Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PTMsite-Finder supports DIA-NN-based PTM DIA proteomics

ABSTRACT: we developed PTMsite-Finder, a user-friendly graphical interface software tool designed to report and quantify multiple PTM sites directly from DIA-NN outputs. We validated PTMsite-Finder’s phosphosite quantification accuracy for phosphoproteomics DIA-MS data and demonstrated its versatility in processing various PTM types, including ubiquitinomics, acetylomics, and biotinylation diaPASEF data. Additionally, PTMsite-Finder outputs are compatible with kinase prediction and PTM site motif analysis tools. Altogether, PTMsite-Finder is a robust and versatile tool for analyzing DIA-NN outputs across multiple types of DIA-MS data.

ORGANISM(S): Homo Sapiens

SUBMITTER: Chuanqi Zhong

PROVIDER: PXD057731 | iProX | Mon Nov 11 00:00:00 GMT 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Boloria dia

Project description:Boloria dia overview

| PRJNA1163491 | ENA

Microflow SWATH data analysed with DIA-NN

Project description:We have developed DIA-NN, an integrated software suite for fully-automated processing of raw SWATH/DIA data. DIA-NN enables deep and confident proteome coverage with fast chromatographic methods, paving the way for a new generation of high-throughput proteomics. This data set illustrates the capabilities of DIA-NN when analysing microflow SWATH data acquired with 19 - 23 minute gradients as well as the use of DIA-NN to generate spectral libraries directly from SWATH/DIA data.

2019-11-06 | PXD014690 | Pride

Benchmarking DIA data analysis workflows

Project description:Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still a lot of possibilities at the data analysis level. By benchmarking different DIA analysis workflows through a ground truth sample mimicking real differential abundance samples, consisting of a differential spike-in of UPS2 in a constant yeast background, we provide a roadmap for DIA data analysis of shotgun samples based on whether sensitivity, precision or accuracy is of the essence. Three different commonly used DIA software tools (DIA-NN, EncyclopeDIA and SpectronautTM) were tested in both spectral library mode and spectral library free mode. In spectral library mode we used the independent spectral library prediction tools Prosit and MS2PIP together with DeepLC, next to the classical DDA-based spectral libraries. In total we benchmarked 12 DIA workflows. DIA-NN in library free mode or using in silico predicted libraries shows the highest sensitivity maintaining a high reproducibility and accuracy.

2024-05-06 | PXD044981 | Pride

Stutzerimonas stutzeri strain:DIA-8

Project description:Stutzerimonas stutzeri strain:DIA-8 Genome sequencing and assembly

| PRJNA1072647 | ENA

Elstera litoralis strain:Dia-1

Project description:Elstera litoralis strain:Dia-1 Genome sequencing and assembly

| PRJNA278930 | ENA

scRNAseq RAT DIA WT and DMD 12months

Project description:scRNAseq RAT DIA WT and DMD 12months

| PRJNA814255 | ENA

Identification of differentially expressed proteins in lung cancer H157 cells after nanocomposite AANL-SeNPs treatment with DIA-MS detection

Project description:H157 cells were treated with nanocomposite AANL-SeNPs and harvested for mass spectrometry detection. The mass spectrum data were obtained by timsTOF Pro combined with UltiMate 3000 RSLCnano liquid chromatograph system. DIA-NN software is used to analyze DIA original data files. The differentially expressed proteins were screened by quantitative proteomics.

2024-05-22 | PXD044000 | Pride

ProteomicAnalysis(DIA)ofmuscleinvasivebladdercancerpatient-derivedxenografts

Project description:Accesstoproteomicfiles(DIA)ofMIBCpatient-derivedxenografts(N=8)

| EGAD00010002512 | EGA

Localisation of Organelle Proteins using Data-Independent Acquisition (DIA-LOP)

Project description:Subcellular localisation within the proteome fundamentally influences cellular processes, however the development of high-throughput techniques to allow proteome-wide mapping of the cell has proven difficult. Here we present DIA-LOP, an approach capable of high-throughput spatial proteome mapping with in-depth subcellular resolution. This unified framework integrates differential-ultracentrifugation with ion-mobility-based data independent acquisition (DIA) mass spectrometry, alongside data processing using DIA-NN and spatial analysis within the pRoloc bioinformatics pipeline. Within the same experimental pipeline, we compare Differential-ultraCentrifugation (DC) fractionation with an alternate detergent-based protocol using both data-dependent (DDA) and data-independent acquisition (DIA) mass spectrometry approaches highlighting the increased subcellular resolution of the DC approach and the increased proteome coverage when DIA is applied. This study thus informs potential users of subcellular proteomics strategies that employ biochemical fractionation of the optimal workflows to achieve high proteome coverage and subcellular resolution.

2025-09-29 | PXD063082 | Pride

Proteomicanalysis(DIA)ofpatientswithnon-muscleinvasiveandmuscleinvasivebladdercancer

Project description:Accesstoproteomicfiles(DIA)ofpatientswithtreatment-naiveMIBC(N=51),treatment-naiveNMIBC(N=17)andneoadjuvantMIBC(N=11)

| EGAD00010002513 | EGA