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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.
We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using
these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ∼3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ∼5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ∼4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. We also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration.
The lead authors failed to name two collaborators as co-authors. The authors listed should include:
Miss Claudia L. Compean-Gonzalez (ORCID:
0000-0002-2367-8450) and Dr. Giacomo Ceccone (ORCID:
0000-0003-4637-0771).
These co-authors participated in VAMAS project A27, provided data that were analyzed and presented in this publication (and supporting information), and reviewed the manuscript before submission.
To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.
Im Rahmen eines von der Kulturstiftung des Bundes und der Kulturstiftung der Länder geförderten
Projektes zum Erhalt naturkundlicher Nasssammlungen wurden 1) der Zustand der Sammlungen bewertet
(Profiling; Analyse der Vergällungsmittel), 2) über Workshops Expertenwissen in das Projekt gebracht,
3) neue archivbeständige Materialien und Managementmaßnahmen eingeführt (Borosilikat-Gläser und -
Röhrchen, Augenwatte, Tefloneinlagen, Japanpapier, archivbeständige Kleber und Papier, Etikettenaufbewahrung;
digitales Dichtemessgerät, Alcomon-Indikator, Kontrollintervalle), 4) Erhaltungsmaßnahmen
zur langfristigen Konservierung in großem Umfange durchgeführt (Messen der Alkoholkonzentration,
Umsetzen von Präparaten in geeignetere Gefäße, Wiederverschluss von Schaugläsern) und 5) Erfahrungen
und Diskussionsergebnisse zusammengestellt, nicht ohne auf Wissenslücken und wünschenswerte
Forschungsaspekte hinzuweisen. Das Projekt profitierte besonders von der Expertise aus den Materialwissenschaften
und der Papierrestaurierung. Das Museum für Naturkunde Berlin kooperierte eng mit
dem Berliner Medizinhistorischen Museum der Charité, der Zoologischen Staatssammlung München und
dem Forschungsinstitut Senckenberg in Frankfurt. Letzteres Museum führte ein eigenes, themenverwandtes
KUR-Projekt Restauration der Sammlungen 'Vergleichende Anatomie, Embryologie und Histologie'
des Naturmuseums Senckenberg durch.
Zur Charakterisierung von luftgekoppelten Ultraschallwandlern werden mehrere verschiedene Methoden und Verfahren angewendet. Durch die unterschiedlichen Herangehensweisen werden oft unterschiedliche Prüfkopfpara-meter und Schallfeldgrößen ermittelt, was einen direkten Vergleich von Datenblättern erschwert. Für die Charakterisierung von Kontakt- und Tauchtechnikprüfköpfen hat sich ISO 22232-2:2021 bereits etabliert, allerdings ist diese Norm nicht auf die luftgekoppelten Wandlertechnologien direkt übertragbar. Daher erkannten Hersteller, Forschungseinrichtungen und Anwender den Bedarf an einer Richtlinie zur einheitlichen Charakterisierung von luftgekoppelten Wandlern. Gemeinsam arbeiten sie aktuell im Rahmen des Unterausschusses „Luftgekoppelte Ultraschallprüfung“ der DGZfP an der Erstellung einer solcher Richtlinie mit dem Anspruch, die bestehende Normung um die luftgekoppelte Prüfung zu erweitern und somit die Vereinheitlichung der Charakterisierung dieser Wandler zu erleichtern.
In diesem Beitrag wird ein Überblick über den geplanten Inhalt der Richtlinie und über die Methoden zur akustischen Charakterisierung von luftgekoppelten Ultraschallwandlern gegeben. Insbesondere werden verschiedene Methoden der Ermittlung von wichtigen Wandlerparametern wie z.B. Empfindlichkeit, Mittenfrequenz, Bandbreite, Fokusgröße und Fokusabstand dargestellt und verglichen.
This guideline was drafted following and complementing the norm ISO 22232-2:2020(E) to include air-coupled ultrasonic transducers. This document specifies the characteristics of probes used for non-destructive air-coupled ultrasonic testing with center frequencies above 20 kHz, with focusing or without focusing means.
Sulphurous additives for polystyrene: Influencing decomposition behavior in the condensed phase
(2015)
The thermal decomposition behaviour of polystyrene (PS) containing sulphur and phosphorus additives was investigated, using thermogravimetry coupled with Fourier transform infrared spectroscopy (TGA-FTIR). It was found that the additives influence the decomposition process of the polymer in the condensed phase, resulting in a decrease in styrene monomer formation and an increase in styrene oligmer derivatives. Via reference measurements with binary mixtures it was found that the presence of sulphur additives influences the radicalic decomposition process of PS. In combination with quantum chemical calculations it was concluded that this is due to the formation of radicals that abstract hydrogen from the polymer matrix at lower temperatures, disfavouring the radicalic decomposition pathway leading to styrene.
The improved Monte-Carlo (MC) method for standard-less analysis in laser induced breakdown spectroscopy (LIBS) is presented. Concentrations in MC LIBS are found by fitting model-generated synthetic spectra to experimental spectra. The current version of MC LIBS is based on the graphic processing unit (GPU) computation and reduces the analysis time down to several seconds per spectrum/sample. The previous version of MC LIBS which was based on the central processing unit (CPU) computation requested unacceptably long analysis times of 10's minutes per spectrum/sample. The reduction of the computational time is achieved through the massively parallel computing on the GPU which embeds thousands of co-processors. It is shown that the number of iterations on the GPU exceeds that on the CPU by a factor > 1000 for the 5-dimentional parameter space and yet requires > 10-fold shorter computational time. The improved GPU-MC LIBS outperforms the CPU-MS LIBS in terms of accuracy, precision, and analysis time. The performance is tested on LIBS-spectra obtained from pelletized powders of metal oxides consisting of CaO, Fe2O3, MgO, and TiO2 that simulated by-products of steel industry, steel slags. It is demonstrated that GPU-based MC LIBS is capable of rapid multi-element analysis with relative error between 1 and 10's percent that is sufficient for industrial applications (e.g. steel slag analysis). The results of the improved GPU-based MC LIBS are positively compared to that of the CPU-based MC LIBS as well as to the results of the standard calibration-free (CF) LIBS based on the Boltzmann plot method.