Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hiroki_et_al_2022_TurboID_Phosphoprotomics_RawData

ABSTRACT: This is the supplemental raw data for Hiroki et al., 2022.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Whole Body

SUBMITTER: Shingo Hiroki

LAB HEAD: Yuichii Iino

PROVIDER: PXD031536 | Pride | 2022-04-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	200615-10elegansTurboID-pkc1nj3_Totalpeptides.msf	Msf
	200615-10elegansTurboID-pkc1nj3_Totalpeptides.raw	Raw
	200615-12elegansTurboID-pkc1nj3_Totalpeptides3.msf	Msf
	200615-12elegansTurboID-pkc1nj3_Totalpeptides3.raw	Raw
	200615-2elegansTurboID-pkc1gf_Totalpeptides.msf	Msf

Items per page:

1 - 5 of 24

Similar Datasets

Abe_etal_2022_NatCom_mass_spectrometry_rawdata

Project description:This is the supplemental raw data for Abe et al., 2022.

2022-05-26 | PXD034068 | Pride

Abe_et_al_Nature_Communications_2022_mass_spectrometry_rawdata

Project description:This is supplemental raw data for Abe et al., 2022. Proteome analysis and phospho-proteome analysis using mouse liver prepared at 6 circadian time points (CT2, 6, 10, 14, 18, 22). In the delta-RRE mutant, two RRE sequences are removed from 5'UTR of mouse Bmal1 gene.

2022-07-20 | PXD035414 | Pride

Substrates of the ATR kinase - Phosphoproteomics

Project description:Identification and validation of substrates of the ATR kinase by quantitative phosphoproteomics

2024-01-15 | PXD041250 | Pride

Nuclear substrates of the CDKL5 kinase - Phosphoproteomics

Project description:Identification of nuclear substrates of the CDKL5 kinase by quantitative phosphoproteomics

2020-12-10 | PXD022916 | Pride

Phosphoproteomic analysis of breast epithelial cells with isogenic knockin of PIK3CA mutations

Project description:The PIK3CA gene is frequently mutated in human cancers. To study the signaling mechanisms responsible for cell growth and invasion phenotypes induced by mutant PIK3CA molecules, we carried out a SILAC-based quantitative phosphoproteomic analysis of MCF10A, a spontaneously immortalized normal mammary epithelial cell line, and two MCF10A knockin cell lines containing different activating mutations of the PIK3CA gene. MCF10A and PIK3CA mutation knock in cells were propagated in DMEM/F12 SILAC media deficient in both L-lysine and L-arginine and supplemented with light lysine (K) and arginine (R) for light, 2H4-K and 13C6-R for medium state and 13C615N2-K and 13C615N4-R for heavy state labeling. Cell lysates were prepared in urea lysis buffer containing 20 mM HEPES pH 8.0, 9 M urea, 1 mM sodium orthovanadate, 2.5 mM sodium pyrophosphate, 1 mM ß-glycerophosphate and 5mM sodium fluoride. The lysates were reduced, alkylated and digested by trypsin. Tryptic peptides were desalted by C18 reverse phase column and followed by strong cation exchange (SCX) fractionation. Fractionated peptides were subjected to TiO2-based phosphopeptide enrichment. LC-MS/MS analysis of enriched phosphopeptides was carried out using a reverse-phase liquid chromatography system interfaced with an LTQ-Orbitrap Velos mass spectrometer. Proteome Discoverer (v 1.3) suite was used for quantitation and database searches. The tandem mass spectrometry data were searched using Mascot (2.2.0) and SEQUEST search algorithms against a Human RefSeq database supplemented with frequently observed contaminants.

2015-07-28 | PXD000599 | Pride

Mass spectrometry study of formaldehyde cross-linking of structured proteins

Project description:Formaldehyde is a widely used fixative in biology and medicine. The current chemical model for formaldehyde cross-linking of proteins is the formation of a methylene bridge that incorporates one carbon atom into the link. Here, we present mass spectrometry data that largely refute this model. Instead, our data show that cross-linking of structured proteins mainly involves a reaction that incorporates two carbon atoms into the link. Under MS/MS fragmentation, the link cleaves symmetrically to yield unusual fragments with a modification of one carbon atom. We apply this new understanding of the underlying cross-linking chemistry to the structural approach of cross-linking coupled to mass spectrometry. First, we cross-linked a mixture of purified proteins with formaldehyde. Our new analysis readily identified tens of cross-links from these proteins, which fit well with their atomic structures. We then perform in-situ cross-linking of human cells in culture. We identified 469 intra-protein and 90 inter-protein cross-links, which also fit well with available atomic structures. Interestingly, many of these cross-links could not be mapped onto a known structure and thus provide new structural insights. We highlight an example in which formaldehyde cross-links localize the binding site of βNAC on the ribosome. We also find several interactions of actin with auxiliary proteins. Our findings not only expand our understanding of formaldehyde reactivity and toxicity, but also clearly demonstrate how to use this potent reagent for structural studies.

2020-06-25 | PXD015435 | Pride

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Project description:The intrinsically disordered protein, α-synuclein, implicated in synaptic vesicle homeostasis and neurotransmitter release, is also associated with several neurodegenerative diseases. The different roles of α-synuclein are characterized by distinct structural states (membrane-bound, dimer, tetramer, oligomer, and fibril), which are originated from its various monomeric conformations. The pathological states, determined by the ensemble of α-synuclein monomer conformations and dynamic pathways of interconversion between dominant states, remain elusive due to their transient nature. Here, we use inter-dye distance distributions from bulk time-resolved Förster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the α-synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of αsynuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.

2022-10-14 | PXD024671 | Pride

Facilitating in situ cross-linking and mass spectrometry by antibody-based protein enrichment

Project description:Cross-linking of living cells followed by mass spectrometry identification of cross-linked peptides (in situ CLMS) is an emerging technology to study protein structures in their native environment. One of the inherent difficulties of this approach is the high complexity of the samples following cell lysis. This difficulty largely limits the identification of cross-links to the more abundant proteins in the cell. Here, we describe a targeted approach in which an antibody pulls a specific protein-of-interest out of the lysate. Mass spectrometry analysis of the protein material that binds to the antibody can then identify considerably more cross-links on the antibody target and its interactors. By using an antibody against the CCT chaperonin, we obtained over two hundred cross-links that provide in situ evidence for the subunit arrangement of CCT and its main interactions with prefoldin. Antibodies against tubulin likewise provided in situ evidence for the structure of the microtubule including the seam. Finally, the approach was also successful in identifying cross-links on a protein expressing at very low amounts (tau in non-neuronal cells). These results demonstrate the general applicability of antibody-based sample simplification for in situ CLMS.

2022-06-09 | PXD025099 | Pride

FACS sorted podocytes, mesangial cells

Project description:FACS sorted glomerular kidney cells from a single mouse were subjected to proteomics.

2022-10-13 | PXD016237 | Pride

Quantitative analysis of YAP effects in podocytes

Project description:Human podocytes were transduced with mouse YAP, with mouse YAP 112A and with empty vector using lentiviral gene transfer. Effects of YAP were measured by quantitative proteomics.

2017-05-02 | PXD005182 | 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