Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AgDAF16D12_Velos

ABSTRACT: Isolation of Protein Aggregates, Daf16, day 12, LTQ Orbi Velos

REANALYSIS of: PXD001364

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Caenorhabditis Elegans (c. Elegans)

SUBMITTER:

PROVIDER: PAe005592 | PeptideAtlas | 2015-12-31

REPOSITORIES: PeptideAtlas

ACCESS DATA

Json Xml

Publications

Widespread Proteome Remodeling and Aggregation in Aging C. elegans.

Walther Dirk M DM Kasturi Prasad P Zheng Min M Pinkert Stefan S Vecchi Giulia G Ciryam Prajwal P Morimoto Richard I RI Dobson Christopher M CM Vendruscolo Michele M Mann Matthias M Hartl F Ulrich FU

Cell 20150501 4

Aging has been associated with a progressive decline of proteostasis, but how this process affects proteome composition remains largely unexplored. Here, we profiled more than 5,000 proteins along the lifespan of the nematode C. elegans. We find that one-third of proteins change in abundance at least 2-fold during aging, resulting in a severe proteome imbalance. These changes are reduced in the long-lived daf-2 mutant but are enhanced in the short-lived daf-16 mutant. While ribosomal proteins de ...[more]

PMID: 25957690

Similar Datasets

AgDAF16D12_Elite

Project description:Isolation of Protein Aggregates, Daf16, day 12, LTQ Orbi Elite

2015-12-31 | PAe005608 | PeptideAtlas

Profiling of HLA-I ligandomes discovers novel cervical cancer-associated antigens

Project description:The product ion scans were acquired with a 2.0-unit isolation width and a normalized collision energy of 35 in an LTQ-Orbitrap Velos Pro MS spectrometer (Orbitrap Velos Pro, Thermo Fisher Scientific, US).

2023-06-05 | PXD042745 |

AgWTD12_Velos

Project description:Isolation of Protein Aggregates, WT, day 12, LTQ Orbi Velos

2015-12-31 | PAe005580 | PeptideAtlas

AgWTD12_Elite

Project description:Isolation of Protein Aggregates, WT, day 12, LTQ Orbi Elite

2015-12-31 | PAe005591 | PeptideAtlas

AgDAF16D06

Project description:Isolation of Protein Aggregates, Daf16, day 6

2015-12-31 | PAe005600 | PeptideAtlas

AgDAF16D01

Project description:Isolation of Protein Aggregates, Daf16, day 1

2015-12-31 | PAe005603 | PeptideAtlas

AgHSF1D12

Project description:Isolation of Protein Aggregates, hsf1, day 12

2015-12-31 | PAe005576 | PeptideAtlas

AgDAF2D12

Project description:Isolation of Protein Aggregates, Daf2, day 12

2015-12-31 | PAe005605 | PeptideAtlas

Tau aggregates are RNA-protein assemblies that mis-localize multiple nuclear speckle components

Project description:We report the isolation and sequencing of tau aggregates from [1] HEK293 cells expressing Tau-RD-P301S-CFP/YFP that have been seeded with preformed fibrils from the brain of P301S mice (B6-Tg(Thy1-MAPT*P301S)2541; referred to as Tg2541 mice). Tau aggregates were isolated by differential centrifugation followed by fluorescence automated particle sorting using a BD FACSaraia. We found that these tau aggregates were enriched for particular small non-coding RNAs, including snoRNAs and snRNAs. [2] the following mice: FvBB6F1-Tg(Camk2a-tTa),(tetO-MAPT*wt)21221 (referred to as rTg21221 or WT tau mice in the paper) and FvBB6F1-Tg(Camk2a-tTA)1Mmay, (tet)-tdTomato-Syp/EGFP)1.1Luo/J,(tetO-MAPT*P301L)4510 (referred to as rTg4510 or P301L mice in the paper). Briefly, tau aggregates were isolated by 1% sarkosyl extraction (to enrich for insoluble proteins) followed by immunoprecipitation of tau using the tau-12 antibody (see Methods section of associated paper for further details). We found that these tau aggregates were enriched for particular small non-coding RNAs, including snRNAs and some snoRNAs. [3] Sequencing of HEK293 tau biosensor cells with and without tau aggregates reveals evidence of significant splicing alterations. Specifically we observed an increase in intron retention events in cells that contain tau aggregates relative to cells without tau aggregates.

2021-04-06 | GSE148716 | GEO

Structural aspects of FOXO4 binding to DAF16 investigated with FPOP using both bottom-up and top-down MS.

Project description:A combination of covalent labelling techniques and mass spectrometry (MS) is currently a progressive approach for the de-riving insights relating to the mapping of protein surfaces or protein-ligand interactions. In this study, we mapped an interac-tion interface between DNA binding domain (DBD) of FOXO4 protein and DNA binding element (DAF16) using the Fast Photochemical Oxidation of Protein (FPOP). Residues involved in protein – DNA interaction were identified using bottom-up approach. To avoid a misinterpretation of obtained data, caused by possible multiple radical oxidation leading to the alter-ing a protein surface and oxidation of deep-buried amino acid residues, a top-down approach was employed for the first time in FPOP analysis. An isolation of singly-oxidized ions allowed their gas-phase separation from multiply oxidized species followed by CID and ECD fragmentation. Application of both fragmentation techniques allowed to obtained complemen-tary fragment sets, out of which the regions shielded in the presence of DNA were deduced. The results obtained by bottom-up and top-down approaches were in a high consistency. Lastly, FPOP results were compared with HDX study of FOXO4-DBD•DAF16 complex. No contradictions were found between both methods. Moreover, their combination provide com-plementary information related to the structure and dynamics of the protein-DNA complex.

2022-02-14 | PXD027624 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data