enabled us to determine the plausible chemical structure of new products originated during γ-irradiation of fullerenes. The radiolytic products are grouped into six principal compound families. We assessed the relative yield, as percentage, for each new radiolytic compound, and designed the reaction schemes that lead to γ-irradiation products. The reactions start with the formation of primary radicals due to the radiolysis of solvents that react with the fullerenes' structures, forming fullerene radical adducts. The fate of these fullerene radical adducts depends on two factors: (i) the nature of radicals formed by irradiation of solvents and consequently by their ability to give secondary reactions, (ii) whether the onset of thermalization energy processes occurs or does not occur. Here, we present the results regarding the fragmentation processes that lead to functionalized carbonaceous chains characterized by lower molecular weight. We identify the chemical nature of functionalized chain products, propose the reaction schemes, and quantify their relative yields.

Structural Characterization of Intact Glycoconjugates by Tandem Mass Spectrometry Using Electron-Induced Dissociation.

Characterizing the structures of glycoconjungates is important because of glycan heterogeneity and structural complexity of aglycon. The presence of relatively weak glycosidic linkages leads to preferential cleavages that limit the acquisition of structural information under typical mass spectrometry dissociation conditions, such as collision-induced dissociation (CID) and infrared multiphoton dissociation. In this paper, we explored the dissociation behaviors of different members of glycoconjugates, including glycopeptides, glycoalkaloids, and glycolipids, under electron-induced dissociation (EID) conditions. Using CID spectra as references, we found that EID is not only a complementary method to CID, but also a method that can generate extensive fragment ions for the structural characterization of all intact glycoconjugates studied. Furthermore, isomeric ganglioside species can be differentiated, and the double bond location in the ceramide moiety of the gangliosides can be identified through the MS3 approach involving sequential CID and EID processes.

Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker.

Cross-linking combined with mass spectrometry (MS) has evolved as an alternative strategy in structural biology for characterizing three-dimensional structures of protein assemblies and for mapping protein-protein interactions. Here, we describe an integrated workflow for an automated identification of cross-linked products that is based on the use of a tandem mass spectrometry (MS/MS) cleavable cross-linker (containing a 1,3-bis-(4-oxo-butyl)-urea group, BuUrBu) generating characteristic doublet patterns upon fragmentation. We evaluate different fragmentation methods available on an Orbitrap Fusion mass spectrometer for three proteins and an E.coli cell lysate. An updated version of the dedicated software tool MeroX was employed for a fully automated identification of cross-links. The strength of our cleavable cross-linker is that characteristic patterns of the cross-linker as well as backbone fragments of the connected peptides are already observed at the MS/MS level, eliminating the need for conducting MS(3) or sequential CID (collision-induced dissociation)- and ETD (electron transfer dissociation)-MS/MS experiments. This makes our strategy applicable to a broad range of mass spectrometers with MS/MS capabilities. For purified proteins and protein complexes, our workflow using CID-MS/MS acquisition performs with high confidence, scoring cross-links at 0.5% false discovery rate (FDR). The cross-links provide structural insights into the intrinsically disordered tetrameric tumor suppressor protein p53. As a time-consuming manual inspection of cross-linking data is not required, our workflow will pave the way for making the cross-linking/MS approach a routine technique for structural proteomics studies.

Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry.

We describe an integrated workflow that robustly identifies cross-links from endogenous protein complexes in human cellular lysates. Our approach is based on the application of mass spectrometry (MS)-cleavable cross-linkers, sequential collision-induced dissociation (CID)-tandem MS (MS/MS) and electron-transfer dissociation (ETD)-MS/MS acquisitions, and a dedicated search engine, XlinkX, which allows rapid cross-link identification against a complete human proteome database. This approach allowed us to detect 2,179 unique cross-links (1,665 intraprotein cross-links at a 5% false discovery rate (FDR) and 514 interprotein cross-links at 1% FDR) in HeLa cell lysates. We validated the confidence of our cross-linking results by using a target-decoy strategy and mapping the observed cross-link distances onto existing high-resolution structures. Our data provided new structural information about many protein assemblies and captured dynamic interactions of the ribosome in contact with different elongation factors.

In-Source Decay and Pseudo Tandem Mass Spectrometry Fragmentation Processes of Entire High Mass Proteins on a Hybrid Vacuum Matrix-Assisted Laser Desorption Ionization-Quadrupole Ion-Trap Time-of-Flight Mass Spectrometer

In-source decay (ISD), although a process known for decades in mass spectrometry, has a renewed interest due to increased theoretical knowledge in fragmentation processes of large biomolecules coupled with technological improvements. We report here an original method consisting of isolating matrix-assisted laser desorption ionization (MALDI)-generated in-source fragments of large proteins and subsequently performing selective fragmentation experiments (up to four cycles) using a hybrid MALDI quadrupole ion-trap time-of-flight mass spectrometer (MALDI-QIT-TOF). This technology takes advantage of keeping high resolution on the selection of precursors and detection of fragments. It allows exhaustive N- and C-terminal sequencing of proteins. In this work, human serum albumin (HSA), β-casein, and recombinant Tau proteins were submitted to in source decay in the MALDI source. The fragments were stored in the ion-trap and submitted to sequential collision-induced dissociation (CID). Finally, ISD and pseudo MS(n) were performed on oxidized Tau protein and acetylated bovine serum albumin to identify amino acid modifications. This work highlights the potential of the MALDI-QIT-TOF instrument for pseudo MS(n) strategies and top down proteomics.

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes

Knowledge of elaborate structures of protein complexes is fundamental for understanding their functions and regulations. Although cross-linking coupled with mass spectrometry (MS) has been presented as a feasible strategy for structural elucidation of large multisubunit protein complexes, this method has proven challenging because of technical difficulties in unambiguous identification of cross-linked peptides and determination of cross-linked sites by MS analysis. In this work, we developed a novel cross-linking strategy using a newly designed MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO). DSSO contains two symmetric collision-induced dissociation (CID)-cleavable sites that allow effective identification of DSSO-cross-linked peptides based on their distinct fragmentation patterns unique to cross-linking types (i.e. interlink, intralink, and dead end). The CID-induced separation of interlinked peptides in MS/MS permits MS(3) analysis of single peptide chain fragment ions with defined modifications (due to DSSO remnants) for easy interpretation and unambiguous identification using existing database searching tools. Integration of data analyses from three generated data sets (MS, MS/MS, and MS(3)) allows high confidence identification of DSSO cross-linked peptides. The efficacy of the newly developed DSSO-based cross-linking strategy was demonstrated using model peptides and proteins. In addition, this method was successfully used for structural characterization of the yeast 20 S proteasome complex. In total, 13 non-redundant interlinked peptides of the 20 S proteasome were identified, representing the first application of an MS-cleavable cross-linker for the characterization of a multisubunit protein complex. Given its effectiveness and simplicity, this cross-linking strategy can find a broad range of applications in elucidating the structural topology of proteins and protein complexes.

Gas phase synthesis and reactivity of dimethylaurate

A combination of multistage mass spectrometry experiments and DFT calculations were used to examine the synthesis and reactivity of dimethylaurate. Collision induced dissociation (CID) of [(CH(3)CO(2))(4)Au](-) proceeded via reductive elimination of acetylperoxide to yield the diacetate [CH(3)CO(2)AuO(2)CCH(3)](-), which in turn underwent sequential CID decarboxylation reactions to yield the organoaurates [CH(3)CO(2)AuCH(3)](-) and [CH(3)AuCH(3)](-). The unimolecular chemistry of the dimethylaurate proceeds via a combination of bond homolysis to yield the methyl aurate radical anion [CH(3)Au] (-) as well as formation of the gold dihydride [HAuH](-). DFT calculations reveal that the latter anion is formed via a 1,2-dyotropic rearrangement to yield the isomer [CH(3)CH(2)AuH](-), followed by a beta-hydride elimination reaction. Ion-molecule reactions of [CH(3)AuCH(3)](-) with methyl iodide did not yield any products even at relatively high concentrations of the neutral substrate and longer reaction times, indicating a reaction efficiency of less than 1 in 20 000 collisions. DFT calculations were carried out on two different potential energy surfaces (PES) for the reaction of [CH(3)AuCH(3)](-) with CH(3)I: (i) an S(N)2 mechanism proceeding via a side-on transition state; and (ii) a stepwise mechanism proceeding via oxidative addition followed by reductive elimination. Both pathways have significant endothermic barriers, consistent with the lack of C-C bond coupling products being formed in the experiments. Finally, the reactivity of [CH(3)AuCH(3)](-) is compared to the previously studied [CH(3)AgCH(3)](-) and [CH(3)CuCH(3)](-), as well as condensed phase studies on dimethylaurate salts.

Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry

Chemical cross-linking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of cross-linked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact cross-linkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under conditions where the native complex structure is stable. In this study, we present a novel compact cross-linker that contains two distinct features: (1) an alkyne tag and (2) a small molecule detection tag (NO(2)) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the cross-linked peptides after proteolytic cleavage and coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO(2) moiety provides a secondary means of detecting cross-linked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this cross-linker, which we termed CLIP (click-enabled linker for interacting proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for cross-linked ubiquitin in highly complex E. coli cell lysates. Sequential collision-induced dissociation tandem mass spectrometry (CID-MS/MS) and electron transfer dissociation (ETD)-MS/MS of intercross-linked peptides (two peptides connected with a cross-linker) are also demonstrated for improved automated identification of cross-linked peptides.

Statistical modeling of sequential collision-induced dissociation thresholds

Thermochemistry determined from careful analysis of the energy dependence of cross sections for collision-induced dissociation (CID) reactions has primarily come from the primary dissociation channel. Higher order dissociations generally have thresholds measured to be higher than the thermodynamic limit because of the unknown internal and kinetic energy distributions of the primary products. A model that utilizes statistical theories for energy-dependent unimolecular decomposition to estimate these energy distributions is proposed in this paper. This permits a straightforward modeling of the cross sections for both primary and secondary dissociation channels. The model developed here is used to analyze data for K+(NH3)x, x=2-5, complexes, chosen because the thermochemistry previously determined by threshold CID studies agrees well with values from theory and equilibrium high pressure mass spectrometry. The model is found to reproduce the cross sections with high fidelity and the threshold values for secondary processes are found to be in excellent agreement with literature values. Furthermore, relative thresholds for higher order dissociation processes appear to provide accurate thermodynamic information as well.

Multi-stage tandem mass spectrometry of metal cationized leucine enkephalin and leucine enkephalin amide.

We have examined the multi-stage collision induced dissociation (CID) of metal cationized leucine enkephalin, leucine enkephalin amide, and the N-acetylated versions of the peptides using ion trap mass spectrometry. In accord with earlier studies, the most prominent species observed during the multi-stage CID of alkali metal cationized leucine enkephalin are the [b(n) + 17 + Cat]+ ions. At higher CID stages (i.e. >MS(4)), however, dissociation of the [b2 + 17 + Cat]+ ion, a cationized dipeptide, results in the production of [a(n) -1 + Cat]+ species. The multi-stage CID of Ag+ cationized leucine enkephalin can be initiated with either the [b(n) -1 + Ag]+ or [b(n) + 17 + Ag]+ ions produced at the MS/MS stage. For the former, sequential CID stages cause, in general, the loss of CO, and then the loss of the imine of the C-terminal amino acid, to reveal the amino acid sequence. Similar to the alkali cationized species, CID of [b2 -1 + Ag]+ produces prominent [a(n) -1 + Ag]+ ions. The multi-stage CID of argentinated peptides is reminiscent of fragmentation observed for protonated peptides, in that a series of (b(n)) and (a(n)) type ions are generated in sequential CID stages. The Ag+ cation is similar to the alkali metals, however, in that the [b(n) + 17 + Ag]+ product is produced at the MS/MS and MS3 stages, and that sequential CID stages cause the elimination of amino acid residues primarily from the C-terminus. We found that N-acetylation of the peptide significantly influenced the fragmentation pathways observed, in particular by promoting the formation of more easily interpreted (in the context of unambiguous sequence determination) dissociation spectra from the [b2 + 17 + Li]+, [b2 + 17 + Na]+ and [b2 -1 + Ag]+ precursor ions. Our results suggest, therefore, that N-acetylation may improve the efficacy of multi-stage CID experiments for C-terminal peptide sequencing in the gas phase. For leucine enkephalin amide, only the multi-stage CID of the argentinated peptide allowed the complete amino acid sequence to be determined from the C-terminal side.