Tanja Holstein
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View article: Limitations of <i>de novo</i> sequencing in resolving sequence ambiguity
Limitations of <i>de novo</i> sequencing in resolving sequence ambiguity Open
De novo peptide sequencing enables peptide identification from fragmentation spectra without relying on sequence databases. However, incomplete spectra create ambiguity, making unambiguous identification challenging. Recent deep learning a…
View article: MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics
MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics Open
The global SARS-CoV-2 pandemic emphasized the need for accurate pathogen diagnostics. While genomics is the gold standard, integrating mass spectrometry-based proteomics offers additional benefits. However, current proteomic and genomic re…
View article: The microbiologist's guide to metaproteomics
The microbiologist's guide to metaproteomics Open
Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiom…
View article: MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing
MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing Open
Motivation A central problem for metaproteomic analysis is the often-unknown taxonomic composition of the analyzed microbiomes. Using a database search, the standard approach requires prior knowledge of which proteins and taxa to include i…
View article: The Microbiologist’s Guide to Metaproteomics
The Microbiologist’s Guide to Metaproteomics Open
Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiom…
View article: Boosting metaproteomics identification rates and taxonomic specificity with MS<sup>2</sup>Rescore
Boosting metaproteomics identification rates and taxonomic specificity with MS<sup>2</sup>Rescore Open
Background Metaproteomics, the study of the collective proteome within microbial ecosystems, has gained increasing interest over the past decade. However, peptide identification rates in metaproteomics remain low compared to single-species…
View article: Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing
Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing Open
Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing p…
View article: The Microbiologist’s Guide to Metaproteomics
The Microbiologist’s Guide to Metaproteomics Open
Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiom…
View article: Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing
Metaproteomics beyond databases: addressing the challenges and potentials of de novo sequencing Open
Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing p…
View article: PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways
PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways Open
Background Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights i…
View article: The Peptonizer2000: bringing confidence to metaproteomics
The Peptonizer2000: bringing confidence to metaproteomics Open
Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of mat…
View article: MultiStageSearch: a multi-step proteogenomic workflow for taxonomic identification of viral proteome samples adressing database bias
MultiStageSearch: a multi-step proteogenomic workflow for taxonomic identification of viral proteome samples adressing database bias Open
The recent years, with the global SARS-Cov-2 pandemic, have shown the importance of strain level identification of viral pathogens. While the gold-standard approach for unkown viral sample identification remains genomics, studies have show…
View article: PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores
PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores Open
Motivation Inferring taxonomy in mass spectrometry-based shotgun proteomics is a complex task. In multi-species or viral samples of unknown taxonomic origin, the presence of proteins and corresponding taxa must be inferred from a list of i…
View article: PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores
PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores Open
Motivation Inferring taxonomy in mass spectrometry-based shotgun proteomics is a complex task. In multi-species or viral samples of unknown taxonomic origin, the presence of proteins and corresponding taxa must be inferred from a list of i…
View article: Optimization of coupling and global collapse in diffusively coupled socio-ecological resource exploitation networks
Optimization of coupling and global collapse in diffusively coupled socio-ecological resource exploitation networks Open
Single- and multi-layer complex networks have been proven as a powerful tool to study the dynamics within social, technological, or natural systems. An often observed common goal is to optimize these systems for specific purposes by minimi…