Project description:Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high throughput experiments. Most importantly, it enables results dependent acquisition (RDA) where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide- and glycan-moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks future development of RDA technology to transcend data acquisition.
2023-03-13 | PXD040716 | Pride
Project description:Early diagnosis of brain abscess using real-time electron microscopy and metagenomics.
| PRJEB40138 | ENA
Project description:Real time detection of AUFI pathogens using Nanopore sequencing: A feasibility and efficacy study
Project description:<p>Commercial low-field (LF) magnetic resonance spectroscopy (MRS) offers a route to rapid and repeated \textit{in vivo} metabolite tracking, however its sensitivity and interpretability at physiological concentrations remain underexplored. Here we evaluate the performance of an 80 MHz benchtop nuclear magnetic resonance (NMR) spectrometer (Bruker Fourier 80) across several key blood metabolites at physiological concentrations, ranging between 0.05 and 10.0 mmol/L. We characterise the relationship between metabolite concentration, acquisition time, and signal-to-noise ratio (SNR) for multiple pulse sequences, and assess how the choice of SNR definition influences reported detection and quantification thresholds. Metabolites present at millimolar levels, such as glucose and lactate, were readily detectable within 20 seconds, with the water-suppressing \texttt{wet} pulse sequence yielding the highest SNR at fixed acquisition time. Concentration differences were also readily distinguishable. In contrast, sub-millimolar metabolites such as citrate require over four minutes to reach conventional detection thresholds, constraining their applicability to rapid metabolite tracking via MRS. To address interpretability in low-SNR data, we introduce a template-fitting approach based on simulated standards from CcpNMR AnalysisAssign, which stabilised relative metabolite quantification under low-SNR conditions. These results establish quantitative benchmarks for LF NMR metabolite detection and demonstrate how simulation-assisted analysis can extend its utility. These findings inform both the selection of target metabolites and optimisation strategies for emerging commercial \textit{in vivo} MRS devices, including the DigiScan™ finger-scanner, supporting their development as accessible tools for real-time metabolic tracking in personalised healthcare.</p><p><br></p><p> </p>
2025-12-29 | MTBLS6262 | MetaboLights
Project description:Real-time Nanopore de novo assembly of ESKAPE pathogens
Project description:Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain.
| PRJEB36528 | ENA
Project description:EMG produced TPA metagenomics assembly of PRJEB36528 data set (Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain.).
Project description:In this project we want to compare ovarian cell cancer treated or non treated with cis-platinum. As acquisition strategy we have used a Real Time Search MS3 method in an Orbitrap Eclipse. The acquisition cycle began with an MS1 scanwhere the most intense ions were selected for fragmentation in the ion trap using CID. MS2 spectra were searched in real time with data acquisition using the sp-human database. MS2 spectra with an Xcorr greater than or equal to 1 and less than 10 ppm precursor mas error, triggered the submission of an MS3 spectrum to the instrument. MS3 spectrum, were collected using the multinotch MS3-based TMT method, in a way were ten MS2 fragment ions were captured in the MS3 precursor population using isolation waveforms with multiple frequency notches
Project description:P. aeruginosa isolates from keratitis and healthy conjunctival sacs were obtained. The transcriptome profile of P. aeruginosa was characterized by a high throughput RNA-seq strategy using the Illumina HiSeq 2500 platform. The DEGs were analyzed with DESeq and validated through quantitative real-time polymerase chain reaction (PCR) and with experimental mice.