Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry.

Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS).

Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins.

Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis.

Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments.

Because of their diverse functionalities in cells, lipids are of primary importance when characterizing molecular profiles of physiological and disease states. Imaging mass spectrometry (IMS) provides the spatial distributions of lipid populations in tissues. Referenced Kendrick mass defect (RKMD) analysis is an effective mass spectrometry (MS) data analysis tool for classification and annotation of lipids.

Infrared Laser Ablation Microsampling with a Reflective Objective.

A Schwarzschild reflective objective with a numerical aperture of 0.3 and working distance of 10 cm was used for laser ablation sampling of tissue for off-line mass spectrometry. The objective focused the laser to a diameter of 5 μm and produced 10 μm ablation spots on thin ink films and tissue sections.

Decontamination of metals from firefighter turnout gear.

Firefighters are exposed to many different contaminants during structural fires. Moreover, if their protective gear is not successfully decontaminated, firefighters are at risk of being repeatedly exposed to contaminants from previous fires. Thus, the successful removal of contaminants from firefighter turnout gear is necessary to prevent or reduce repeated exposure risks.

Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue.

Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m.

Trihydroxycholanoyl-taurine in brains of rodents with hepatic encephalopathy.

Hepatic encephalopathy (HE), a neurological disease resulting from liver failure, is difficult to manage and its causes are unclear. Bile acids have been postulated to be involved in the provenance and progression of various diseases including HE. Hence, the characterization of bile acid profiles in the brains of subjects with and without liver failure can provide important clues for the potential treatment of HE.

Supercharging Prions via Amyloid-Selective Lysine Acetylation.

Repulsive electrostatic forces between prion-like proteins are a barrier against aggregation. In neuropharmacology, however, a prion's net charge (Z) is not a targeted parameter. Compounds that selectively boost prion Z remain unreported.

Using isotopic envelopes and neural decision tree-based in silico fractionation for biomolecule classification.

Untargeted mass spectrometry (MS) workflows are more suitable than targeted workflows for high throughput characterization of complex biological samples. However, analysis workflows for untargeted methods are inadequate for characterization of complex samples that contain multiple classes of compounds as each chemical class might require a different type of data processing approach. To increase the feasibility of analyzing MS data for multi-class/component complex mixtures (i.

MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics.

A multimodal workflow for mass spectrometry imaging was developed that combines MALDI imaging with protein identification and quantification by liquid chromatography tandem mass spectrometry (LC-MS/MS). Thin tissue sections were analyzed by MALDI imaging, and the regions of interest (ROI) were identified using a smoothing and edge detection procedure. A midinfrared laser at 3-μm wavelength was used to remove the ROI from the brain tissue section after MALDI mass spectrometry imaging (MALDI MSI).

Characterization of Electrospray Ionization (ESI) Parameters on In-ESI Hydrogen/Deuterium Exchange of Carbohydrate-Metal Ion Adducts.

The conformations of glycans are crucial for their biological functions. In-electrospray ionization (ESI) hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is a promising technique for studying carbohydrate conformations since rapidly exchanging functional groups, e.g.

Identification of a panel of genes as a prognostic biomarker for glioblastoma.

Background: Glioblastoma multiforme (GBM) is a fatal disease without effective therapy. Identification of new biomarkers for prognosis would enable more rational selections of strategies to cure patients with GBM and prevent disease relapse.

Methods: Seven datasets derived from GBM patients using microarray or next generation sequencing in R2 online database (http://r2.

Improving Accuracy and Confidence of Chemical Identification by Gas Chromatography/Vacuum Ultraviolet Spectroscopy-Mass Spectrometry: Parallel Gas Chromatography, Vacuum Ultraviolet, and Mass Spectrometry Library Searches.

Chemical identification often relies on matching measured chemical properties and/or spectral "fingerprints" of unknowns against their precompiled libraries. Chromatography, absorption spectroscopy, and mass spectrometry are all among analytical approaches that provide chemical measurement databases amenable to library searching. Occasionally, using conventional single-library or single-domain searches can lead to misidentification of unknowns.

Infrared laser ablation sampling coupled with data independent high resolution UPLC-IM-MS/MS for tissue analysis.

Infrared laser ablation microsampling was used with data-dependent acquisition (DDA) and ion mobility-enhanced data-independent acquisition (HDMS) for mass spectrometry based bottom-up proteomics analysis of rat brain tissue. Results from HDMS and DDA analyses of the 12 laser ablation sampled tissue sections showed that HDMS consistently identified approximately seven times more peptides and four times more proteins than DDA. To evaluate the impact of ultra-performance liquid chromatography (UPLC) peak congestion on HDMS and DDA analysis, whole tissue digests from rat brain were analyzed at six different UPLC separation times.

Broadband ion mobility deconvolution for rapid analysis of complex mixtures.

High resolving power ion mobility (IM) allows for accurate characterization of complex mixtures in high-throughput IM mass spectrometry (IM-MS) experiments. We previously demonstrated that pure component IM-MS data can be extracted from IM unresolved post-IM/collision-induced dissociation (CID) MS data using automated ion mobility deconvolution (AIMD) software [Matthew Brantley, Behrooz Zekavat, Brett Harper, Rachel Mason, and Touradj Solouki, J. Am.

The reaction between GSNO and HS: On the generation of NO, HNO and NO.

Several recent reports suggest that HNO may be produced endogenously by reaction of HS and S-nitrosoglutathione (GSNO). This hypothesis was tested using deoxymyoglobin (MbFe) to trap the expected HNO released from the target reaction, which should generate the stable HNO adduct, HNO-Mb, under anaerobic conditions. Under numerous experimental conditions, the sole globin product was NO-Mb, as characterized by absorbance, EPR, and NMR spectroscopies.

Vacuum Ultraviolet Spectroscopy and Mass Spectrometry: A Tandem Detection Approach for Improved Identification of Gas Chromatography-Eluting Compounds.

For wide class characterizations of volatile organic compounds (VOCs), conventional gas chromatography mass spectrometry (GC-MS)-based techniques are utilized. These GC-MS-based chemical identification approaches typically rely on library searches against ion fragmentation patterns of known compounds. Although MS library searches can often provide correct chemical identities, erroneous chemical assignments of structurally similar unknown compounds are also possible.

Automated peak width measurements for targeted analysis of ion mobility unresolved species.

Peak broadening in ion mobility (IM) is a relatively predictable process and abnormally broad peaks can be indicative of the presence of unresolved species. Here, we introduce a new ion mobility peak fitting (IM_FIT) software package for automated and systematic determination of traveling wave ion mobility (TWIM) unresolved species. To identify IM unresolved species, the IM_FIT software generates a trend line by plotting ions' mobility peak widths as a function of their arrival times.

Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution.

Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J.

Evidence for electron-based ion generation in radio-frequency ionization.

Radio-frequency ionization (RFI) is a novel ionization method coupled to mass spectrometry (MS) for analysis of semi-volatile and volatile organic compounds (VOCs). Despite the demonstrated capabilities of RFI MS for VOC analysis in both positive- and negative-ion modes, mechanism of RFI is not completely understood. Improved understanding of the ion generation process in RFI should expand its utility in MS.

Competing noncovalent host-guest interactions and H/D exchange: reactions of benzyloxycarbonyl-proline glycine dipeptide variants with ND3.

A combination of density functional theory calculations, hydrogen/deuterium exchange (HDX) reactions, ion mobility-mass spectrometry, and isotope labeling tandem mass spectrometry was used to study gas-phase "host-guest" type interactions of a benzyloxycarbonyl (Z)-capped proline (P) glycine (G) model dipeptide (i.e., Z-PG) and its various structural analogues with ND3.

Collision-energy resolved ion mobility characterization of isomeric mixtures.

Existing instrumental resolving power limitations in ion mobility spectrometry (IMS) often restrict adequate characterization of unresolved or co-eluting chemical isomers. Recently, we introduced a novel chemometric deconvolution approach that utilized post-IM collision-induced dissociation (CID) mass spectrometry (MS) data to extract "pure" IM profiles and construct CID mass spectra of individual components from a mixture containing two IM-overlapped components [J. Am.

DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation.

Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5' phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5' phosphate group in w type ions and 5' phosphorylated DNA to generate sequence permuted [phosphopurine](-) fragment ions.

Automated deconvolution of overlapped ion mobility profiles.

Presence of unresolved ion mobility (IM) profiles limits the efficient utilization of IM mass spectrometry (IM-MS) systems for isomer differentiation. Here, we introduce an automated ion mobility deconvolution (AIMD) computer software for streamlined deconvolution of overlapped IM-MS profiles. AIMD is based on a previously reported post-IM/collision-induced dissociation (CID) deconvolution approach [J.

Loss of internal backbone carbonyls: additional evidence for sequence-scrambling in collision-induced dissociation of y-type ions.

It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported.