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Metaproteomics, the study of the collective proteome within a microbial ecosystem, has substantially grown over the past few years. This growth comes from the increased awareness that it can powerfully supplement metagenomics and metatranscriptomics analyses. Although metaproteomics is more challenging than single-species proteomics, its added value has already been demonstrated in various biosystems, such as gut microbiomes or biogas plants. Because of the many challenges, a variety of metaproteomics workflows have been developed, yet it remains unclear what the impact of the choice of workflow is on the obtained results. Therefore, we set out to compare several well-established workflows in the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. In this benchmarking study, we evaluated the influence of different workflows on sample preparation, mass spectrometry acquisition, and bioinformatic analysis on two samples: a simplified, lab-assembled human intestinal sample and a complex human fecal sample. We find that the same overall biological meaning can be inferred from the metaproteome data, regardless of the chosen workflow. Indeed, taxonomic and functional annotations were very similar across all sample-specific data sets. Moreover, this outcome was consistent regardless of whether protein groups or peptides, or differences at the spectrum or peptide level were used to infer these annotations. Where differences were observed, those originated primarily from different wet-lab methods rather than from different bioinformatic pipelines. The CAMPI study thus provides a solid foundation for benchmarking metaproteomics workflows, and will therefore be a key reference for future method improvement. [doi:10.25345/C5SX64D9M] [dataset license: CC0 1.0 Universal (CC0 1.0)]
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.
In 2019 the Bundesanstalt für Materialforschung und –prüfung (BAM) conducted a benchmarking to compare the operations of European accreditation bodies and to identify best practices, with the aim of improving key processes in accreditation. Ten European accreditation bodies attended the comparison, four of which had already taken part in the pilot phase of the benchmarking project, which was conducted in 2017 by the German accreditation body Deutsche Akkreditierungsstelle GmbH (DAkkS) and BAM.
The study, designed to examine and compare the operation of accreditation bodies in Europe, used a management tool called Process Maturity Benchmarking Tool, which was especially elaborated and validated for this purpose in the pilot phase, in order to determine the values of indicators, thus enabling a comparison of the accreditation bodies despite different operational processes and organizational forms. The management tool is based on the analysis of selected processes with high relevance for the operation of accreditation bodies. The processes are derived from a process map designed for accreditation bodies in a universally applicable way. The indicators used to characterize the processes come from two sources: The first source relates to data already available from internal databases, reports, financial audits, and others. The second source is derived from the self-evaluation of process maturity performed by the accreditation bodies. The criteria for evaluating process maturities were designed by applying the criteria of the EFQM excellence model 2013 of the European Foundation for Quality Management (EFQM) to the processes identified in the process map.
The results of the analysis were presented to and discussed with representatives of the ten accreditation bodies at a Results-Workshop that took place at BAM on 21/22 January 2020.
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
ACEnano is an EU-funded project which aims at developing, optimising and validating methods for the detection and characterisation of nanomaterials (NMs) in increasingly complex matrices to improve confidence in the results and support their use in regulation. Within this project, several interlaboratory comparisons (ILCs) for the determination of particle size and concentration have been organised to benchmark existing analytical methods. In this paper the results of a number of these ILCs for the characterisation of NMs are presented and discussed. The results of the analyses of pristine well-defined particles such as 60 nm Au NMs in a simple aqueous suspension showed that laboratories are well capable of determining the sizes of these particles. The analysis of particles in complex matrices or formulations such as consumer products resulted in larger variations in particle sizes within technologies and clear differences in capability between techniques. Sunscreen lotion sample analysis by laboratories using spICP-MS and TEM/SEM identified and confirmed the TiO2 particles as being nanoscale and compliant with the EU definition of an NM for regulatory purposes. In a toothpaste sample orthogonal results by PTA, spICP-MS and TEM/SEM agreed and stated the TiO2 particles as not fitting the EU definition of an NM. In general, from the results of these ILCs we conclude that laboratories are well capable of determining particle sizes of NM, even in fairly complex formulations.
This study was designed to examine and compare the operation of accreditation bodies in Europe. A management tool, the Process Maturity Benchmarking Tool (PMBT), was elaborated and validated by applying it to various accreditation bodies. By applying the tool, the values of indicators were determined, thus enabling a comparison of the accreditation bodies despite different operational processes and organizational forms.
The management tool PMBT is based on the analysis of selected processes with high relevance for the operation of accreditation bodies. The processes are derived from a process map designed for accreditation bodies in a universally applicable way. The indicators used to characterize the processes come from two sources: The first source relates to data already available from internal databases, reports, financial audits etc. The second source is derived from a self-evaluation of process maturity performed by the accreditation bodies. The criteria for evaluating process maturity were designed by applying the criteria of the EFQM excellence model 2013 of the European Foundation for Quality Management (EFQM) to the processes identified in the process map.
The project Comparison of the Operation of Accreditation Bodies in Europe comprised three stages. In the first stage, the processes of accreditation bodies were systematically analyzed. A process map was developed and processes of special relevance for the performance of accreditation bodies were identified and underpinned by indicators as described above. In the second stage, the processes of the German accreditation body DAkkS were assigned to the tool. This stage was used to check and modify the indicators when necessary. In the third stage, the transferability of the model was analyzed by extension to seven other accreditation bodies operating in Europe. The third stage of the project ended with a workshop attended by the eight accreditation bodies, which was used to present and discuss the results of the comparison and to identify best practices.
Accreditation is one of the pillars of a national Quality Infrastructure, as the competence of conformity assessment bodies is assured through accreditation performed by accreditation bodies. To compare the operation of accreditation bodies in Europe and to identify best practices, a management tool, the Process Maturity Benchmarking Tool, was developed and validated by applying it to European accreditation bodies. The benchmarking project comprised two major phases: In the first phase, the processes of accreditation bodies were systematically analyzed. A process map was developed, and processes of special relevance were identified and underpinned by indicators. In the second phase, the practical applicability of the theoretical model was demonstrated by analyzing the processes of eight European accreditation bodies. The results of this comparative assessment were subsequently discussed in a workshop with experts from those accreditation bodies, giving the opportunity to identify best practices.
This article has a twofold objective. First, to present a method to benchmark European accreditation bodies, based on the European Foundation for Quality Management excellence model. The successful application of the Process Maturity Benchmarking Tool gives evidence that it is a suitable and capable management tool to assess the processes of the European accreditation bodies and to benchmark them. Second, the article presents the results of the first adaption of the Process Maturity Benchmarking Tool. A general trend of process maturity was identified: While processes based on stakeholder involvement tend to have an overall lower maturity on average, internal processes are more mature.
In 2019 the German federal institute Bundesanstalt für Materialforschung und –prüfung (BAM) conducted a benchmarking to compare the operations of European accreditation bodies and to identify best practices, with the aim of improving key processes in accreditation. Ten European accreditation bodies attended the comparison, four of which had already taken part in the pilot phase of the benchmarking project, which was conducted in 2017 by the German accreditation body Deutsche Akkreditierungsstelle GmbH (DAkkS) and the BAM.
The study, designed to examine and compare the operation of accreditation bodies in Europe, used a management tool called Process Maturity Benchmarking Tool, which was especially elaborated and validated for this purpose in the pilot phase, in order to determine the values of indicators, thus enabling a comparison of the accreditation bodies despite different operational processes and organizational forms. The management tool is based on the analysis of selected processes with high relevance for the operation of accreditation bodies. The processes are derived from a process map designed for accreditation bodies in a universally applicable way. The indicators used to characterize the processes come from two sources: The first source relates to data already available from internal databases, reports, financial audits, and others. The second source is derived from the self-evaluation of process maturity performed by the accreditation bodies. The criteria for evaluating process maturities were designed by applying the criteria of the EFQM excellence model 2013 of the European Foundation for Quality Management (EFQM) to the processes identified in the process map.
The results of the analysis were presented to and discussed with representatives of the ten accreditation bodies at a Results-Workshop that took place at BAM on 21/22 January 2020.
In this presentation a wrap-up of the results was given to the HHC of EA
Accreditation is one of the relevant tasks in a modern Quality Infrastructure, as the competence of conformity assessment bodies is assured through accreditation performed by accreditation bodies. To compare the operation of accreditation bodies in Europe and identify best practices a management tool was elaborated and validated by applying it to eight accreditation bodies. The tool made a comparison of the operations of the accreditation bodies possible, despite different sizes, operational processes and organizational forms.
The benchmarking project comprised three stages. In the first stage, the processes of accreditation bodies were systematically analyzed. A process map was developed and processes of special relevance for the performance of accreditation bodies were identified and underpinned by indicators. In the second stage, the processes of the German accreditation body Deutsche Akkreditierungsstelle GmbH (DAkkS) were assigned to the tool. This validation stage was used to check and modify the indicators when necessary. In the third stage, the transferability of the model was analyzed by extension to seven other accreditation bodies operating in Europe. The third stage of the project resulted in a workshop attended by experts from the participating ABs, which was used to discuss the results of the comparison and to identify best practices.
The long-term goal of the benchmarking project for European accreditation bodies is twofold: First of all, the project is supposed to help the European accreditation attending bodies to improve their processes by identifying best practices and by learning from others. Possibly Secondly, the results of the analysis can be used by the European Cooperation for Accreditation (EA) to identify differences in the operation of the European accreditation bodies and based on this knowledge to promote harmonization of accreditation activities in Europe.