Veit Schwämmle

DORSSAA: Drug-target interactOmics Resource based on Stability/Solubility Alteration Assay

DORSSAA provides a platform for analyzing stability and solubility alteration data to identify drug-protein interactions and therapeutic targets.

Modeling Synaptic Maturation from Growth Cone to Synapse in Human Organoids

This study develops a centrifugation protocol to isolate growth cones and immature synapses from human organoids, capturing synaptic development stages and enabling models for studying synaptic function and dysfunction.

Informative Missingness in Nominal Data: A Graph-Theoretic Approach to Revealing Hidden Structure

The paper presents a graph-theoretic approach to analyze missing data in nominal datasets, revealing hidden structures by treating missingness as informative signals.

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

How to deal with internal fragment ions?

The paper introduces a graph-based method to annotate internal fragment ions in tandem mass spectra, improving proteoform sequencing and modification localization.

Data mining antibody sequences for database searching in bottom-up proteomics

The paper extends antibody databases for mass spectrometry by mining millions of sequences from the OAS database to improve antibody peptide identification in SARS-CoV-2 plasma samples.

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

WOMBAT-P benchmarks label-free proteomics workflows by comparing four analysis pipelines using standardized metrics and datasets.

Variance Analysis of LC-MS Experimental Factors and Their Impact on Machine Learning

The paper analyzes variance sources in LC-MS data and evaluates transfer learning's impact on ML performance across public datasets.

VIQoR: a web service for Visually supervised protein Inference and protein Quantification

VIQoR provides a web service for protein inference and quantification with interactive visualization, using algorithms and visualization tools to analyze proteomics data.

MS2AI: Automated repurposing of public peptide LC-MS data for machine learning applications

The paper introduces MS2AI, a pipeline that automates the collection and preparation of LC-MS data for machine learning, and presents a CNN for oxidized peptide identification.

A proteomics sample metadata representation for multiomics integration, and big data analysis.

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.

Synaptic transmission induces site-specific changes in sialylation on N-linked glycoproteins in rat nerve terminals

This study identifies site-specific changes in sialylation of N-linked glycoproteins in rat nerve terminals following brief depolarization.

PolySTest: Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features

PolySTest improves proteomics data analysis by detecting differentially regulated proteins with missing values, increasing confidence and sensitivity in muscle differentiation studies.

Visualization of the Dynamics of Histone Modifications and Their Crosstalk Using PTM-CrossTalkMapper

The paper introduces PTM-CrossTalkMapper, a tool to visualize histone PTM dynamics and crosstalk across experimental conditions, showing its application in mouse aging studies.

ComplexBrowser: a tool for identification and quantification of protein complexes in large scale proteomics datasets

ComplexBrowser identifies and quantifies protein complexes in proteomics datasets using a supervised approach, revealing coordinated regulation and providing insights into biological processes.

Quantitative behavior of protein complexes in human cells

The paper develops a computational tool to analyze protein complex behavior across human cell types using mass spectrometry data and provides a web service for co-regulation analysis.

IsoProt: A complete and reproducible workflow to analyse iTRAQ/TMT experiments

IsoProt provides a reproducible workflow for analyzing iTRAQ/TMT proteomics data using open-source tools and a containerized environment.