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ProteomicsFidelity of translation initiation is required for coordinated respiratory complex assembly
Mammalian mitochondrial ribosomes are unique molecular machines that translate 11 leaderless mRNAs. To date it is not clear how mitoribosomes recognize and initiate translation in the absence of untranslated regions in the mitochondrial mRNAs. Translation initiation in mitochondria shares similariti...
ORGANISM(S): Mus musculus (Mouse) 
2020-01-02 | PXD015521 | Pride
Ribosome Translation Cardiomyopathy Rna-seq 
ProteomicsMitochondrial mistranslation is modulated by metabolic stress
Changes in the rate and fidelity of mitochondrial protein synthesis impact the metabolic and physiological roles of mitochondria. Here we explored how environmental stress in the form of a high fat diet modulates mitochondrial translation using mutant mice with error-prone (Mrps12ep/ep) or hyper-acc...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-09 | PXD021762 | Pride
Metabolism Mitochondria Protein synthesis 
ProteomicsCysteine alkylating methods in shotgun proteomics and their possible effects on methionine residues
Neatly every proteomic protocol has a Cysteine reduction and alkylation step in it preceding the trypsin digestion. It needs to be done in order to remove the s-s bonds and prevent proteins from folding, thus, provide better access for trypsin. Among various reagents used for alkylation, iodoacetami...
ORGANISM(S): Homo sapiens (Human) 
2020-10-28 | PXD013973 | Pride
Cysteine Proteomics Alkylation Methionine 
ProteomicsCysteine alkylating methods in shotgun proteomics and their possible effects on methionine residues
Neatly every proteomic protocol has a Cysteine reduction and alkylation step in it preceding the trypsin digestion. It needs to be done in order to remove the s-s bonds and prevent proteins from folding, thus, provide better access for trypsin. Among various reagents used for alkylation, iodoacetami...
ORGANISM(S): Homo sapiens (Human) 
2024-02-14 | PXD015889 | Pride
Cysteine Proteomics Alkylation Methionine Reduction 
TranscriptomicsHierarchical RNA processing is rate limiting for mitochondrial ribosome assembly
In animals the organization of the compact mitochondrial genome and lack of introns have necessitated a unique mechanism for RNA processing. To date the regulation of mitochondrial RNA processing and its importance for ribosome biogenesis and energy metabolism are not clear. To understand the in viv...
ORGANISM(S): Mus musculus 
2016-08-04 | E-GEOD-83471 | biostudies-arrayexpress
ProteomicsProteogenomics of adenosine-to-inosine RNA editing in fruit fly
This dataset is a part of a bigger work on RNA editing in D. melanogaster brain. We present Orbitrap spectra searched against a customized database of Drosophila proteome with introduction of variants provided by RNA editing. Tree files reflect 3 technical replicates.
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2019-03-13 | PXD004949 | Pride
Proteomics Ls-msms Rna editing Drosophila melanogaster 
ProteomicsStress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation
The fidelity of translation is crucial in prokaryotes and for the nuclear-encoded proteins of eukaryotes, however little is known about the role of mistranslation in mitochondria and its effects on metabolism. We generated yeast and mouse models with error-prone and hyperaccurate mitochondrial trans...
ORGANISM(S): Mus musculus (Mouse) 
2019-11-08 | PXD015456 | Pride
Oxidative phosphorylation Mitochondrial ribosome  mrps12 Stress response abbreviations used: mitoribosome Mitochondrial ribosomal protein of the small subunit 12  oxphos Mitochondria Metabolism Protein synthesis 
ProteomicsProteogenomics of adenosine-to-inosine RNA editing in fruit fly
This dataset is a part of a bigger work on RNA editing in D. melanogaster brain. We present Orbitrap spectra searched against a customized database of Drosophila proteome with introduction of variants provided by RNA editing. Three files reflect 3 technical replicates.
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2018-10-25 | PXD009590 | Pride
Rna editing Proteogenomics Drosophila melanogaster 
ProteomicsExome-based proteogenomics of HEK-293 human cell line: coding genomic variants identified at the level of shotgun proteome
Genomic and proteomic data were integrated into the proteogenomic workflow to identify coding genomic variants of Human Embryonic Kidney 293 (HEK-293) standard cell line at the proteome level. Shotgun proteome data published by Geiger et al (2012) and obtained in this work for HEK-293 were searched ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-28 | MSV000080712 | MassIVE
ProteomicsSequence coverage by multiple reads in shotgun proteomics to validate single amino acid variants
Mass spectrometry-based shotgun proteomics is currently based on assigning matches between mass-spectra of protein fragments resulting from protease digestion and amino acid sequences predicted from nucleic acid sequences. At the same time, the method lacks reliability in identification of every sin...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-12-07 | MSV000088536 | MassIVE
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