Quantitative Analysis of Mass Spectrometry Data

Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"

Reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the *flex series

Collaborative workflow for untargeted metabolomics data processing and analysis using open-source tools. https://doi.org/10.3390/metabo13040463

Library that implements "Automatic antibiotic resistance prediction in Klebsiella pneumoniae based on MALDI-TOF mass spectra"

SPUTNIK R package

Application of Machine Learning with MALDI-TOF MS for Rapid Differentiation between Methicillin-susceptible and Methicillin-resistant Staphylococcus aureus

S2P is an open source application for fast and easy processing of 2D-gel and MALDI-based mass spectrometry protein data.

Dereplicate And Cherry-pick Mass Spectrometry Spectra

Script for analyzing intensity of olefin species from AgLDI IMS data. Uses MALDIquant, Cardinal and Tidyverse

Python library for analyzing MALDI-ToF Mass Spectrometry experiments

R codes for plotting heatmap and line plots for MALDI TOF MS data from sublimated liver tissue. Uses MALDIquant and ggplot2

Data analysis pipeline for strawberry imaging mass spectrometry data in Food Chemistry publication. Uses Cardinal, MALDIquant and Tidyverse

Script for unsupervised analysis of microdissected fly tubule phospholipid signals as well as fly sections. Uses Cardinal

Detects high variance signals and generates dose-response curves to futher investigate candidate signals.

M²ara, a R shiny web app for feature selection in cell-based assays.

Codes for analyzing the relative ganglioside intensities MS results of brain sections. Calculates total ion current using MALDIquant.

In this study, I present a deep learning framework that utilizes raw MALDI-TOF-MS proteomic profiles as the input data source, trained strictly against high-fidelity labels derived from WGS ground truth, facilitating the detection of certain clonal complex and genes of Staphylococcus aureus.

Differentiation of Penicillium Species (Series Viridicata) Using MALDI-TOF MS & Machine Learning

Machine learning detection tool for Chagas disease using MALDI-TOF proteomic profiles and mass spectra.