Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Antibody N-linked glycosylation profiling with PEAKS GlycanFinder

ABSTRACT: We conducted a new mass spectrometry experiment for antibody N-linked glycosylation profiling that could distinguish isomeric peptides and glycans in four immunoglobulin G subclasses.

INSTRUMENT(S): Orbitrap Eclipse, timsTOF Pro 2

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Serum

SUBMITTER: Weiping Sun

LAB HEAD: Jun Ma

PROVIDER: PXD039787 | Pride | 2023-05-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform

Project description:Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high throughput experiments. Most importantly, it enables results dependent acquisition (RDA) where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide- and glycan-moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks future development of RDA technology to transcend data acquisition.

2023-03-13 | PXD040716 | Pride

Immunopeptidomics by use of a microfluidics chip.

Project description:A microfluidics technology was implemented to the immunoaffinity purification process of MHC peptides in Ligandomics/Immunopeptidomics. The thus purified HLA peptides were analysed by LCMS with the nanoElute LC and TimsTOF Pro Mass Spectrometer from Bruker. The aim of the microfluidics implementation was to improve the sensitivity and robustness while also reducing antibody and other material requirements in the immunoaffinity purification protocol.

2022-02-17 | PXD022194 | Pride

Exploiting trogocytosis by Immunopeptidomics to profile tumor associated antigens (TAA) actively targeted by tumor specific T cells in leukemia.

Project description:We employed PeptiCHIP Immunopeptidomics to profile tumor associated antigens (TAA) actively targeted by tumor specific T cells by exploiting the trogocytosis effect, whereby antigen presenting cells (APCs) nibble portions of the cognate T cell containing the TCR. The antigen presenting cells were then processed by Immunoaffinity purification by peptiCHIP to identify the relevant HLA-I peptides by LCMS on the Bruker Tims TOF Pro instrument.

2023-09-07 | PXD035344 | Pride

First direct observation of elongated conformational states in alpha-synuclein upon liquid-liquid phase separation

Project description:α-Synuclein (α-syn) is an intrinsically disordered protein (IDP) that undergoes liquid-liquid phase separation (LLPS), fibrillation, and forms insoluble intracellular Lewy’s bodies in neurons, which are the hallmark of Parkinson’s Disease (PD). Neurotoxicity precedes the formation of aggregates and is probably related to LLPS of α-syn in the cell. The molecular mechanisms underlying the early stages of LLPS are still elusive. To obtain structural insights into α-syn upon LLPS, we take advantage of cross-linking/mass spectrometry (XL-MS) and introduced an innovative new approach, termed COMPASS (COMPetitive PAiring StatisticS). COMPASS unravels transient interactions between α-syn molecules in liquid droplets to derive structural information of α-syn upon LLPS. In this work, we show that the conformational ensemble of α-syn shifts towards more elongated conformational states upon LLPS. We obtain insights into the critical initial stages of PD and establish a novel mass spectrometry-based approach that will aid to solve open questions in LLPS structural biology.

2024-03-18 | PXD033205 | Pride

Iimmunopeptidomics pipeline for generation of personalized oncolytic cancer vaccines.

Project description:We used a streamlined pipeline for the generation of personalized cancer vaccines starting from the isolation and selection of the most immunogenic peptide candidates expressed on the tumour cells and ending in the generation of efficient therapeutic oncolytic cancer vaccines. We used MHC-I immunoaffinity purification in a murine colon tumor model from CT26 cells. The selection of the target candidates was then based on two separate approaches: RNAseq analysis and HEX software.

2022-04-06 | PXD026463 | Pride

Immunopeptidomics of malignant mesothelioma to identify target antigens for T cell Immunotherapy

Project description:Immunoaffinity purification was performed on human mesothelioma cell lines NCI-H2452, NCI-H28, MSTO-211H and JL1, on murine mesothelioma cell line AB12, as well as on mesothelioma samples from two patients (including tumor and benign tissues). Thereafter Immunopeptidomics by Mass Spectrometry on a Tims TOF Pro revealed the MHC peptide landscape of mesothelioma.

2023-09-08 | PXD038273 | Pride

Deregulated Expression of the 14q32 miRNA Cluster in Clear Cell Renal Cell Carcinomas

Project description:Clear cell renal cell carcinomas (ccRCC) are characterized by arm-wide chromosomal alterations. Loss at 14q is associated with disease aggressiveness in ccRCC, which responds poorly to chemotherapeutics. The 14q locus contains one of the largest miRNA clusters in the human genome; however, little is known about the contribution of these miRNAs to ccRCC pathogenesis. In this regard, we investigated the expression pattern of selected miRNAs at the 14q32 locus in TCGA kidney tumors and in ccRCC cell lines. We validated that the miRNA cluster is downregulated in ccRCC (and cell lines) as well as in papillary kidney tumors relative to normal kidney tissues and primary renal proximal tubule epithelial (RPTEC) cells. We demonstrated that agents modulating expression of DNMT1 (e.g., 5-Aza-deoxycytidine) could modulate miRNA expression in ccRCC cell lines. Lysophosphatidic acid (LPA, a Lysophospholipid mediator elevated in ccRCC) not only increased labile iron content but also modulated expression of 14q32 miRNAs. Through an overexpression approach targeting a subset of 14q32 miRNAs (specifically at subcluster A: miR-431, miR-432, miR-127, and miR-433) in 769-P cells, we uncovered changes in cellular viability and claudin-1, a tight junction marker. A global proteomic approach was implemented using these miRNA overexpressing cell lines which uncovered ATXN2 as a highly downregulated target, which has a role in chronic kidney disease pathogenesis. Collectively, these findings support a contribution of miRNAs at 14q32 in ccRCC pathogenesis.

2023-05-10 | PXD036428 | Pride

CSF glycoproteomics reveals brain-specific changes in glyco-sylation in congenital disorders of glycosylation

Project description:In this project, CSF samples from healthy volunteers and patients diagnosed with congenital disorders of glycosylation (CDG) were analyzed with MS-based glycoproteomics to characterize the glycoproteome in the two cohorts. In order to identify highly truncated glycopeptides and glycopeptides that show the complete loss of glycosylation, we chose to not perform a glycopeptide enrichment. Using the high identification rate of the timsTOF Pro including PASEF fragmentation, we were able to detect over 800 unique glycopeptides. We show that changes in protein N-glycosylation of CDG patients can be different on brain-derived proteins compared to blood derived proteins.

2023-01-18 | PXD038787 | Pride

A peptide-derived strategy for specifically targeting the mitochondrial-ER network of cancer cells: a new paradigm in fighting cancer

Project description:An effective anti-cancer therapy should exclusively target cancer cells and trigger in them a broad spectrum of cell death pathways that will prevent avoidance. Here, we present a novel paradigm in cancer therapy that specifically targets the mitochondria and ER of cancer cells. We developed a peptide derived from the flexible and transmembrane domains of the human protein NAF-1/CISD2. This peptide (NAF-1) specifically permeated through the plasma membranes of human epithelial breast cancer cells, abolished their mitochondrial-ER network, and triggered cell death with characteristics of apoptosis, ferroptosis and necroptosis. In vivo analysis revealed that the peptide significantly decreased tumor growth in mice carrying xenograft human tumors. Computational simulations of cancer vs. normal cells membranes revealed that the specificity of the peptide to cancer cells is due to its selective recognition of their membrane composition. NAF-1 represents therefore a promising anti-cancer lead compound that acts via a unique mechanism.

2022-08-12 | PXD030509 | Pride

MS Annika: A new Cross-Linking Search Engine

Project description:A cross linking mass spectrometry search engine was developed and implemented into Thermo Proteome Discoverer. The search engine is capable to handle several linker types as well as data input formats. To demonstrate its ability processing Bruker -ion mobility data, synthetic peptides (Beveridge, et. al., Nat. Commun., 2020, doi: 10.1038/s41467-020-14608-2) were analyzed and the respective files are availible here.

2021-05-27 | PXD022772 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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