Browse
Submit Data
Databases
API
Help

Dataset Information

211 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments, part 2

ABSTRACT: We propose a new pipeline for the refinement of spectrum-peptide assignment, designed specifically for MHC ligand identification. By modeling the peptidome as a collection of a limited number of specificities, corresponding to the MHC alleles of the cell line, our method achieves increased sequencing depth, while at the same time removing potential experimental outliers and contaminants.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Nicola Ternette

LAB HEAD: Nicola Ternette

PROVIDER: PXD011794 | Pride | 2019-01-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	FL812_mouse_A1_even.mgf	Mgf
	FL812_mouse_A1_even.pride.mgf.gz	Mgf
	FL812_mouse_A1_even.raw	Raw
	FL812_mouse_A1_odd.mgf	Mgf
	FL812_mouse_A1_odd.pride.mgf.gz	Mgf

Items per page:

1 - 5 of 50

Publications

MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments.

Andreatta Massimo M Nicastri Annalisa A Peng Xu X Hancock Gemma G Dorrell Lucy L Ternette Nicola N Nielsen Morten M

Proteomics 20190118 4

LC-MS/MS has become the standard platform for the characterization of immunopeptidomes, the collection of peptides naturally presented by major histocompatibility complex molecules to the cell surface. The protocols and algorithms used for immunopeptidomics data analysis are based on tools developed for traditional bottom-up proteomics that address the identification of peptides generated by tryptic digestion. Such algorithms are generally not tailored to the specific requirements of MHC ligand ...[more]

PMID: 30578603

Similar Datasets

Transcription profiling of mouse basal-like mammary tumors of luminal origin

Project description:MS_LuminalOriginBasalLikeMammaryTumours

2011-05-03 | E-TABM-684 | biostudies-arrayexpress

Gene expression - GLI1 induced mammary gland tumours

Project description:Increased expression of GLI1 is associated with poor prognosis for some breast cancer subtypes. A conditional transgenic GLI1 expressing mouse model, with or without heterozygous deletion of Trp53, was used to generate and study GLI1 induced mammary gland tumours. Tumour tissue was serially orthotopically transplanted for at least 10 generations in NSG mice.

2019-06-30 | E-MTAB-7531 | biostudies-arrayexpress

RNA-seq analysis of CD8 tumour infiltrating lymphocytes from GFP-Egr2 Knockin and hCD2-Cre Egr2loxP/loxP Egr3-/- mice

Project description:To determine the effect of Egr2 and Egr3 on tumour infiltrating lymphocyte gene expression, GFP-Egr2 knockin (Egr2 Kin) and hCD2-Cre Egr2loxP/loxP Egr3-/- (Egr2/3 DKO) mice were inoculated with MC38 or B16 tumour cells. Fourteen days later, GFP-Egr2high and Egr2-/-Egr3-/- CD8+ tumour infiltrating lymphocytes were isolated from Egr2 Kin and Egr2/3 DKO mice, respectively, and analysed by RNA-seq.

2023-01-31 | E-MTAB-11672 | biostudies-arrayexpress

The use of Nitric Oxide as a Radiosensitiser of Hypoxic Prostate Cancer Characterized by Data Independent Label-free Ion Mobility LC-MS

Project description:The use of Nitric Oxide as a Radiosensitiser of Hypoxic Prostate Cancer Characterized by Data Independent Label-free Ion Mobility LC-MS

2020-02-27 | PXD009047 | Pride

RNA of Small Cell Lung Cancer Circulating Tumour Cells Derived Explants

Project description:RNA-seq data characterising small cell lung cancer within circulating tumour cell (CTC) derived explants, generated within immune compromised mice. Both chemo naive and progression models were taken from patients and their drug sensitivity tested within the mouse models. Blood samples were taken from patients, and RosetteSep CTC Enrichment was used to implant these cells into mice. Tumours were allowed to grow, then extracted and re-implanted into second and third generations of mice, before finally being subjected to molecular profiling.

2020-04-26 | E-MTAB-8465 | biostudies-arrayexpress

MS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments

Project description:We propose a new pipeline for the refinement of spectrum-peptide assignment, designed specifically for MHC ligand identification. By modeling the peptidome as a collection of a limited number of specificities, corresponding to the MHC alleles of the cell line, our method achieves increased sequencing depth, while at the same time removing potential experimental outliers and contaminants.

2019-01-02 | PXD011723 | Pride

Restoring PD-1 immune checkpoint inhibitor response following IFNγ-driven adaptive resistance

Project description:Immune checkpoint inhibitors (ICIs) are a type of cancer treatment that work by targeting molecules on immune cells that can inhibit the immune system's ability to attack cancer cells. One such checkpoint molecule is PD-1, which is found on the surface of T cells (a type of immune cell) and helps to prevent them from attacking healthy cells. When PD-1 binds to its ligand (a molecule on the surface of some cells), it sends a signal to the T cell to \\"turn off\\" and not attack the cell. This mechanism is important in preventing the immune system from attacking healthy cells, but it can also be exploited by cancer cells to avoid detection and destruction by the immune system. In this study YUMM2.1 mouse tumour cells were implanted subcutaneously. The effect of IFN-γ-pre-treatment, PARP14 inhibition and PD-1 antibody treatment are reported by RNA-seq.

2023-08-22 | E-MTAB-12872 | biostudies-arrayexpress

Transcription profiling by array of mouse mammary epithelial stem cell tumours.

Project description:The aim of the experiment was to analyse gene expression profiles in Brca1 tumours arising from different mammary epithelial cell populations use a Cre-loxP based conditional knockout system. K14 promoter driving Cre expression caused Brca1 knockout in basal stem cells and thus stem cell origin tumours whereas Blg promoter driving Cre expression caused Brca1 knockout in luminal progenitor cells and thus progenitor origin tumours. Individual arrays were carried out on labelled cDNA made from RNA isolated from mouse mammary tumours. Only cDNA passing Almac diagnostics QC criteria were hybridised to arrays. Only arrays passing QC criteria after hybrisiation were subsequently analysed.

2011-05-20 | E-TABM-997 | biostudies-arrayexpress

A combinatorial extracellular matrix platform identifies cell-extracellular matrix interactions that correlate with metastasis

Project description:Extracellular matrix interactions play essential roles in normal physiology and many pathological processes. Here, we report a novel screening platform capable of measuring phenotypic responses to combinations of ECM molecules. While the importance of ECM interactions in metastasis is well documented, systematic approaches to identify their roles in distinct stages of tumorigenesis have not been described. Using a genetic mouse model of lung adenocarcinoma, we measured the ECM-dependent adhesion of tumor-derived cells. Hierarchical clustering of adhesion profiles generated using this platform differentially segregated metastatic cell lines from primary tumor lines. Furthermore, we uncovered that metastatic cells selectively associate with fibronectin when in combination with galectin-3, galectin-8, or laminin. These interactions appear to be mediated in part by Î±3Î²1 integrin both in vitro and in vivo. We show that these galectins also correlate with human disease at both a transcriptional and histological level. Thus, our in vitro platform allowed us to interrogate the interactions of metastatic cells with their surrounding environment, and identified ECM and integrin interactions that could lead to therapeutic targets for metastasis prevention. Cell lines derived from murine lung primary adenocarcinomas and their metastases (Winslow et al., 2011 Nature 473:101-104)

2012-10-11 | E-GEOD-40222 | biostudies-arrayexpress

RNA-seq of intestinal cancer GEMMs

Project description:Intestinal tumours from genetically engeenierd mouse modesl (GEMMs), of various gentopyes, were isolated at endpoint and RNA was isolated. In an additional experiment, epithelial tumour organoids were isolated at end point and grown in vitro. These organoids were harvested 72 hours after seeding and RNA was isolated.

2019-09-16 | E-MTAB-6363 | biostudies-arrayexpress

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