Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PulseLabeling_Velos

ABSTRACT: SILAC pulse labeling, LTQ Orbi Velos

REANALYSIS of: PXD001364

INSTRUMENT(S): LTQ Orbitrap Elite

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

SUBMITTER:

PROVIDER: PAe005595 | PeptideAtlas | 2015-12-31

REPOSITORIES: PeptideAtlas

ACCESS DATA

Json Xml

Publications

Recurrent Chagas' disease meningomyelitis in an HIV-infected patient.

de Almeida Igor Melo IM da Rocha Aline Borges Moreira ABM Lindoso José Angelo Lauletta JAL de Freitas Vera Lúcia Teixeira VLT Oliveira Augusto Cp AC Vidal Jose E JE

Practical neurology 20240913 5

Chagas' disease reactivation leading to monophasic acute or subacute meningoencephalitis or space-occupying lesions is a well-described AIDS-defining condition in Latin America. We report a 59-year-old man native from the Northeast region of Brazil, with a second episode of subacute chagasic meningomyelitis. He had long-term multidrug-resistant HIV and had abandoned combined antiretroviral therapy (CD4+ lymphocyte count, 16 cells/mm³, and HIV viral load 169 403 copies/mL). He initially received ...[more]

PMID: 38653547

Similar Datasets

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 |

PulseLabeling_Elite

Project description:SILAC pulse labeling, LTQ Orbi Elite

2015-12-31 | PAe005559 | PeptideAtlas

Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and their interacting stromal fibroblast cells

Project description:Communication and interaction between carcinoma associated fibroblast (CAF) cells and tumor epithelium cells plays a critical role in cancer initiation and progression. However, a mechanistic understanding of how CAFs communicate with tumor cells to promote their proliferation and invasion is far from complete. In this study, we employed a SILAC labeling based co-culture system coupled with mass spectrometry analysis to identify and quantify the early phospho-signaling transductions induced by the crosstalk between CAFs and tumor cells. We performed three-state SILAC labeling for MDA-MB-231 and 82T. 9 million light labeled 82-L cells were co-cultured with medium labeled MDA-MB-231-M cells for 30 minutes. 9 million heavy labeled 82T-H cells were individually cultured in heavy SILAC media with for 30 minutes. Both individually cultured and co-cultured cells were quickly harvested with 9 M urea lysis buffer and mixed together. Mixed lysates were sonicated, reduced, alkylated and digested by trypsin. Tryptic peptides were desalted using SepPak C18 cartridge and followed by phosphotyrosine peptide enrichment using immunoaffinity purification with pY100 antibody. The enriched phosphopeptides were analyzed using a reverse-phase liquid chromatography system interfaced with an LTQ-Orbitrap Velos mass spectrometer. The Proteome Discoverer (v2.0; Thermo Fisher Scientific) suite was used for quantitation and database searches. The tandem mass spectrometry data were searched using SEQUEST search algorithm against a Human RefSeq database supplemented with frequently observed contaminants. The probability of phosphorylation sites was determined from the PhosphoRS algorithm.

2018-10-26 | PXD003544 | Pride

Combined transcriptomic and proteomic analysis of chicken DF-1 cells following innate immune stimulations

Project description:The goal of our study was to experimentally quantify both at the transcriptomic and proteomic level the effects of comprehensive innate immune stimulations in chicken. To this end, SILAC-labeled chicken DF-1 cells were mock-treated or treated with either ChIFN1 (1000 IU/mL for 6h), transfected poly (I:C) (4,25 ug/mL for 6 h) or infected with Infectious Bursal Disease Virus strain PBG-98 (IBDV, MOI 5 for 8h). Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN) and Illumina libraries were prepared and sequenced. In parallel, proteins were extracted and processed for SILAC-based quantitative mass-spectrometry. Samples were run on a LTQ-Velos Orbitrap tandem mass spectrometer and the data processing and quantification were performed by the MaxQuant software.

2026-05-26 | PXD057686 | Pride

Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP

Project description:Post-transcriptional gene regulation relies on hundreds of RNA binding proteins (RBPs) but the function of most RBPs is unknown. The human RBP HuR/ELAVL1 is a conserved mRNA stability regulator. We used PAR-CLIP, a method based on RNA-protein crosslinking, to identify transcriptome wide ~26,000 HuR binding sites. These sites were on average highly conserved, enriched for HuR binding motifs and mainly located in 3' untranslated regions. Surprisingly, many sites were intronic, implicating HuR in splicing. Upon HuR knock down, mRNA levels and protein synthesis of thousands of target genes was down regulated, validating functionality. HuR and miRNA binding sites tended to reside nearby but generally did not overlap. Additionally, HuR knock down triggered strong and specific up regulation of miR-7. In summary, we identified thousands of direct and functional HuR targets, found a human miRNA controlled by HuR, and propose a role for HuR in splicing. PolyA mRNA was extracted from anti HuR siRNA treated and mock transfected HeLa cells to identify changes in mRNA expression and splicing. 2x100 paired end sequencing was performed according to the protocol on the Illumina HiSeq. PARCLIP was performed as in Hafner et. Al 2010 but with an antibody against endogenous HuR (3A2, Santa Cruz, sc-5261) in unstressed HeLa cells. We used, independently, 4-thiouridine (4SU) and 6-thioguanosine (6SG) to assess a possible nucleotide bias. As our proteomics measurements required labeling of cells in a special medium we also performed PAR-CLIP on cells grown in SILAC medium. Altogether we performed three PAR-CLIP experiments: 4SU labeling in standard DMEM medium, 4SU labeling in SILAC medium (as a replicate) and 6SG labeling in SILAC medium. Small RNA was extracted from anti HuR siRNA treated and mock transfected HeLa cells to identify changes in mRNA expression. Sequencing was performed on Illumina GAII using the standard sRNA 36cycle protocol.

2011-06-29 | E-GEOD-29943 | biostudies-arrayexpress

Dynamic profiling of the protein life cycle in response to pathogens (protein)

Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress

Analytical framework for peptidomics applied to large scale neuropeptide identification

Project description:Endogenous peptides are extracted and seperated with nLC with HCD fragmentation on a LTQ Orbitrap Velos. Data analysis was done with Mascot and MaxQuant

2016-05-03 | PXD002431 | 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

Proteomic analysis of integrin adhesion complex-mediated mechanotransduction

Project description:Integrin adhesion complexes were isolated from mouse fibroblasts treated with or without blebbistatin. Adhesion complexes were resolved by SDS-PAGE, digested with trpysin and analysed by LC-MS/MS using an LTQ Velos mass spectrometer

2015-10-19 | PXD000018 | Pride

Chick utricle hair bundles and utricular epithelium—Velos

Project description:Purified hair bundles and utricular epithelium from E19-E20 chick inner ears were analyzed by LC-MS/MS to determine the abundant and enriched proteins of the hair bundle. This dataset used a Thermo LTQ Velos mass spectrometer for protein detection.

2015-11-17 | PXD002414 | 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