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MetabolomicsThermal Profiling Maps Multilayered Organization of the Mitochondrial Proteome

Mitochondria execute essential metabolic, biosynthetic, and signaling functions, yet the regulatory principles governing their proteome remain incompletely understood. Here, we develop a thermal proteome profiling (TPP) workflow applied directly to purified mitochondria, enabling systematic analy...

2025-12-08 | MTBLS7386 | MetaboLights
MetabolomicsProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis

Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the...

2021-09-01 | MTBLS1903 | MetaboLights
MetabolomicsLongitudinal Deep Multi-Omics Profiling in aCLN3Δex7/8Minipig Model Reveals Novel Biomarker Signatures for Batten Disease
Development of therapies for CLN3 Batten disease, a rare pediatric lysosomal storage disorder, has been hindered by the lack of etiological insights and translatable biomarkers to clinics. Here, we used a deep multi-omics approach to discover new biomarkers using longitudinal serum samples from a po...
2025-08-13 | MTBLS1107 | MetaboLights
TranscriptomicsRNA-seq of A431 cell line after gefitinib treatment
RNA sequencing of A431 cell line samples before and after gefitinib treatment, at 0, 2, 6 and 24 hours, was performed in order to characterize the cell line's early and late response to this drug, and to compare against proteomics (mass spectrometry) characterization of the cell line using the same ...
ORGANISM(S): Homo sapiens 
2016-12-01 | E-MTAB-5285 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by high throughput sequencing of HeLa human cancer cell line
Illumina single-end sequencing of Hela_2 (HeLa cell line). While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. On-line liquid chromatography coupled to hi...
ORGANISM(S): Homo sapiens 
2011-11-12 | E-MTAB-823 | biostudies-arrayexpress
GenomicsSimultaneous deep transcriptome and proteome profiling in single mouse oocytes
Simultaneous deep transcriptome and proteome profiling in single mouse oocytes
PRJNA997259 | ENA
ProteomicsDeep learning neural network prediction method improves proteome profiling of vascular sap of grapevines during Pierces disease development
Plant secretome studies have shown the importance of plant defense proteins in the vascular system against pathogens. Studies on Pierces disease of grapevines caused by the xylem-limited bacteria Xylella fastidiosa Xf have detected proteins and pathways associated to its pathobiology. Despite the bi...
ORGANISM(S): Vitis Vinifera (ncbitaxon:29760) Xylella Fastidiosa Temecula1 (ncbitaxon:183190) 
2020-08-12 | MSV000085942 | MassIVE
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): Drosophila Melanogaster (ncbitaxon:7227) Escherichia Coli (ncbitaxon:562) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) Caenorhabditis Elegans (ncbitaxon:6239) 
2021-03-12 | MSV000087047 | MassIVE
ProteomicsA deep proteome and transcriptome abundance atlas of 29 healthy human tissues
We generated a systematic, quantitative and deep proteome and transcriptome abundance atlas from 29 paired healthy human to serve as a molecular baseline to study human biology.
ORGANISM(S): Homo sapiens (Human) 
2019-07-10 | PXD010154 | Pride
Human proteome 
TranscriptomicsSimultaneous deep transcriptome and proteome profiling in single mouse oocytes
Nowadays, although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform bas...
ORGANISM(S): Mus musculus 
2023-10-18 | GSE237932 | GEO
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