Timo T. Sachsenberg

onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

The paper introduces onsite, a framework for estimating false localization rates in phosphoproteomics, showing pyLucXor achieves high accuracy and localization count.

mzQC: a versatile way to communicate quality information for biological mass spectrometry

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

π-MSNet: A large-scale, AI-ready and continuously reprocessed proteomics data resource

The paper introduces π-MSNet, a large-scale proteomics dataset for AI training and benchmarking, showing performance improvements when models are retrained on it.

Deep learning enables direct HLA typing from immunopeptidomics data

This paper introduces Immunotype, a deep learning model that directly types HLA alleles from immunopeptidomics data with 87.2% accuracy.

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

pmultiqc generates metadata-aware QC reports for proteomics data using standardized metrics and integrates with existing workflows and cloud services.

quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments.

quantms-rescoring improves proteomics analysis by integrating multiple search engines and machine learning, increasing identified spectra and quantifying more phosphorylated peptides and modification sites.

Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry

The paper introduces chemical crosslinking with mass spectrometry and a new search engine, NuXL, to identify nucleic acid-protein crosslinks at amino acid resolution, enhancing structural analysis.

ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

ibaqpy computes iBAQ values for proteomics data using SDRF metadata, improving scalability and reproducibility in large-scale experiments.

Unified and standardized mass spectrometry data processing in Python using spectrum_utils

The paper updates the spectrum_utils Python package to integrate mass spectrometry standards, enhance data processing, and unify visualization across proteomics and metabolomics applications.

A Universal Language for Finding Mass Spectrometry Data Patterns

MassQL, an open-source query language, lets users search raw mass spectrometry data from any vendor for isotope, fragmentation and neutral-loss patterns, from one file to entire public repositories.

A comprehensive evaluation of consensus spectrum generation methods in proteomics

The paper evaluates consensus spectrum generation methods in proteomics, finding BEST and BIN to be the most reliable for peptide identification.

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

The paper introduces tools to generate proteogenomics databases using ENSEMBL resources, revealing non-canonical peptides in public datasets.

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.

DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics

DIAproteomics is an automated pipeline for analyzing DIA proteomics and peptidomics data, offering tools for spectral library generation, alignment, and statistical analysis.

SmartPeak automates targeted and quantitative metabolomics data processing

SmartPeak automates metabolomics data processing with algorithms for alignment, calibration, and peak integration, improving reproducibility and throughput.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

The paper introduces NASE, a database search engine for RNA mass spectrometry data, demonstrating its ability to identify modified RNA sequences in three datasets.

EPIFANY - A method for efficient high-confidence protein inference

EPIFANY improves protein inference accuracy and efficiency by combining loopy belief propagation with convolution trees, outperforming existing methods on benchmark data.

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

ThermoRawFileParser converts Thermo RAW files to open formats like mzML, enabling broader use with workflow systems and providing a user-friendly interface.