Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Detection and relative quantification of proteins by surface enhanced Raman using isotopic labels.

ABSTRACT: Accurate quantification of protein content and composition has been achieved using isotope-edited surface enhanced resonance Raman spectroscopy. Synthesis of isotopomeric Rhodamine dye-linked bioconjugation reagents enabled direct labeling of surface lysines on a variety of proteins. When separated in polyacrylamide gels and stained with silver nanoparticles. The spectral signatures reflect the expected statistical distribution of isotopomeric labels on the labeled proteins in the gel matrix format without interference from protein features.

SUBMITTER: Deb SK

PROVIDER: S-EPMC2646756 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Detection and relative quantification of proteins by surface enhanced Raman using isotopic labels.

Deb Shirshendu K SK Davis Brandon B Knudsen Giselle M GM Gudihal Ravindra R Ben-Amotz Dor D Davisson V Jo VJ

Journal of the American Chemical Society 20080701 30

Accurate quantification of protein content and composition has been achieved using isotope-edited surface enhanced resonance Raman spectroscopy. Synthesis of isotopomeric Rhodamine dye-linked bioconjugation reagents enabled direct labeling of surface lysines on a variety of proteins. When separated in polyacrylamide gels and stained with silver nanoparticles. The spectral signatures reflect the expected statistical distribution of isotopomeric labels on the labeled proteins in the gel matrix for ...[more]

PMID: 18593116

Similar Datasets

Rapid Detection and Quantification of Novel Psychoactive Substances (NPS) Using Raman Spectroscopy and Surface-Enhanced Raman Scattering.

Project description:With more than a million seizures of illegal drugs reported annually across Europe, the variety of psychoactive compounds available is vast and ever-growing. The multitude of risks associated with these compounds are well-known and can be life threatening. Hence the need for the development of new analytical techniques and approaches that allow for the rapid, sensitive, and specific quantitative detection and discrimination of such illicit materials, ultimately with portability for field testing, is of paramount importance. The aim of this study was to demonstrate the application of Raman spectroscopy and surface-enhanced Raman scattering (SERS) combined with chemometrics approaches, as rapid and portable techniques for the quantitative detection and discrimination of a wide range of novel psychoactive substances (methcathinone and aminoindane derivatives), both in powder form and in solution. The Raman spectra of the psychoactive compounds provided clear separation and classification of the compounds based on their core chemical structures; viz. methcathinones, aminoindanes, diphenidines, and synthetic cannabinoids. The SERS results also displayed similar clustering patterns, with improved limits of detections down to ~2 mM (0.41 g L-1). As mephedrone is currently very popular for recreational use we performed multiplexed quantitative detection of mephedrone (4-methylmethcathinone), and its two major metabolites (nor-mephedrone and 4-methylephedrine), as tertiary mixtures in water and healthy human urine. These findings readily illustrate the potential application of SERS for simultaneous detection of multiple NPS as mixtures without the need for lengthy prior chromatographic separation or enrichment methods.

| S-EPMC6593286 | biostudies-literature

Quantification of isotope encoded proteins in 2-D gels using surface enhanced resonance Raman.

Project description:A strategy for quantification of multiple protein isoforms from a complex sample background is demonstrated, combining isotopomeric rhodamine 6G (R6G) labels and surface-enhanced Raman in polyacrylamide matrix. The procedure involves isotope-encoding by lysine-labeling with (R6G) active ester reagents, isoform separation by 2-DGE, fluorescence quantification using internal standardization to water, and silver nanoparticle deposition followed by surface-enhanced Raman detection. R6G sample encoding and standardization enabled the determination of total protein concentration and the distribution of specific isoforms using the combined detection approach of water-referenced fluorescence spectral imaging and ratiometric quantification. A detection limit of approximately 13.5 picomolar R6G-labeled protein was determined for the surface-enhanced Raman in a gel matrix (15-fold lower than fluorescence). High quantification accuracies for small differences in protein populations at low nanogram abundance were demonstrated for human GMP synthetase (hGMPS) either as purified protein samples in a single-point determination mode (3% relative standard deviation, RSD%) or as HCT116 human cancer cellular lysate in an imaging application (with 16% RSD%). These results represent a prototype for future applications of isotopic surface-enhanced resonance Raman scatter to quantification of protein distributions.

| S-EPMC2654710 | biostudies-literature

Sensitive carbohydrate detection using surface enhanced Raman tagging.

Project description:Glycomic analysis is an increasingly important field in biological and biomedical research as glycosylation is one of the most important protein post-translational modifications. We have developed a new technique to detect carbohydrates using surface enhanced Raman spectroscopy (SERS) by designing and applying a Rhodamine B derivative as the SERS tag. Using a reductive amination reaction, the Rhodamine-based tag (RT) was successfully conjugated to three model carbohydrates (glucose, lactose, and glucuronic acid). SERS detection limits obtained with a 633 nm HeNe laser were ?1 nM in concentration for all the RT-carbohydrate conjugates and ?10 fmol in total sample consumption. The dynamic range of the SERS method is about 4 orders of magnitude, spanning from 1 nM to 5 ?M. Ratiometric SERS quantification using isotope-substituted SERS internal references allows comparative quantifications of carbohydrates labeled with RT and deuterium/hydrogen substituted RT tags, respectively. In addition to enhancing the SERS detection of the tagged carbohydrates, the Rhodamine tagging facilitates fluorescence and mass spectrometric detection of carbohydrates. Current fluorescence sensitivity of RT-carbohydrates is ?3 nM in concentration while the mass spectrometry (MS) sensitivity is about 1 fmol, achieved with a linear ion trap electrospray ionization (ESI)-MS instrument. Potential applications that take advantage of the high SERS, fluorescence, and MS sensitivity of this SERS tagging strategy are discussed for practical glycomic analysis where carbohydrates may be quantified with a fluorescence and SERS technique and then identified with ESI-MS techniques.

| S-EPMC3010869 | biostudies-literature

Designing dendronic-Raman markers for sensitive detection using surface-enhanced Raman spectroscopy.

Project description:Surface-Enhanced Raman Spectroscopy (SERS) is well-established as a tool for bio-diagnostics but is often limited by analyte sensitivity and the need for specialized substrates. Signal enhancement can be achieved by attaching multiple Raman markers to a single analyte. Dendronic frameworks with multiple Raman markers attached to the periphery offer an opportunity to examine this idea. In this article, dendrons with thiophenol groups on their periphery were synthesized and tested as a SERS analyte. For this study, simple gold nanoparticles (∼60 nm) were used as a substrate. A 102 fold enhancement in detection was observed upon going from a mono-thiophenol (MT) to a tetra-thiophenol (TT). Dendronic Raman markers increased the probability of SERS occurrence at lower concentrations when compared to a single Raman active molecule. This strategy extends the applicability of SERS, as these analyte molecules can be just mixed or drop-casted on any kind of SERS substrate.

| S-EPMC9071040 | biostudies-literature

Mathematical Model for Biomolecular Quantification Using Large-Area Surface-Enhanced Raman Spectroscopy Mapping.

Project description:Surface-enhanced Raman spectroscopy (SERS) based on nanostructured platforms is a promising technique for quantitative and highly sensitive detection of biomolecules in the field of analytical biochemistry. Here, we report a mathematical model to predict experimental SERS signal (or hotspot) intensity distributions of target molecules on receptor-functionalized nanopillar substrates for biomolecular quantification. We demonstrate that by utilizing only a small set of empirically determined parameters, our general theoretical framework agrees with the experimental data particularly well in the picomolar concentration regimes. This developed model may be generally used for biomolecular quantification using Raman mapping on SERS substrates with planar geometries, in which the hotspots are approximated as electromagnetic enhancement fields generated by closely spaced dimers. Lastly, we also show that the detection limit of a specific target molecule, TAMRA-labeled vasopressin, approaches the single molecule level, thus opening up an exciting new chapter in the field of SERS quantification.

| S-EPMC4852715 | biostudies-literature

Nanofluidic biosensing for beta-amyloid detection using surface enhanced Raman spectroscopy.

Project description:Trace detection of the conformational transition of beta-amyloid peptide (Abeta) from a predominantly alpha-helical structure to beta-sheet could have a large impact in understanding and diagnosing Alzheimer's disease. We demonstrate how a novel nanofluidic biosensor using a controlled, reproducible surface enhanced Raman spectroscopy active site was developed to observe Abeta in different conformational states during the Abeta self-assembly process as well as to distinguish Abeta from confounder proteins commonly found in cerebral spinal fluid.

| S-EPMC2587305 | biostudies-literature

Detection of ethyl carbamate in liquors using surface-enhanced Raman spectroscopy.

Project description:Ethyl carbamate (EC), a potential carcinogen, can be formed during the fermentation and storage of alcoholic beverages. In this work, quantitative detection of EC in alcoholic beverages by using surface-enhanced Raman spectroscopy (SERS) is reported. Flower-shaped silver nanostructure substrates and silver nanocube substrates were prepared and employed as SERS platform. Flower-like silver substrates had better Raman enhancement effect on EC and were selected for further EC detection. In EC SERS spectra based on flower-shaped silver substrates, the strongest and reproducible characteristic band at 857 cm-1 was chosen for establishing a linear regression model in the concentrations ranging from 10-5 to 10-9 M, which effectively extended the application scope of the quantitative model for determination EC. Furthermore, a real alcoholic beverage was tested to verify the feasibility and reliability of the method.

| S-EPMC6304119 | biostudies-literature

Detection of Silver Nanoparticles in Seawater Using Surface-Enhanced Raman Scattering.

Project description:Nanomaterials significantly contribute to the development of new solutions to improve consumer products properties. Silver nanoparticles (AgNPs) are one of the most used, and as human exposure to such NPs increases, there is a growing need for analytical methods to identify and quantify nanoparticles present in the environment. Here we designed a detection strategy for AgNPs in seawater using surface-enhanced Raman Scattering (SERS). Three commercial AgNPs coated with polyvinylpyrrolidone (PVP) were used to determine the relative impact of size (PVP-15nmAgNPs and PVP-100nmAgNPs) and aggregation degree (predefined Ag aggregates, PVP-50-80nmAgNPs) on the SERS-based detection method. The study of colloidal stability and dissolution of selected AgNPs into seawater was carried out by dynamic light scattering and UV-vis spectroscopy. We showed that PVP-15nmAgNPs and PVP-100nmAgNPs remained colloidally stable, while PVP-50-80nmAgNPs formed bigger aggregates. We demonstrated that the SERS-based method developed here have the capacity to detect and quantify single and aggregates of AgNPs in seawater. The size had almost no effect on the detection limit (2.15 ± 1.22 mg/L for PVP-15nmAgNPs vs. 1.51 ± 0.71 mg/L for PVP-100nmAgNPs), while aggregation caused an increase of 2.9-fold (6.08 ± 1.21 mg/L). Our results demonstrate the importance of understanding NPs transformation in seawater since this can influence the detection method performance.

| S-EPMC8308189 | biostudies-literature

NeuCode labels for relative protein quantification.

Project description:We describe a synthesis strategy for the preparation of lysine isotopologues that differ in mass by as little as 6 mDa. We demonstrate that incorporation of these molecules into the proteomes of actively growing cells does not affect cellular proliferation, and we discuss how to use the embedded mass signatures (neutron encoding (NeuCode)) for multiplexed proteome quantification by means of high-resolution mass spectrometry. NeuCode SILAC amalgamates the quantitative accuracy of SILAC with the multiplexing of isobaric tags and, in doing so, offers up new opportunities for biological investigation. We applied NeuCode SILAC to examine the relationship between transcript and protein levels in yeast cells responding to environmental stress. Finally, we monitored the time-resolved responses of five signaling mutants in a single 18-plex experiment.

| S-EPMC4159665 | biostudies-literature

Surface enhanced Raman spectroscopy detection of biomolecules using EBL fabricated nanostructured substrates.

Project description:Fabrication and characterization of conjugate nano-biological systems interfacing metallic nanostructures on solid supports with immobilized biomolecules is reported. The entire sequence of relevant experimental steps is described, involving the fabrication of nanostructured substrates using electron beam lithography, immobilization of biomolecules on the substrates, and their characterization utilizing surface-enhanced Raman spectroscopy (SERS). Three different designs of nano-biological systems are employed, including protein A, glucose binding protein, and a dopamine binding DNA aptamer. In the latter two cases, the binding of respective ligands, D-glucose and dopamine, is also included. The three kinds of biomolecules are immobilized on nanostructured substrates by different methods, and the results of SERS imaging are reported. The capabilities of SERS to detect vibrational modes from surface-immobilized proteins, as well as to capture the protein-ligand and aptamer-ligand binding are demonstrated. The results also illustrate the influence of the surface nanostructure geometry, biomolecules immobilization strategy, Raman activity of the molecules and presence or absence of the ligand binding on the SERS spectra acquired.

| S-EPMC4401373 | biostudies-literature

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