Biology subjects

van der Zwaan, R.

Publications and source records attributed to van der Zwaan, R..

3 recordsLinked to original sources

bioRxiv2025

Meta-PepView: a metaproteomics performance evaluation and visualization platform

Microbial community proteomics is rapidly gaining traction as it allows exploration of functional processes in microbial ecosystems. Consequently, there is a growing need for user-friendly tools that enable performance evaluation and interactive visualization of the increasingly complex community proteomics data. We introduce meta-PepView, a web-based platform that enables performance evaluation and interactive visualization of metaproteomics data, ensuring transparent and reproducible metaproteomics experiments. Meta-PepView integrates spectral sequencing outputs and databases from common proteomics search engines and classification tools. It runs efficiently on laptop or desktop PCs and can be deployed as a Docker container or installed with pip, from which it is operated through the web browser. Its modular design allows easy expansion with new data sources and annotation databases. Meta-PepView is an open-source Python platform that is freely available under the Apache License 2.0. The code is available on GitHub: https://github.com/ramonzwaan/metapepview/. Here, we showcase the meta-PepView platform with data from synthetic communities and previously published microbiome studies.

systems biology↗

bioRxiv2024

NovoLign: metaproteomics by sequence alignment

Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.

systems biology↗

bioRxiv2022

Comparative metaproteomics demonstrates different views on the complex granular sludge microbiome

The tremendous progress in sequencing technologies has made 16S amplicon and whole metagenome sequencing routine in microbiome studies. Furthermore, advances in mass spectrometric techniques has expanded conventional proteomics into the field of microbial ecology. Commonly referred to as metaproteomics, this approach measures the gene products (i.e., proteins) to subsequently identify the actively-expressed metabolic pathways and the protein-biomass composition of complete microbial communities. However, more systematic studies on metaproteomic and genomic approaches are urgently needed, to determine the orthogonal character of these approaches. Here we describe a deep, comparative metaproteomic study on the complex aerobic granular sludge microbiome obtained from different wastewater treatment plants. Thereby, we demonstrate the different views that can be obtained on the central nutrient-removing organisms depending on the omic approach and reference sequence databases. Furthermore, we demonstrate a homogenized Genome Taxonomy Database (GTDB) that subsequently enables a more accurate interpretation of data from different omics approaches. Ultimately, our systematic study underscores the importance of metaproteomics in the characterization of complex microbiomes; and the necessity of accurate reference sequence databases to improve the comparison between approaches and accuracy in scientific reporting.

systems biology↗