Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Non-small cell lung cancer global proteomics

ABSTRACT: We present data of global proteomes for non-small cell lung cancer for squamous cell and adenocarcinoma, and for normal adjacent tissue.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

SUBMITTER: Alistair Bailey

LAB HEAD: Paul J Skipp

PROVIDER: PXD054390 | Pride | 2024-12-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	BLN_040521_TL0367T_peptides.pepxml	Pepxml
	BLN_040521_TL0367T_peptides_1_1_0.mzid.gz	Mzid
	BLN_040521_TL0367Tglob_003.mgf	Mgf
	BLN_040521_TL0367Tglob_003.mzxml	Mzxml
	BLN_040521_TL0367Tglob_003.raw	Raw

Items per page:

1 - 5 of 183

Similar Datasets

Immunopeptidomics of a brain tumour cell line to identify HLA presented Zika peptides

Project description:We present data of a brain tumour cell line (USP7) infected with Zika virus (Strain: BeH819966, GenBank: KU365779.1) to identify CD8 T cell epitopes eluted from the cell surface using mass spectrometry (immunopeptidomics) of presented HLA bound Zika peptides.

2025-11-10 | PXD037627 | Pride

Immunopeptidomics of ex-vivo tissues to identify T cell vaccine candidates for influenza

Project description:We present data comparing an immortal macrophage-like cell lines with ex-vivo infected lung tissues as the presentation models of direct observation of CD4 and CD8 T cell epitopes eluted from the cell surface using mass spectrometry (immunopeptidomics) of presented HLA bound peptides.

2022-01-13 | PXD022884 | Pride

Proteomic screening for potentially amyloidogenic proteins of Rhizobium leguminosarum in effective and ineffective root nodules of Pisum sativum L.

Project description:We studied potentially amyloidogenic proteins (e.g. protein forming polymers and complexes that are resistant to treatment with ionic detergents) in root nodules formed by two lines of garden pea (P. sativum L.): Sprint-2 (Fix+ phenotype) and Sprint-2Fix- (sym31) (Fix- phenotype) inoculated with the Rhizobium leguminosarum bv. viciae RCAM1026 root nodule bacteria. The Fix+ phenotype is characterized by effective (ability to fix nitrogen) root nodules formation. The Fix- line is a descendant of the Fix+ line and forms ineffective root nodules (unable to fix nitrogen) with undifferentiated bacteroids. We demonstrated the presence of both plant and bacterial proteins in detergent resistant fractions, including previously identified amyloid proteins RopA and RopB of R. leguminosarum and vicilin of P. sativum L.

2022-10-25 | PXD035724 | Pride

The kidney releases in the urine and circulation a non-polymerizing form of Uromodulin that retains the external hydrophobic patch domain

Project description:Uromodulin (Tamm-Horsfall protein, THP) is a glycoprotein uniquely produced in the kidney. It is released by cells of the thick ascending limbs (TAL) apically in the urine, and basolaterally in the renal interstitium and systemic circulation. Processing of mature urinary THP, which polymerizes into supra-molecular filaments, requires cleavage of an external hydrophobic patch (EHP) at the C terminus. However, THP in the circulation is not polymerized, and it remains unclear if non-aggregated forms of THP exist natively in the urine. We propose that an alternative processing path, which retains the EHP domain, can lead to a non-polymerizing form of THP. We generated an antibody that specifically recognizes THP with retained EHP (THP+EHP) and established its presence in the urine in a non-polymerized native state. Proteomic characterization of urinary THP+EHP revealed its C-terminus to end at F617. In the human kidney, THP+EHP was not only detected in TAL cells, but also diffusely in the renal parenchyma. Using C-terminus proteomic sequencing and immunoblotting, we then demonstrated that serum THP has also retained EHP. In a small cohort of patients at risk for acute kidney injury (AKI), admission urinary THP+EHP was significantly lower in patients who subsequently developed AKI during hospitalization. Our findings uncover novel insights into uromodulin biology by establishing the presence of an alternative path for cellular processing, which could explain the release of non-polymerizing THP in the circulation. Larger studies as needed to establish the utility of urinary THP+EHP as a sensitive biomarker of kidney health and susceptibility to injury.

2022-11-08 | PXD027914 | Pride

Cryo-EM Structures of Prion protein filaments from Gerstmann-Sträussler-Scheinker disease

Project description:Aggregation of the prion protein (PrP) and formation of PrP amyloid (APrP) is severe in some Prion diseases. In the dominantly inherited prion protein amyloidosis known as Gerstmann-Sträussler-Scheinker (GSS) disease, plaques made of PrP amyloid are a distinct feature. The TTC to TCC mutation in Prion protein gene (PRNP), resulting in a phenylalanine to serine amino acid substitution at PrP residue 198, causes a severe amyloidosis in a well-studied GSS variant. The neuropathologic phenotype of this neurodegenerative disease is characterized by the presence of numerous extracellular APrP plaques and intracytoplasmic tau neuronal inclusions which are identical to neurofibrillary tangles of Alzheimer disease. Using cryogenic electron microscopy (cryo-EM), we determined for the first time the structures of filaments of human APrP, isolated post-mortem from the brain of a symptomatic PRNP F198S mutation carrier. We report that in GSS (F198S) APrP filaments are composed of dimeric, trimeric and tetrameric left-handed protofilaments with their protomers sharing a common protein fold. The protomers in the cross-β spines consist of sixty-two amino acids and span from glycine 80 to phenylalanine 141, adopting a previously unseen spiral fold with a thicker outer layer and a thinner inner layer. Each protomer comprises nine short β-strands. The β1 and β8 strands as well as the β4 and β9 strands are engaged in a steric zipper. The new data, obtained by Cryo-EM, provide insights into the complexity of the structure of pathogenic PrP, and reveal the difference of PrP’s structure in brain disease versus that of recombinant PrP, highlighting the urgency of extending our knowledge of the structure of the amyloid filaments involved in human neurodegenerative diseases.

2022-07-18 | PXD032402 | Pride

DRAK2 alters IL-2 sensitivity and Treg development

Project description:Drak2¬-deficient (Drak2-/-) mice are resistant to multiple models of autoimmunity, yet effectively eliminate pathogens and tumors. Thus, DRAK2 is an ideal target to treat autoimmune diseases. However, the mechanisms by which DRAK2 contributes to autoimmunity, particularly type 1 diabetes (T1D), remain unresolved. Our data indicate that DRAK2 contributes to autoimmunity in multiple ways by regulating thymic Treg development and by impacting the sensitivity of conventional T cells to Treg-mediated suppression.

2023-02-09 | PXD037922 | Pride

Human plasma LC-MS/MS from children with bacterial and viral infections

Project description:LC-MS/MS proteomic profiling was performed on children with bacterial and viral infections using plasma samples. Protein biomarkers indiciative of bacterial or viral infection were identified.

2023-11-14 | PXD041960 | Pride

Human plasma LC-MS/MS from children with bacterial and viral infections

2023-11-14 | PXD042003 | Pride

Label-free LC-MS/MS analysis of proteins associated with expanded G4C2 hexanucleotide repeat-containing transcripts in human induced pluripotent stem cells

Project description:Proteins co-localizing with RNA targets of interest in human induced pluripotent stem cells (iPSCs) were identified using our recently optimized hybridization-proximity labeling approach (HyPro2) combined with label-free mass spectrometry. Briefly, fixed and permeabilized iPSCs from an ALS patient (DN19V4) or a healthy donor (C0053) were hybridized with a digoxigenin-labeled antisense oligonucleotide probe targeting transcripts containing the G4C2 hexanucleotide repeat expansion, which is present in the C9orf72 gene in DN19V4 but not in C0053. Alternatively, a control probe set was used to target ACTB pre-mRNA, expressed in both DN19V4 and C0053. The purified HyPro2 enzyme, which contains a digoxigenin-binding domain and a modified ascorbate peroxidase domain, was then recruited to the RNA targets, enabling in vitro biotinylation of target-proximal proteins. Following streptavidin pull-down, biotinylated proteins were fragmented using a Trypsin/Lys-C protease mix and identified by label-free LC-MS/MS analysis. All experiments were performed in triplicate

2025-08-12 | PXD063192 | Pride

Label-free LC-MS/MS analysis of proteins associated with specific RNAs in HeLa cells

Project description:Proteins co-localizing with RNA targets of interest in HeLa cells were identified using our recently optimized hybridization-proximity labeling approach (HyPro2) combined with label-free mass spectrometry. Briefly, fixed and permeabilized cells were hybridized with digoxigenin-labeled antisense oligonucleotide probes targeting the long noncoding RNA PNCTR or pre-mRNAs encoding ACTB and FUS proteins. A no-probe negative control was also included. The purified HyPro2 enzyme, which contains a digoxigenin-binding domain and a modified ascorbate peroxidase domain, was then recruited to the RNA targets, enabling in vitro biotinylation of target-proximal proteins. Following streptavidin pull-down, biotinylated proteins were fragmented using a Trypsin/Lys-C protease mix and identified by label-free LC-MS/MS analysis. All experiments were performed in triplicate.

2025-08-04 | PXD063191 | 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