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Metaproteomics has substantially grown over the past years and supplements other omics approaches by bringing valuable functional information, enabling genotype- phenotype linkages and connections to metabolic outputs. Currently, a wide variety of metaproteomic workflows is available, yet their impact on the results remains to be thoroughly assessed.
Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry acquisition, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.
Although bioinformatic pipelines contributed to variability in peptide identification, wet-lab workflows were the most important source of differences between analyses. Overall, these peptide-level differences largely disappeared at the protein group level. Differences were observed between peptide- and protein-centric approaches for the predicted community composition but similar functional profiles were found across workflows.
The CAMPI findings demonstrate the robustness of current metaproteomics research and provide a perspective for future benchmarking studies.
The use of inorganic lanthanide-doped upconversion nanoparticles (UCNP) in bioimaging and cellular studies requires biocompatible particles. One possible cause of UCNP toxicity is the release of potentially harmful fluoride and lanthanide ions as revealed by dilution studies in aqueous environments, particularly under high dilution conditions. To address this issue, suitable surface coatings preventing such effects in combination with fast screening methods suited for online monitoring and in situ analyses are desired.
Here we present systematic studies of differently sized β-NaYF4:Yb,Er UCNP stabilized with different surface coatings and hydrophilic ligands varying in binding strength to the particle surface in various aqueous environments at different temperatures and UCNP concentrations. The concentration of the fluoride and lanthanide ions released upon particle dissolution was quantified electrochemically with a fluoride ion-sensitive electrode and inductively coupled plasma optical emission spectrometry (ICP-OES) and monitored fluorometrically, thereby exploiting the sensitivity of the upconversion luminescence to changes in size and surface chemistry. Moreover, changes in surface chemistry were determined with X-Ray photoelectron spectroscopy (XPS). Based upon our results, we could derive optimum screening parameters for UCNP stability studies and determine conditions and coating procedures and ligands for enhancing UCNP stability in aqueous environments.