Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optical Fiber-Enabled Photoactivation of Peptides and Proteins.

ABSTRACT: Photoactivation and photodissociation have long proven to be useful tools in tandem mass spectrometry, but implementation often involves cumbersome and potentially dangerous configurations. Here, we redress this problem by using a fiber-optic cable to couple an infrared (IR) laser to a mass spectrometer for robust, efficient, and safe photoactivation experiments. Transmitting 10.6 μm IR photons through a hollow-core fiber, we show that such fiber-assisted activated ion-electron transfer dissociation (AI-ETD) and IR multiphoton dissociation (IRMPD) experiments can be carried out as effectively as traditional mirror-based implementations. We report on the transmission efficiency of the hollow-core fiber for conducting photoactivation experiments and perform various intact protein and peptide analyses to illustrate the benefits of fiber-assisted AI-ETD, namely, a simplified system for irradiating the two-dimensional linear ion trap volume concurrent with ETD reactions to limit uninformative nondissociative events and thereby amplify sequence coverage. We also describe a calibration scheme for the routine analysis of IR laser alignment and power through the fiber and into the dual cell quadrupolar linear ion trap. In all, these advances allow for a more robust, straightforward, and safe instrumentation platform, permitting implementation of AI-ETD and IRMPD on commercial mass spectrometers and broadening the accessibility of these techniques.

SUBMITTER: Peters-Clarke TM

PROVIDER: S-EPMC8008966 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Etching-enabled extreme miniaturization of graded-index fiber-based optical coherence tomography probes.

Project description:We introduced and validated a method to miniaturize graded-index (GRIN) fiber-based optical coherence tomography (OCT) probes down to 70???m in diameter. The probes consist in an assembly of single-mode (SM), coreless (CL), and graded-index (GRIN) fibers. We opted for a probe design enabling controlled size reduction by hydrogen fluoride etching. The fabrication approach prevents nonuniform etching for both the GRIN and SM fiber components, while it requires no probe polishing postetching. We found that the miniaturized probes present insignificant loss of sensitivity (?1??dB) compared to their thicker (125???m) counterparts. We also showed that their focusing capabilities remain tunable and highly predictable. The fabrication process is simple and can be carried out by using inexpensive telecom equipment. Both the fabrication process and the developed probes can benefit the prototyping of minimally invasive endoscopic tools.

| S-EPMC7010983 | biostudies-literature

Protein detection enabled using functionalised silk-binding peptides on a silk-coated optical fibre.

Project description:We present a new coating procedure to prepare optical fibre sensors suitable for use with protein analytes. We demonstrate this through the detection of AlexaFluor-532 tagged streptavidin by its binding to D-biotin that is functionalised onto an optical fibre, via incorporation in a silk fibroin fibre coating. The D-biotin was covalently attached to a silk-binding peptide to provide SBP-biotin, which adheres the D-biotin to the silk-coated fibre tip. These optical fibre probes were prepared by two methods. The first involves dip-coating the fibre tip into a mixture of silk fibroin and SBP-biotin, which distributes the SBP-biotin throughout the silk coating (method A). The second method uses two steps, where the fibre is first dip-coated in silk only, then SBP-biotin added in a second dip-coating step. This isolates SBP-biotin to the outer surface of the silk layer (method B). A series of fluorescence measurements revealed that only the surface bound SBP-biotin detects streptavidin with a detection limit of 15 μg mL-1. The fibre coatings are stable to repeated washing and long-term exposure to water. Formation of silk coatings on fibres using commercial aqueous silk fibroin was found to be inhibited by a lithium concentration of 200 ppm, as determined by atomic absorption spectroscopy. This was reduced to less than 20 ppm by dialysis against water, and was found to successfully form a coating on optical fibres.

| S-EPMC9034238 | biostudies-literature

Catalyst-Free Decarbonylative Trifluoromethylthiolation Enabled by Electron Donor-Acceptor Complex Photoactivation.

Project description:A catalyst- and additive-free decarbonylative trifluoromethylthiolation of aldehyde feedstocks has been developed. This operationally simple, scalable, and open-to-air transformation is driven by the selective photoexcitation of electron donor-acceptor (EDA) complexes, stemming from the association of 1,4-dihydropyridines (donor) with N-(trifluoromethylthio)phthalimide (acceptor), to trigger intermolecular single-electron transfer events under ambient- and visible light-promoted conditions. Extension to other electron acceptors enables the synthesis of thiocyanates and thioesters, as well as the difunctionalization of [1.1.1] propellane. The mechanistic intricacies of this photochemical paradigm are elucidated through a combination of experimental efforts and high-level quantum mechanical calculations [dispersion-corrected (U)DFT, DLPNO-CCSD(T), and TD-DFT]. This comprehensive study highlights the necessity for EDA complexation for efficient alkyl radical generation. Computation of subsequent ground state pathways reveals that SH2 addition of the alkyl radical to the intermediate radical EDA complex is extremely exergonic and results in a charge transfer event from the dihydropyridine donor to the N-(trifluoromethylthio)phthalimide acceptor of the EDA complex. Experimental and computational results further suggest that product formation also occurs via SH2 reaction of alkyl radicals with 1,2-bis(trifluoromethyl)disulfane, generated in-situ through combination of thiyl radicals.

| S-EPMC8903066 | biostudies-literature

Topologically enabled optical nanomotors.

Project description:Shaping the topology of light, by way of spin or orbital angular momentum engineering, is a powerful tool to manipulate matter on the nanoscale. Conventionally, such methods focus on shaping the incident beam of light and not the full interaction between the light and the object to be manipulated. We theoretically show that tailoring the topology of the phase space of the light particle interaction is a fundamentally more versatile approach, enabling dynamics that may not be achievable by shaping of the light alone. In this manner, we find that optically asymmetric (Janus) particles can become stable nanoscale motors even in a light field with zero angular momentum. These precessing steady states arise from topologically protected anticrossing behavior of the vortices of the optical torque vector field. Furthermore, by varying the wavelength of the incident light, we can control the number, orientations, and the stability of the spinning states. These results show that the combination of phase-space topology and particle asymmetry can provide a powerful degree of freedom in designing nanoparticles for optimal external manipulation in a range of nano-optomechanical applications.

| S-EPMC5493414 | biostudies-literature

Optical manipulation and binding of microrods with multiple traps enabled in an inclined dual-fiber system.

Project description:We present experimental demonstrations of optical manipulation and optical binding of microscopic glass rods using the multiple traps created by a dual-fiber optical trapping system. Trapping, alignment, rotation, and stacking of glass rods were realized. To the best of our knowledge, this is the first time that cylindrical particles are optically trapped and bound by an optical fiber-based system. The optical manipulation of rods is also investigated through numerical simulations, which are used to quantitatively explain the experimental results. The ability of manipulating multiple particles of different shapes, as well as the integrable nature of the fiber-based setup, bestows the system the potential to be used in microfluidic systems for versatile particle manipulations.

| S-EPMC3026032 | biostudies-other

EGaIn Fiber Enabled Highly Flexible Supercapacitors.

Project description:Attributed to their soft and stretchable feature, flexible supercapacitors have attracted increasing attention in areas of soft electronics, wearable devices, and energy storage systems. However, it is a challenge to manufacture all-soft supercapacitors with highly flexible properties and excellent electrochemical performance. Here, an EGaIn-based fibrous supercapacitor, which is composed of two paralleled stretchable fibers, is designed and demonstrated first with flexible and stretchable properties. EGaIn coated on the surface of polyurethane (PU)@polymethacrylate (PMA) fibers can serve as a current collector. The prepared supercapacitor is measured with an areal specific capacitance of 26.71 mF·cm-2 by mixing Fe3O4 microparticles with EGaIn. This value can increase up to 61.34 mF·cm-2 after vacuum pumping, the mechanism of which is further revealed to be related with the coarser surface and airhole formation on the fibers. The supercapacitor maintains an excellent electrochemical performance when stretched to 120% strain and exhibits a long cycling life through a charge-discharge cycle of over 1000 times. Finally, the supercapacitors are adopted to light the LED, demonstrating that those supercapacitors can work successfully. All these characteristics indicate the huge potential of EGaIn-based supercapacitors in the field of flexible electronics and wearable devices.

| S-EPMC8482390 | biostudies-literature

Optical Fiber Delivered Ultrafast Plasmonic Optical Switch.

Project description:Ultrafast optical switch based on plasmonic nanostructures has large application potentials in optical logic circuits and optical communication systems. Integration of plasmonic optical switching devices with optical fibers is a breakthrough for realizing practical applications in long-range optical data transmission or communication techniques. Here, the incorporation of plasmonic optical switch devices onto the end facets of optical fibers is reported, so that the switched optical signals are generated by interaction between femtosecond laser pulses and plasmonic nanostructures on one end of the fiber, and are delivered via the fiber waveguide to the other end for detection or decoding. "Quenching" of localized surface plasmon in the gold nanowires by its interaction with band-edge modulation in gold through strong optical excitation is the responsible photophysics. This work accomplishes for the first time the implementation of ultrafast plasmonic optical switch device on optical fiber tips for logic data transmission.

| S-EPMC8132049 | biostudies-literature

Optical fiber meta-tips.

Project description:We report on the first demonstration of a proof-of-principle optical fiber 'meta-tip', which integrates a phase-gradient plasmonic metasurface on the fiber tip. For illustration and validation purposes, we present numerical and experimental results pertaining to various prototypes implementing generalized forms of the Snell's transmission/reflection laws at near-infrared wavelengths. In particular, we demonstrate several examples of beam steering and coupling with surface waves, in fairly good agreement with theory. Our results constitute a first step toward the integration of unprecedented (metasurface-enabled) light-manipulation capabilities in optical-fiber technology. By further enriching the emergent 'lab-on-fiber' framework, this may pave the way for the widespread diffusion of optical metasurfaces in real-world applications to communications, signal processing, imaging and sensing.

| S-EPMC6062173 | biostudies-literature

Quantitative visualization of endocytic trafficking through photoactivation of fluorescent proteins.

Project description:Endocytic trafficking controls the density of molecules at the plasma membrane and by doing so, the cell surface profile, which in turn determines how cells interact with their environment. A full apprehension of any cellular process necessitates understanding how proteins associated with the plasma membrane are endocytosed, how they are sorted after internalization, and if and how they are recycled to the plasma membrane. To date, it is still difficult to experimentally gain access to this information, even more to do it in a quantitative way. Here we present a toolset based on photoactivation of fluorescent proteins that enabled us to generate quantitative information on endocytosis, incorporation into sorting and recycling endosomes, delivery from endosomes to the plasma membrane, and on the type of vesicles performing intracellular transport. We illustrate these approaches by revealing striking differences in the endocytic trafficking of T-cell receptor and CD4, which bind to the same molecule at the surface of antigen-presenting cells during T-cell activation.

| S-EPMC8108533 | biostudies-literature

Macrocyclisation of small peptides enabled by oxetane incorporation.

Project description:Cyclic peptides are an important source of new drugs but are challenging to produce synthetically. We show that head-to-tail peptide macrocyclisations are greatly improved, as measured by isolated yields, reaction rates and product distribution, by substitution of one of the backbone amide C[double bond, length as m-dash]O bonds with an oxetane ring. The cyclisation precursors are easily made by standard solution- or solid-phase peptide synthesis techniques. Macrocyclisations across a range of challenging ring sizes (tetra-, penta- and hexapeptides) are enabled by incorporation of this turn-inducing element. Oxetane incorporation is shown to be superior to other established amino acid modifications such as N-methylation. The positional dependence of the modification on cyclisation efficiency is mapped using a cyclic peptide of sequence LAGAY. We provide the first direct experimental evidence that oxetane modification induces a turn in linear peptide backbones, through the observation of d NN (i, i + 2) and d αN (i, i + 2) NOEs, which offers an explanation for these improvements. For cyclic peptide, cLAGAY, a combination of NMR derived distance restraints and molecular dynamics simulations are used to show that this modification alters the backbone conformation in proximity to the oxetane, with the flexibility of the ring reduced and a new intramolecular H-bond established. Finally, we incorporated an oxetane into a cyclic pentapeptide inhibitor of Aminopeptidase N, a transmembrane metalloprotease overexpressed on the surface of cancer cells. The inhibitor, cCNGRC, displayed similar IC50 values in the presence or absence of an oxetane at the glycine residue, indicating that bioactivity is fully retained upon amide C[double bond, length as m-dash]O bond replacement.

| S-EPMC6385813 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data