Vincenth Brennsteiner

FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics

AlphaPeptTools provides a scverse-native Python package for analyzing MS-based proteomics data, enabling scalable analysis and integration with other modalities.

Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data

The paper introduces spatialproteomics, a Python toolbox for analyzing highly multiplexed fluorescence images, demonstrating its use on lymph node and lymphoma data.

HIP-MS: An ultra-high-throughput, sensitive, and versatile affinity enrichment platform for static and dynamic interactome profiling

HIP-MS is an automated platform for high-throughput interactome profiling that improves sensitivity and throughput compared to traditional AE-MS methods.

A simplified perchloric acid workflow with neutralization (PCA-N) for democratizing deep plasma proteomics at population scale

This paper introduces PCA-N, a simplified perchloric acid workflow for plasma proteomics that enables high-throughput, cost-effective analysis of large population samples.

AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics

AlphaDIA enables end-to-end transfer learning for feature-free proteomics, improving identification and quantification of post-translational modifications.