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MetabolomicsMassVision: An open-source end-to-end platform for AI-driven mass spectrometry image analysis

This dataset contains 10 Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) slides from cross-sections of surgically resected colorectal tissues with cancer and adjacent normal. The data is released with MassVision software platform for exploration and analysis of MSI data. P...

2025-09-19 | MTBLS12868 | MetaboLights
MetabolomicsStreamlining LC-MS/MS Data Analysis in R with Open-Source *xcms* and *RforMassSpectrometry*: An End-to-End Workflow

Despite untargeted LC-MS/MS data being a powerful approach for large-scale metabolomics analysis, a significant challenge in the field lies in the reproducible and efficient analysis of such data, in particular. The power of R-based analysis workflows lies in their high customizability and adapta...

2024-08-26 | MTBLS8735 | MetaboLights
ProteomicsA flexible end-to-end automated sample preparation workflow enables reproducible large-scale bottom-up proteomics - Part 2
Bottom-up proteomics holds significant promise for clinical applications due to its high sensitivity and precision, but is limited by labor-intensive, low-throughput sample preparation meth-ods. Advanced automation is essential to enhance throughput, reproducibility, and accuracy and to allow standa...
ORGANISM(S): Homo sapiens (Human) 
2025-10-17 | PXD063636 | Pride
Automated sample preparation End-to-end 
ProteomicsA flexible end-to-end automated sample preparation workflow enables reproducible large-scale bottom-up proteomics - Part 1
Bottom-up proteomics holds significant promise for clinical applications due to its high sensi-tivity and precision, but is limited by labor-intensive, low-throughput sample preparation meth-ods. Advanced automation is essential to enhance throughput, reproducibility, and accuracy and to allow stand...
ORGANISM(S): Homo sapiens (Human) 
2025-10-17 | PXD063610 | Pride
Automated sample preparation End-to-end 
ProteomicsA flexible end-to-end automated sample preparation workflow enables reproducible large-scale bottom-up proteomics - Part 4
Bottom-up proteomics holds significant promise for clinical applications due to its high sensitivity and precision, but is limited by labor-intensive, low-throughput sample preparation meth-ods. Advanced automation is essential to enhance throughput, reproducibility, and accuracy and to allow standa...
ORGANISM(S): Homo sapiens (Human) 
2025-10-17 | PXD063831 | Pride
Automated sample preparation End-to-end 
ProteomicsA flexible end-to-end automated sample preparation workflow enables reproducible large-scale bottom-up proteomics - Part 3
Bottom-up proteomics holds significant promise for clinical applications due to its high sensitivity and precision, but is limited by labor-intensive, low-throughput sample preparation meth-ods. Advanced automation is essential to enhance throughput, reproducibility, and accuracy and to allow standa...
ORGANISM(S): Homo sapiens (Human) 
2025-10-17 | PXD063679 | Pride
Automated sample preparation End-to-end 
ProteomicsDDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics
This project provides a large-scale training dataset for DDA-BERT, an end-to-end transformer-based deep learning model developed for PSM rescoring in data-dependent acquisition (DDA) proteomics. The dataset comprises curated PSMs generated using established database search engines, including FragPip...
ORGANISM(S): Chlamydomonas reinhardtii Glycine max Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) Mus musculus (Mouse) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) Caenorhabditis elegans Rattus norvegicus (Rat) Bacillus cereus Bacillus subtilis 
2026-08-24 | PXD072999 | Pride
Deep learning Dda proteomics Peptide-spectrum matches (psms) rescoring Dda-bert Peptide identification 
GenomicsAn end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae
An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae
PRJNA1085387 | ENA
ModelsPalaniappan2021 - Cell free modelling of second generation Toehold switches
Cervical cancer is a global public health subject as it affects women in the reproductive ages, and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50% mortality rate. Poor awareness and access to effective diagnosis have led to this enormous disease burden...
2025-03-31 | BIOMD0000001103 | BioModels
GenomicsMuscle Transcriptomic Circuits Linked to Periarticular Physiology in End-Stage Osteoarthritis.
Muscle Transcriptomic Circuits Linked to Periarticular Physiology in End-Stage Osteoarthritis.
PRJNA845210 | ENA
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