LC-MS data processing tool for large-scale metabolomics experiments.

Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing

The MetaRbolomics book. A review of R packages in BioC, CRAN, gitlab and github.

AutoRT: Peptide retention time prediction using deep learning

Python module for lipidomics LC MS/MS data analysis

A Bioconductor R package - Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

https://taxonomicallyinformedannotation.github.io/tima

A python package for protein inference in Mass Spectrometric data analysis.

LipidHunter is capable to perform bottom up identification of lipids from LC-MS/MS and shotgun lipidomics data by resembling a workflow of manual spectra annotation. LipidHunter generates interactive HTML output with its unique six-panel-image, which provides an easy way to review, store, and share the identification results.

Code, Data and Results of the publication: "Probabilistic Framework for Integration of Tandem-Mass Spectrum and Retention Time Information in Small Molecule Identification" by Bach et al. 2020

High-throughput MS/MS annotation with a in-house database

BMDMS-NP

tools collection of Sipros for stable isotopic mass spectrum metaproteomics proteomics research

https://adafede.github.io/cascade

Python & R scripts collection for AdipoAtlas project

R package for annotation of glycans in MS1 and MS2 data

Predict and match digested peptides sequences, their mass m/z and MS/MS spectra with chemical derivatization or post-translational modification.

LC-MS/MS derived peptide retention time deviation calculator across replicates for DDA and DIA derived result files.

Generate annotated Peptide Spectrum Matches (PSMs) from proteomic database search result

Sipros5, a proteomics tool designed for identifying and quantifying isotopically labeled proteins—especially 13C-15N-18O-2H-labeled—in complex microbial communities using scalable and modular high-performance computation.

Extracts the features of peptide spectral library for better understanding and its efficient usage in DIA database search

High performance computing solution for mass-spectrometry based metabolomics data analysis pipeline that combines traditional numerical methods with advanced computer vision methods for high volume data using AI-driven metacognitive orchestration layers

MFQL files for Natural Products Dereplication

Predicting ion-mobility and spectra for labeled peptides

MSCA-PF project NeuroTOm

PCIIS data on DBS sample for volume detection

AI web application to diagnose the malignancy of adrenocortical tumors based on LC-MS/MS

https://adafede.github.io/sapid

Automatic identify sphingolipids through PreIS and MRM

Visualization of Immunopeptides Mapped to Source Proteins Across Multiple Samples