A comprehensive description of overall brain architecture at the molecular level is essential for understanding behavioral and cognitive processes in health and diseases. Although fluorescent labeling of target proteins has been successfully established to visualize a brain connectome, the molecular basis for diverse neurophysiological phenomena remains largely unknown. Here we report a brain-wide, molecular-level, and microscale imaging of endogenous metabolites, in particular, lipids of mouse brain by using laser activated electron tunneling (LAET) and mass spectrometry. In this approach, atomic electron emission along with finely tuned laser beam size provides high resolution that can be down to the sub-micrometer level to display spatial distribution of lipids in mouse brain slices. Electron-directed soft ionization has been achieved through exothermal capture of tunneling photoelectrons as well as unpaired electron-initiated chemical bond cleavages. Regionally specific lipids including saturated, mono-unsaturated, and poly-unsaturated fatty acids as well as other lipids, which may be implicated in neurological signaling pathways, have been discovered by using this laser activated electron tunneling based mass spectrometric imaging (LAET-MSI) technique.

•Ultraviolet irradiation on semiconductor nanoparticles produces electron–hole pairs.•Hole oxidization results in the formation of hydroxyl radicals.•Fluorine atoms of PFOSF can be specifically substituted with hydroxyl radicals.•Capture of photoelectrons causes dissociation and fragmentation.•Fragments are detected in negative ion mode.A rapid and solvent free substitution reaction of a fluorine atom in perfluorooctane sulfonyl fluoride (PFOSF) with a hydroxyl radical is reported. Under irradiation of ultraviolet laser on semiconductor nanoparticles or metal surfaces, hydroxyl radicals can be generated through hole oxidization. Among all fluorine atoms of PFOSF, highly active hydroxyl radicals specifically substitute the fluorine of sulfonyl fluoride functional group. Resultant perfluorooctane sulfonic acid is further ionized through capture of photo-generated electrons that switch the neutral molecules to negatively charged odd electron hypervalent ions. The unpaired electron subsequently initiates α O–H bond cleavage and produces perfluorooctane sulfonate negative ions. Hydroxyl radical substitution and molecular dissociation of PFOSF have been confirmed by masses with high accuracy and resolution. It has been applied to direct mass spectrometric imaging of PFOSF adsorbed on surfaces of plant leaves.

Identification of endogenous and exogenous chemicals contained in latent fingerprints is important for forensic science in order to acquire evidence of criminal identities and contacts with specific chemicals. Mass spectrometry has emerged as a powerful technique for such applications without any derivatization or fluorescent tags. Among these techniques, MALDI (Matrix Assisted Laser Desorption Ionization) provides small beam size but has interferences with MALDI matrix materials, which cause ion suppressions as well as limited spatial resolution resulting from uneven distribution of MALDI matrix crystals with different sizes. LAET (Laser Activated Electron Tunneling) described in this work offers capabilities for chemical imaging through electron-directed soft ionization. A special film of semiconductors has been designed for collection of fingerprints. Nanoparticles of bismuth cobalt zinc oxide were compressed on a conductive metal substrate (Al or Cu sticky tape) under 10 MPa pressure. Resultant uniform thin films provide tight and shining surfaces on which fingers are impressed. Irradiation of ultraviolet laser pulses (355 nm) on the thin film instantly generates photoelectrons that can be captured by adsorbed organic molecules and subsequently cause electron-directed ionization and fragmentation. Imaging of latent fingerprints is achieved by visualization of the spatial distribution of these molecular ions and structural information-rich fragment ions. Atomic electron emission together with finely tuned laser beam size improve spatial resolution. With the LAET technique, imaging analysis not only can identify physical shapes but also reveal endogenous metabolites present in females and males, detect contacts with prohibited substances, and resolve overlapped latent fingerprints.

•Chelation of Cu2+ with histones changes migration patterns in gel electrophoresis.•Histone variants were first separated by charge differences.•Charge-separated histone variants were further separated by their mass differences.•Two dimensional separations significantly resolve histone variants.Abundant isoforms and dynamic posttranslational modifications cause the separation and identification of histone variants to be experimentally challenging. To meet this need, we employ two-dimensional electrophoretic gel separation followed by mass spectrometric detection which takes advantage of the chelation of Cu2+ with amino acid residues exposed on the surfaces of the histone proteins. Acid-extracted rat liver histones were first mixed with CuSO4 solution and then separated in one dimension with triton–acid–urea (TAU) gel electrophoresis and in a second dimension using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The separations result from both the changes in charge and mass upon Cu2+ chelation. Identities of each separated gel bands were obtained by using matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). It was found that the migration of H3 histone isoforms of rat liver is markedly affected by the use of Cu2+ ions.

•Matrix materials were compressed into a thin film for MALDI mass spectrometric analysis.•Improved shot-to-shot reproducibility was achieved.•CMTF allows in situ salt washing and enhances detection sensitivity.•CMTF can be used for direct tissue analysis.The inhomogeneous re-crystallization process of matrix materials is the major concerns associated with matrix assisted laser desorption/ionization (MALDI) analysis. We describe here the approach termed compressed matrix thin film (CMTF) in order to make a uniform matrix deposition. In this approach, solid matrix particles are compressed under 10 MPa of pressure by a compressor that is regularly used in infrared spectroscopic analysis. Then aqueous samples can be deposited on the surface of the matrix film. Major advantages of the CMTF approach are summarized as follows. (1) Reproducible sample preparation procedure. Size and thickness of matrix thin films can be controlled by using a fixed mold.force and known amount of matrix materials. (2) Significantly decreased shot-to-shot variations and enhanced reproducibility. (3) Tolerance for in situ salt washing. Because matrix materials are hydrophobic, salts can be washed away while proteins or peptides are retained on the surface of matrix thin films through hydrophobic interactions. (4) Improved sensitivity. The hydrophobic coating of MALDI sample plate by matrix thin films prevents the spreading of samples across the plate and confines analytes to a small area, leading to increased local concentration. (5) A new means for tissue analysis. Tissue sections can be directly transferred to the uniform surface of matrix materials for reproducible and quantitative comparison of different molecules in different localization. The proposed CMTF should be an enabling technique for mass spectrometric analysis with improved correlations between signal intensities and sample quantities.

Nanosized carbon based sorbents have been widely used for separation, enrichment and desalting of biological samples because of their distinguished characteristics. In this work, magnetic nanoparticles of nitrogen enriched carbon (mnNEC) have been developed for enrichment of organochlorine pesticide DDT and metabolite DDE that have been accumulated in zebrafish during the course of environmental exposure. Polymerization of pyrrole was performed in the aqueous suspension of Fe3O4 nanoparticles. Resultant core–shell nanoparticules coated with polypyrrole were then subjected to a process of carbonization under high temperature and nitrogen atmospheric condition. The presence of nitrogen atoms in carbon nanoparticles increases the hydrophilicity and dispersability in aqueous samples. It has been experimentally demonstrated that mnNEC can be effectively dispersed in aqueous samples and rapidly isolated by the application of an external magnetic field. Recoveries of DDT and DDE from water range from 90% to 102% and 85–97% respectively. In combination with Selected Ion Monitoring (SIM) experiments of gas chromatography–mass spectrometry, the detection limit can be down to low ng/mL level. By using mnNEC approach, two interesting results have been found for zebrafish with 60 days exposure to DDT (1 μg/l). (1) There is higher concentration of DDT (37–143 ng/g) and DDE (173–1108 ng/g) in male zebrafish body tissues than that of female (7–52 ng/g and 146–362 ng/g for DDT and DDE respectively). (2) There is high ratio of DDE/DDT for both female and male zebrafish, implying high environmental persistence and ongoing bioaccumulation.Highlights► Magnetic nanoparticles of Fe3O4 were coated by in situ polymerization of pyrrole. ► Carbonization of polypyrrole coated magnetic nanoparticles at high temperature and nitrogen atmospheric condition. ► Magnetic nanoparticles of nitrogen enriched carbon (mnNEC) can be readily dispersed in aqueous solutions. ► The mnNEC can be used for enrichment of environmental pollutants such as pesticide residues and metabolites.

Desalting and concentration of peptides using reverse phase (RP) C18 chromatographic material based on hydrophobic interaction is a routine approach used in mass spectrometry (MS)-based proteomics. However, MS detection of small hydrophilic peptides, in particular, phosphopeptides that bear multiple negative charges, is challenging due to the insufficient binding to C18 stationary phase. We described here the development of a new desalting method that takes the unique properties of polypyrrole (PPY). The presence of positively charged nitrogen atoms under acidic conditions and polyunsaturated bonds in polypyrrole provide a prospect for enhanced adsorption of phosphopeptides or hydrophilic peptides through extra electrostatic and Π–Π stacking interactions in addition to hydrophobic interactions. In tandem with reversed phase C18 chromatographic material, the new type of desalting method termed as TMTipPPY-C18 can significantly improve the MS detection of phosphopeptides with multiple phosphate groups and other small hydrophilic peptides. It has been applied to not only tryptic digest of model proteins but also the analysis of complex lysates of zebrafish eggs. The number of detected phosphate groups on a peptide ranged from 1 to 6. Particularly, polypyrrole based method can also be used in basic condition. Thus it provides a useful means to handle peptides that may not be detectable in acidic condition. It can be envisioned that the TMTipPPY-C18 should be able to facilitate the exploration of large scale phosphoproteome.Graphical abstractHighlights► A new micropipette tip TMTipPPY-C18 was developed for desalting of phosphopeptides. ► TMTipPPY-C18 is based on polypyrrole in tandem with C18 chromatographic material. ► TMTipPPY-C18 combines electrostatic, Π–Π stacking and hydrophobic interactions. ► TMTipPPY-C18 can be used in both acidic and basic experimental conditions.

Measurement of light induced heterogeneous electron transfer is important for understanding of fundamental processes involved in chemistry, physics and biology, which is still challenging by current techniques. Laser activated electron tunneling (LAET) from semiconductor metal oxides was observed and characterized by a MALDI (matrix assisted laser desorption ionization) mass spectrometer in this work. Nanoparticles of ZnO were placed on a MALDI sample plate. Free fatty acids and derivatives were used as models of organic compounds and directly deposited on the surface of ZnO nanoparticles. Irradiation of UV laser (λ = 355 nm) with energy more than the band gap of ZnO produces ions that can be detected in negative mode. When TiO2 nanoparticles with similar band gap but much lower electron mobility were used, these ions were not observed unless the voltage on the sample plate was increased. The experimental results indicate that laser induced electron tunneling is dependent on the electron mobility and the strength of the electric field. Capture of low energy electrons by charge-deficient atoms of adsorbed organic molecules causes unpaired electron-directed cleavages of chemical bonds in a nonergodic pathway. In positive detection mode, electron tunneling cannot be observed due to the reverse moving direction of electrons. It should be able to expect that laser desorption ionization mass spectrometry is a new technique capable of probing the dynamics of electron tunneling. LAET offers advantages as a new ionization dissociation method for mass spectrometry.Graphical abstractHighlights► Irradiation of photons with energies more than the band gap generates electron–hole pairs. ► Electron tunneling probability is dependent on the electron mobility. ► Tunneling electrons are captured by charge deficient atoms. ► Unpaired electrons induce cleavages of chemical bonds.

Rapid identification of unknown microorganisms of clinical and agricultural importance is not only critical for accurate diagnosis of infections but also essential for appropriate and prompt treatment. We describe here a rapid method for microorganisms typing based on quantitative analysis of fatty acids by iFAT approach (Isotope-coded Fatty Acid Transmethylation). In this work, lyophilized cell lysates were directly mixed with 0.5 M NaOH solution in d3-methanol and n-hexane. After 1 min of ultrasonication, the top n-hexane layer was combined with a mixture of standard d0-methanol derived fatty acid methylesters with known concentration. Measurement of intensity ratios of d3/d0 labeled fragment ion and molecular ion pairs at the corresponding target fatty acids provides a quantitative basis for hierarchical clustering. In the resultant dendrogram, the Euclidean distance between unknown species and known species quantitatively reveals their differences or shared similarities in fatty acid related pathways. It is of particular interest to apply this method for typing fungal species because fungi has distinguished lipid biosynthetic pathways that have been targeted for lots of drugs or fungicides compared with bacteria and animals. The proposed method has no dependence on the availability of genome or proteome databases. Therefore, it is can be applicable for a broad range of unknown microorganisms or mutant species.

As primary endogenous ligands of serum albumin, free fatty acids exert versatile effects on the albumin conformation through cooperative or competitive interactions with exogenous chemicals. Based on equilibrium partition between n-hexane and aqueous phases, we have established three indexes, defined as RA, RV, and RT, for quantitative assessment of the intrinsic binding affinity, the affinitive variation induced by exogenous chemicals, and the topological dependence of albumin affinity, respectively. When albumin molecules in the aqueous phase are in native or denatured forms, or disturbed by exogenous chemicals, corresponding changes of free fatty acids in the n-hexane phase can be quantified by an iFFAM (isotope-coded free fatty acid methylation) approach. Free fatty acids from the control and the sample are differentially derived by d0- or d3-methanol and analyzed by gas chromatography–mass spectrometry. Changes of fatty acids can be revealed by peak ratios of d0- or d3-labeled fragment ions of fatty acid methyl esters.Keywords: exogenous chemicals; free fatty acids; interactions; Mass spectrometry; serum albumin

Reversible protein palmitoylation is one of the most important posttranslational modifications that has been implicated in the regulation of protein signaling, trafficking, localizing and enzymatic activities in cells and tissues. In order to achieve a precise understanding of mechanisms and functions of protein palmitoylation as well as its roles in physiological processes and disease progression, it is necessary to develop techniques that can qualitatively and quantitatively monitor the dynamic protein palmitoylation in vivo and in vitro. This review will highlight recent advances in both chemical and genetic encoded probes that have been developed for accurate analysis of protein palmitoylation, including identification and quantification of acyl moieties and palmitoylated proteins, localization of amino acid residues on which acyl moieties are attached, and imaging of cellular distributions of palmitoylated proteins. The role of major techniques of fluorescence microscopy and mass spectrometry in facilitating the analysis of protein palmitoylation will also be explored.

Accurate measurement of pesticides in biological fluids such as blood is important for quantifying environmental exposures. Beyond sample enrichment and separation, the method presented here is focused on studies of interactions between pesticides and co-existed proteins. It was experimentally demonstrated that entrapped or adsorbed pesticide residues within the folded native structures of proteins were poorly recovered using direct solvent extraction solely. We described here an effective approach termed Enzymatic Digestion-Organic Solvent Extraction (eDOSE) that utilizes the enzymatic approach to disrupt the folded structures of proteins and release entrapped or adsorbed pesticide residues. In this approach, samples were first reduced, alkylated, tryptically digested and then diluted 10 times before the subsequent extraction using an n-hexane solution. Resultant pesticide residues were determined by capillary gas chromatography coupled with a mass spectrometer. Mean recoveries of the 5 organophosphorus pesticides pre-spiked in fish blood including diazinon, parathion-methyl, malathion, parathion-ethyl and ethion were 85%, 95%, 84%, 103%, and 43% respectively using eDOSE strategy but only 24%, 45%, 40%, 27%, and 29% respectively using direct solvent extraction approach. The eDOSE approach was effective for demonstrating the critical role of folded native structure of serum albumin in adsorption of exogenous chemicals. It provides an alterative means for denaturation of proteins when the target analytes are not stable in acidic solution or entrapped within the protein aggregates caused by organic solvents such as acetone that have been applied for protein denaturation. The eDOSE approach should be able to combine with other advanced techniques of enrichment and separation for more efficient and accurate measurement of target compounds present in the context of complex biological systems. This approach can provide wide applications to the analysis of a variety of small molecules including environmental pesticide residues and metabolites as well as other toxins present in cells, tissues and biofluids.

Fatty acids covalently bonded with other molecules have been implicated in many important biological processes. We describe here a rapid approach termed isotope-coded fatty acid transmethylation (iFAT) that integrates extraction, transmethylation, and isotopic labeling into a single step with the aid of ultrasonic irradiation for comparative analysis of fatty acids by mass spectrometry. In this approach, samples without any prefractionation were mixed with a methanol solution of 0.5 M NaOH and an n-hexane solution. The intense wave shocks and cavitations generated by ultrasonic irradiation not only speed the alkaline-catalyzed transmethylation reaction but also facilitate the simultaneous mass transfer of fatty acid methyl esters into the top n-hexane extraction phase that was injected into a GC/MS system. By using commercially available d3-methanol, we were able to compare the intensity of labeled and unlabeled methyl esters and their corresponding fragment ions. The detection limit can be down to the picogram level. Major advantages of the iFAT strategy are summarized in the following: (1) Efficient heterogeneous reactions. Solid samples such as dried cell lysates or detergent-resistant fractions can be readily transformed and analyzed with the aid of ultrasound irradiation. (2) Accurate quantification of fatty acids. Evaluation of the completeness or losses of transformation reactions across lipid classes has been hampered due to a lack of suitable methods. Isotope labeling can be used as an internal standard for accurate comparison of the fatty acid composition in different cell states. (3) Reduced interferences from complex biological context. The iFAT strategy not only differentially labels fatty acids in different samples, but also volatilizes those molecules, and thus, they are isolated from the bulk background and analyzed by GC/MS. This proposed approach has been applied to quantitatively determine the fatty acid composition in plant oil and in budding yeast cell lysates and detergent-resistant fractions. It should provide a widely applicable means for quantitative comparison of the fatty acid composition in cells and tissues.