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UnknownAlphaPept: a modern and open framework for MS-based proteomics.
Not available
S-EPMC10924963 | biostudies-literature
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 
ProteomicsSpatial characterization and stratification of colorectal adenomas by Deep Visual Proteomics
Background and Aims: Colorectal adenomas (CRAs) are precursor lesions that can progress to adenocarcinomas. Current clinical guidelines categorize patients into risk groups based on adenoma characteristics observed during index colonoscopy, but this may lead to overtreatment. Our aim was to establis...
ORGANISM(S): Homo sapiens (Human) 
2024-08-04 | PXD046999 | Pride
Spatial Mass spectrometry Pathology Cancer Colorectal adenoma Proteomics Dvp 
UnknownAlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics.
Not available
S-EPMC10415174 | biostudies-literature
UnknownAccurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.
Not available
S-EPMC10315922 | biostudies-literature
UnknownAlphaTims: Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization.
Not available
S-EPMC8526765 | biostudies-literature
ProteomicsAlphaTims: Indexing unprocessed trapped ion mobility spectrometry - time of flight data for fast and easy accession and visualization
High resolution mass spectrometry-based proteomics generates large amounts of data, even in the standard liquid chromatography (LC) – tandem mass spectrometry configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipe...
ORGANISM(S): Homo sapiens (Human) 
2021-07-30 | PXD027359 | Pride
Software. Time of flight Ion mobility spectrometry Data indexing Mass spectrometry Data visualization 
ProteomicsAlphaViz: Visualization and validation of critical proteomics data directly at the raw data level
Although current mass spectrometry (MS)-based proteomics identifies and quantifies thousands of proteins and (modified) peptides, only a minority of them are subjected to in-depth downstream analysis. With the advent of automated processing workflows, biologically or clinically important results wit...
ORGANISM(S): Homo sapiens (Human) 
2022-07-11 | PXD034223 | Pride
Tims Dia-nn Validation Tof Python Quality control Maxquant Open source Data visualization Alphapept 
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