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UnknownAnalysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities.
Not available
S-EPMC6055662 | biostudies-literature
UnknownComparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools.
Not available
S-EPMC8280745 | biostudies-literature
ProteomicsComparative Evaluation of MaxQuant and Proteome Discoverer MS1-based Protein Quantification Tools
MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool....
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-05-31 | PXD022169 | Pride
Dynamic range Proteomics Mass spectrometry Specificity Sensitivity Accuracy Precision Label-free quantification Differential analysis 
ProteomicsReanalysis of Thermal Proteome Profiling in Zebrafish Reveals Effects of Napabucasin on Retinoic Acid Metabolism in Proteome Discoverer 2.5
This is a reanalysis of PXD017419 performed in Proteome Discoverer version 2.5
ORGANISM(S): Danio Rerio (ncbitaxon:7955) 
2021-12-06 | MSV000088522 | MassIVE
ProteomicsErastin and ferrostatin induced protein expression change in HepG2 cells
Project description: HepG2 cells were treated with DMSO, erastin and ferrostatin, respectively. Protein was extracted and separated using SDS-PAGE electrophoresis. MS analysis was performed and protein was identified and quantified using Proteome Discoverer™ 1.3 software using the SEQUEST® search en...
ORGANISM(S): Homo sapiens (Human) 
2019-11-12 | PXD010761 | Pride
Erastin Ferroptosis Liver cancer 
ProteomicsMS Annika: A new Cross-Linking Search Engine
A cross linking mass spectrometry search engine was developed and implemented into Thermo Proteome Discoverer. The search engine is capable to handle several linker types as well as data input formats. To demonstrate its ability processing Bruker -ion mobility data, synthetic peptides (Beveridge, et...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2021-05-27 | PXD022772 | Pride
Xl-ms Proteome-discoverer Ion-mobility Search-engine 
ProteomicsSecretome proteomic dataset of Filobasidium magnum PLANB_3024 cultured with poly(lactic acid)
This dataset contains bottom-up LC-MS/MS data from the culture-supernatant-derived extracellular protein fraction of Filobasidium magnum PLANB_3024 cultivated in the presence of poly(lactic acid) (PLA). Proteins were identified using Proteome Discoverer v3.0 with Sequest HT against a strain-specific...
ORGANISM(S): Filobasidium magnum 
2026-09-06 | PXD083739 | Pride
Pla Cutinase Filobasidium magnum Secretome 
UnknownSpectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.
Not available
S-EPMC6456873 | biostudies-literature
ProteomicsNovel interconnections of HOG signaling revealed by combined use of two proteomic software packages
Modern quantitative mass spectrometry (MS)-based proteomics enables researchers to unravel signaling networks by monitoring proteome-wide cellular responses to different stimuli. MS-based analysis of signaling systems usually requires an integration of multiple quantitative MS experiments, which rem...
ORGANISM(S): Saccharomyces Cerevisiae 
PXD013789 | panorama
UnknownDataset of quantitative proteomic analysis to understand aging processes in rabbit liver.
Not available
S-EPMC7262418 | biostudies-literature
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