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ProteomicsProsit: Proteome-wide prediction of peptide tandem mass spectra by deep learning
In this study, we extended the ProteomeTools peptide library (PROPEL, see PXD004732 and PXD010595) to train a deep neural network resulting in chromatographic retention time and fragment ion intensity predictions for (tryptic) peptides that exceed the quality of the experimental data.
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) Drosophila melanogaster (Fruit fly) Caenorhabditis elegans 
2019-05-30 | PXD010871 | Pride
Dia Prosit Retention time Predicted spectra Irt Machine learning Proteometools Spectral library Synthetic peptides Dda 
ProteomicsProteomic analysis of synovial fibroblasts from patients with Juvenile idiopathic arthritis
The aim was to characterize the proteomic alterations in synovial fibroblasts from patients with juvenile idiopathic arthritis, with or without prior priming with inflamed synovial fluid. Synovial fibroblasts were isolated from the synovial fluid of patients with oligoarticular juvenile idiopathic a...
ORGANISM(S): Homo sapiens (Human) 
2026-04-13 | PXD041459 | Pride
Synovial fluid Inflammation Juvenile idiopathic arthritis Synovial fibroblasts 
ProteomicsProteome characterization of synovial fluid polarized healthy monocytes
This project involves proteome characterization of healthy monocytes polarized (activated) with synovial fluid (SF) versus serum from patients with juvenile idiopathic arthritis (JIA). The objective is to investigate the influence of SF on monocytes at the proteome level, using serum polarized monoc...
ORGANISM(S): Homo sapiens (Human) 
2023-07-20 | PXD033983 | Pride
Monocytes Inflammation Juvenile idiopathic arthritis Synovial fluid 
ProteomicsYeast phosphofructokinase subunit 2 has ATP-dependent RNA unwinding activity and modulates cell cycle progression
Phosphofructokinase (PFK) is a rate-limiting glycolytic enzyme that also possesses an unexplored polyadenylated RNA binding activity. Here, we show that the two PFK subunits, Pfk1 and Pfk2, in budding yeast bind a large number of mRNAs in cells, including ones coding for proteins involved in regulat...
ORGANISM(S): Saccharomycetales (ncbitaxon:4892) 
2024-12-04 | MSV000096586 | MassIVE
TranscriptomicsPrepubertal Human Spermatogonia and Mouse Gonocytes Share Conserved Gene Expression of Germline Stem Cell Regulatory
Full title: Prepubertal Human Spermatogonia and Mouse Gonocytes Share Conserved Gene Expression of Germline Stem Cell Regulatory Molecules Oligonucleotide Microarray Analysis Reveals Novel Genes Expressed in Prepubertal Human Spermatogonia and Mouse Gonocytes Four hundred cells were selected for ea...
ORGANISM(S): Homo sapiens 
2009-11-06 | E-GEOD-18914 | biostudies-arrayexpress
UnknownImpairment of Motor Function Correlates with Neurometabolite and Brain Iron Alterations in Parkinson's Disease.
Not available
S-EPMC6406520 | biostudies-literature
MetabolomicsConsistency across multi-omics layers in a drug-perturbed gut microbial community
Multi-omics analyses are increasingly employed in microbiome studies to obtain a holistic view of molecular changes occurring within microbial communities exposed to different conditions. However, it is not always clear to what extent each omics data type contributes to our understanding of the comm...
2022-12-08 | MTBLS3129 | MetaboLights
UnknownActivation of beta-catenin signaling programs embryonic epidermis to hair follicle fate.
Not available
S-EPMC2516408 | biostudies-literature
ProteomicsSystematic characterization of 21 post-translational modification using synthetic peptides
The data presented in this study in the - context of the ProteoemTools project - is based on the synthesis of about 5000 synthetic peptides carrying 21 different post-translational modifications to systematically characterize their chromatographic and mass spectrometric properties using multimodal L...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-04-05 | MSV000091649 | MassIVE
ProteomicsPlasmodium falciparum Kelch13, Eps15 and Clathrin HC interactomes obtained using a dimerisation-induced quantitative BioID (DiQ-BioID)
In order to identify Kelch13 interaction partners in living P. falciparum parasites, we established a new type of BioID we termed dimerisation-induced quantitative BioID (DiQ-BioID) that takes advantage of the FKBP-FRB heterodimerisation system. For DiQ-BioID the target is endogenously tagged with F...
ORGANISM(S): Plasmodium falciparum 
2021-12-02 | PXD008219 | Pride
Eps15 Dimerisation-induced quantitative bioid (diq-bioid) Plasmodium falciparum Artemisinin resistance Vesicle trafficking Kelch13 Clathrin hc 
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