Nanocapillaries for open tubular chromatographic separations of proteins in femtoliter to picoliter samples.
Ontology highlight
ABSTRACT:
SUBMITTER: Wang X
PROVIDER: S-EPMC2802834 | biostudies-literature | 2009 Sep
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Microreactor technology has attracted tremendous interest due to its features of a large specific surface area, low consumption of reagents and energy, and flexible control of the reaction process. As most of the current microreactors have volumes of microliters or even larger, effective methods to reduce the microreactors' sizes and improve their flexibility and controllability have become highly demanded. Here we propose an optical method of coalescence and splitting of femto-/pico-liter droplets for application in microreactors. Firstly, two different schemes are adopted to stably trap and directionally transport the microdroplets (oil and water) by a scanning optical tweezing system. Then, optically controlled coalescence and splitting of the microdroplets are achieved on this basis, and the mechanism and conditions are explored. Finally, the microdroplets are used as microreactors to conduct the microreactions. Such microreactors combine the advantages of miniaturization and the multi-functions of microdroplets, as well as the precision, flexibility, and non-invasiveness of optical tweezers, holding great potential for applications in materials synthesis and biosensing.
| S-EPMC9215165 | biostudies-literature
Project description:Computer-assisted optimization of chromatographic separations is still a fruitful activity. In fact, advances in computerized data handling should make the application of systematic optimization strategies much easier. However, in most contemporary applications, the optimization criterion is not considered to be a key issue (Vanbel, J Pharm Biomed, 21:603-610, 1999). In this paper, an update of the importance of selecting adequate criteria in chromatographic separation is presented.
| S-EPMC2694924 | biostudies-other
Project description:Nanoflow liquid chromatography-mass spectrometry is key to enabling in-depth proteome profiling of trace samples such as single cells, but these separations can lack robustness due to the use of narrow-bore columns that are susceptible to clogging. In the case of single-cell proteomics, offline cleanup steps are generally omitted to avoid losses to additional surfaces, and online solid-phase extraction/trap columns frequently provide the only opportunity to remove salts and insoluble debris before the sample is introduced to the analytical column. Trap columns are traditionally short, packed columns used to load and concentrate analytes at flow rates greater than those employed in analytical columns, and since these first encounter the uncleaned sample mixture, trap columns are also susceptible to clogging. We hypothesized that clogging could be avoided by using large-bore porous layer open tubular trap columns (PLOTrap). The low back pressure ensured that the PLOTraps could also serve as the sample loop, thus allowing sample cleanup and injection with a single 6-port valve. We found that PLOTraps could effectively remove debris to avoid column clogging. We also evaluated multiple stationary phases and PLOTrap diameters to optimize performance in terms of peak widths and sample loading capacities. Optimized PLOTraps were compared to conventional packed trap columns operated in forward and backflush modes, and were found to have similar chromatographic performance of backflushed traps while providing improved debris removal for robust analyses of trace samples.
2024-02-09 | PXD048565 | Pride
Project description:The search for biomarkers allowing the assessment of disease by early diagnosis is facilitated by liquid chromatography. However, it is not clear how many components are lost due to being present in concentrations below the detection limit and/or being obscured by chromatographic peak overlap. First, we extend the study of missing components undertaken by Enke and Nagels, who employed the log-normal probability density function (pdf) for the distribution of signal intensities (and concentrations) of three mixtures. The Weibull and exponential pdfs, which have a higher probability of small-concentration components than the log-normal pdf, are also investigated. Results show that assessments of the loss of low-intensity signals by curve fitting are ambiguous. Next, we simulate synthetic chromatograms to compare the loss of peaks from superposition (overlap) with neighboring peaks to the loss arising from lying below the limit of detection (LOD) imposed by a finite signal-to-noise ratio (SNR). The simulations are made using amplitude pdfs based on the Enke-Nagels data as functions of relative column efficiency, i.e., saturation, and SNR. Results show that at the highest efficiencies, the lowest-amplitude peaks are lost below the LOD. However, at small and medium efficiencies, peak overlap is the dominant loss mechanism, suggesting that low-level components will not be found easily in liquid chromatography with single channel detectors regardless of SNR. A simple treatment shows that a multichannel detector, e.g., a mass spectrometer, is necessary to expose more low-level components.
| S-EPMC7748966 | biostudies-literature
Project description:This work presents the first example of utilization of amphiphilic block copolymer PCL-PEG-PCL as a stationary phase for capillary gas chromatographic (GC) separations. The PCL-PEG-PCL capillary column fabricated by static coating provides a high column efficiency of 3951 plates/m for n-dodecane at 120 °C. McReynolds constants and Abraham system constants were also determined in order to evaluate the polarity and possible molecular interactions of the PCL-PEG-PCL stationary phase. Its selectivity and resolving capability were investigated by using a complex mixture covering analytes of diverse types and positional, structural, and cis-/trans-isomers. Impressively, it exhibits high resolution performance for aliphatic and aromatic isomers with diverse polarity, including those critical isomers such as butanol, dichlorobenzene, dimethylnaphthalene, xylenol, dichlorobenzaldehyde, and toluidine. Moreover, it was applied for the determination of isomer impurities in real samples, suggesting its potential for practical use. The superior separation performance demonstrates the potential of PCL-PEG-PCL and related block copolymers as stationary phases in GC and other separation technologies.
| S-EPMC6749289 | biostudies-literature
Project description:High-throughput screening (HTS) using multiwell plates and fluorescence plate readers is a powerful tool for drug discovery and evaluation by allowing tens of thousands of assays to be completed in 1 day. Although this method has been successful, electrophoresis-based methods for screening are also of interest to avoid difficulties associated fluorescence assays such as requirements to engineer fluorogenic reactions and false positives. We have developed a method using droplet microfluidics to couple multiwell plate-based assays to microchip electrophoresis (MCE) to screen enzyme modulators. Samples contained in multiwell plates are reformatted in to plugs with a sample volume of 8 nL segmented by an immiscible oil. The segmented flow sample streams are coupled to a hybrid polydimethylsiloxane-glass microfluidic device capable of selectively extracting the aqueous samples from the droplet stream and rapidly analyzing by MCE with laser-induced fluorescence detection. This system was demonstrated by screening a test library of 140 compounds against using protein kinase A. For each sample in the screen, two droplets are generated, allowing approximately 6 MCE injections per sample. Using a 1 s separation at 2000 V/cm, we are able to analyze 96 samples in 12 min. Separation resolution between the internal standard, substrate, and product is 1.2 and average separation efficiency is 16,000 plates/s using real samples. Twenty-five compounds were identified as modulators during primary screening and verified using dose-response curves.
| S-EPMC4204908 | biostudies-other
Project description:A study was initiated to construct a micro-reactor for protein digestion based on trypsin-coated fused-silica capillaries. Initially, surface plasmon resonance was used both for optimization of the surface chemistry applied in the preparation and for monitoring the amount of enzyme that was immobilized. The highest amount of trypsin was immobilized on dextran-coated SPR surfaces which allowed the covalent coupling of 11 ng mm(-2) trypsin. Fused-silica capillaries were modified in a similar manner and the resulting open-tubular trypsin-reactors having a pH optimum of pH 8.5, display a high activity when operated at 37 degrees C and are stable for at least two weeks when used continuously. Trypsin auto-digestion fragments, sample carry-over, and loss of signal due to adsorption of the protein were not observed. On-line digestion without prior protein denaturation, followed by micro-LC separation and photodiode array detection, was tested with horse-heart cytochrome C and horse skeletal-muscle myoglobin. The complete digestion of 20 pmol microL(-1) horse cytochrome C was observed when the average residence time of the protein sample in a 140 cm x 50 microm capillary immobilized enzyme reactor (IMER) was 165 s. Mass spectrometric identification of the injected protein on the basis of the tryptic peptides proved possible. Protein digestion was favorable with respect to reaction time and fragments formed when compared with other on-line and off-line procedures. These results and the easy preparation of this micro-reactor provide possibilities for miniaturized enzyme-reactors for on-line peptide mapping and inhibitor screening.
| S-EPMC2117336 | biostudies-other
Project description:BackgroundHigh-throughput peptide and protein identification technologies have benefited tremendously from strategies based on tandem mass spectrometry (MS/MS) in combination with database searching algorithms. A major problem with existing methods lies within the significant number of false positive and false negative annotations. So far, standard algorithms for protein identification do not use the information gained from separation processes usually involved in peptide analysis, such as retention time information, which are readily available from chromatographic separation of the sample. Identification can thus be improved by comparing measured retention times to predicted retention times. Current prediction models are derived from a set of measured test analytes but they usually require large amounts of training data.ResultsWe introduce a new kernel function which can be applied in combination with support vector machines to a wide range of computational proteomics problems. We show the performance of this new approach by applying it to the prediction of peptide adsorption/elution behavior in strong anion-exchange solid-phase extraction (SAX-SPE) and ion-pair reversed-phase high-performance liquid chromatography (IP-RP-HPLC). Furthermore, the predicted retention times are used to improve spectrum identifications by a p-value-based filtering approach. The approach was tested on a number of different datasets and shows excellent performance while requiring only very small training sets (about 40 peptides instead of thousands). Using the retention time predictor in our retention time filter improves the fraction of correctly identified peptide mass spectra significantly.ConclusionThe proposed kernel function is well-suited for the prediction of chromatographic separation in computational proteomics and requires only a limited amount of training data. The performance of this new method is demonstrated by applying it to peptide retention time prediction in IP-RP-HPLC and prediction of peptide sample fractionation in SAX-SPE. Finally, we incorporate the predicted chromatographic behavior in a p-value based filter to improve peptide identifications based on liquid chromatography-tandem mass spectrometry.
| S-EPMC2254445 | biostudies-literature
Project description:Cannabis sativa L. is widely used as recreational illegal drugs. Illicit Cannabis profiling, comparing seized samples, is challenging due to natural Cannabis heterogeneity. The aim of this study was to use GC-FID and GC-MS herbal fingerprints for intra (within)- and inter (between)-location variability evaluation. This study focused on finding an acceptable threshold to link seized samples. Through Pearson correlation-coefficient calculations between intra-location samples, 'linked' thresholds were derived using 95% and 99% confidence limits. False negative (FN) and false positive (FP) error rate calculations, aiming at obtaining the lowest possible FP value, were performed for different data pre-treatments. Fingerprint-alignment parameters were optimized using Automated Correlation-Optimized Warping (ACOW) or Design of Experiments (DoE), which presented similar results. Hence, ACOW data, as reference, showed 54% and 65% FP values (95 and 99% confidence, respectively). An additional fourth root normalization pre-treatment provided the best results for both the GC-FID and GC-MS datasets. For GC-FID, which showed the best improved FP error rate, 54 and 65% FP for the reference data decreased to 24 and 32%, respectively, after fourth root transformation. Cross-validation showed FP values similar as the entire calibration set, indicating the representativeness of the thresholds. A noteworthy improvement in discrimination between seized Cannabis samples could be concluded.
| S-EPMC8587667 | biostudies-literature
Project description:While encouraging progress has been made on switchable nanopores to mimic biological channels and pores, it remains a great challenge to realize long tubular pores with a dynamic open-closed motion. Here we report μm-long, dynamic tubular pores that undergo rapid switching between open and closed states in response to a thermal signal in water. The tubular walls consist of laterally associated primary fibrils stacked from disc-shaped molecules in which the discs readily tilt by means of thermally regulated dehydration of the oligoether chains placed on the wall surfaces. Notably, this pore switching mediates a controlled water-pumping catalytic action for the dehydrative cyclization of adenosine monophosphate to produce metabolically active cyclic adenosine monophosphate. We believe that our work may allow the creation of a variety of dynamic pore structures with complex functions arising from open-closed motion.
| S-EPMC4633957 | biostudies-literature