Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic profiling to predict therapeutic response to anti-PD1 therapy in advanced melanoma – SWATH MS dataset - glycopeptides

ABSTRACT: MS-based proteomics based on data-independent acquisition / SWATH MS was used to study the response of melanoma patients to anti-PD1 therapy. Human serum samples were collected from patients at the start of their therapy and later categorized into responders and non-responders based on clinical outcome. Samples were subjected to glycocapture and glycopeptides were quantified by SWATH MS followed by analysis using mapDIA to protein levels.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Serum

DISEASE(S): Melanoma

SUBMITTER: Ludovic Gillet

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD027933 | Pride | 2023-08-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E1712141754_feature_alignment_requant.tsv	Tabular
	PD1_lib32_171215_mapDIA_input.txt	Txt
	SampleAnnotation.txt	Txt
	analysis_output.txt	Txt
	checksum.txt	Txt

Items per page:

1 - 5 of 64

Similar Datasets

Glycoprotein Signatures for Aggressive Prostate Cancer via SWATH mass spectrometry

Project description:The identification of biomarkers indicating the level of aggressiveness of prostate cancer (PCa) addresses an urgent clinical need to minimize the general over-treatment of patients with non-aggressive PCa, which account for the majority of PCa cases. In this study we combined N-glycopeptide isolation and SWATH-MS towards the molecular characterization of tumor malignancy and aggressiveness. Here, we isolated formerly N-linked glycopeptides from normal prostate (n=10), non-aggressive (n=22), aggressive (n=16) and metastatic PCa (n=25) tumor tissues and analyzed the samples by SWATH-MS, an emerging data independent mass spectrometric acquisition method that generates a single MS file containing fragment ion spectra of all ionized species of a sample. The resulting datasets were searched using a targeted data analysis strategy where a priori spectral reference library representing known N-glycosites of the human proteome was used to identify groups of signals in the SWATH-MS data. On-average we identified 1430 N-glycosites from each SWATH map of which 1057 were quantified across all samples. The 220 glycoproteins that showed significant quantitative changes associated diverse biological processes with the level of PCa aggressiveness and metastasis and indicated functional relationships with common PCa genomic mutations.

2014-04-23 | PXD000704 | Pride

A magnetic bead-based workflow for sensitive and streamlined cell surface proteomics

Project description:Cell-surface proteins represent an important class of molecules for therapeutic targeting and defining cellular phenotypes. However, their enrichment and detection via mass spectrometry-based proteomics remains challenging due to low abundance, posttranslational modifications, hydrophobic regions, and processing requirements. To improve the identification of cell-surface proteins via their corresponding N-linked glycopeptides (N-glycopeptides), we optimized a Cell-Surface Capture (CSC) workflow which incorporates magnetic bead-based processing. Using this approach, we evaluated labeling conditions (biotin tags and catalysts), enrichment specificity (streptavidin beads), missed cleavages (lysis buffers), non-enzymatic deamidation (digestion and de-glycosylation buffers), and data acquisition methods. Our findings support the use of alkoxyamine-PEG4-biotin plus 5-methoxy-anthranilic acid and streptavidin magnetic beads for maximal N-glycopeptide detection. Furthermore, single-pot solid-phased-enhanced sample-preparation (SP3) circumvented the need to isolate cell membranes by affording the use of strong detergents and chaotropes for protein extraction. Notably, with semi-automated processing, sample handling was simplified and between ~600-900 N-glycoproteins were identified from only 25-200µg of HeLa protein. Overall, the improved efficiency of the magnetic-based CSC workflow allowed us to identify both previously reported and novel N-glycosites with less material and high reproducibility, and should help advance the field of surfaceomics by providing insight in cellular phenotypes not previously documented.

2024-01-21 | PXD043678 | Pride

Proteomic profiling of NCI60 cell lines from Cancer Cell Line Encyclopedia

Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.

2017-01-27 | E-PROT-2 | biostudies-arrayexpress

Project description:The plasma of the sepsis patient survivors and non-survivors (n=10/group) were analyzed using glycoproteomics approach.

2018-10-19 | PXD001425 | Pride

Total Proteome Analysis in RNAi treated C. elegans

Project description:A SWATH-based worflow has been developed for C. elegans proteome profiling, including sample preparation, SWATH spectral library generation and downstream data treatment. The influence of mrps-5 RNAi treatment on C. elegans total proteome were studied.

2019-12-11 | PXD009223 | Pride

Total Proteome Analysis in RNAi treated C. elegans (mrps5, fzo1, drp1, eat3)

Project description:A SWATH-based worflow has been developed for C. elegans proteome profiling, including sample preparation, SWATH spectral library generation and downstream data treatment. The influences of several RNAi treatments (including mrps5, fzo1, drp1, eat3) on C. elegans total proteome were studied.

2020-04-03 | PXD009256 | Pride

Project Grandiose, cell surface protein capture

Project description:The aim of Project Grandiose has been to examine the process of somatic cell (specifically, murine fibroblast) conversion to induced pluripotent stem cells, at many levels (proteome, mRNA, DNA methylation, etc.), over the time course of the conversion. This dataset represents the cell surface proteome portion of the project, namely the set of cell surface glycoproteins that were detected over theproject time course.

2014-11-27 | PXD001456 | Pride

urinary glycopeptide profile differentiates early cardiorenal risk in subjects not meeting criteria for chronic kidney disease

Project description:Early diagnosis and treatment of chronic kidney disease (CKD) is a worldwide challenge. Albuminuria is defined as urinary albumin:creatinine ratio (ACR) ≥30 mg/g. Subjects with ACR values below this cut-off and preserved renal function are considered at no cardiorenal risk, but increased risk is established even at the 10-30 mg/g ACR range, supporting the need to identify other molecular indicators for early assessment of normoalbuminuric patients at higher risk. Following our previous studies, here we aimed to stratify the normoalbuminuria range according to cardiorenal risk and identify glycoproteins and N-glycosylation sites associated to kidney damage in subclinical CKD.

2025-06-02 | PXD049688 | Pride

Glycoproteome of Elongating cotton fiber cells

Project description:Glycoproteins isolated from elongating cotton fiber cells were analyzed using 2D-PAGE followed by MALDI TOF/TOF based protein identification. Protein isoforms were identified using Tandem mass spectrometry. Lectin based Glycopeptide enrichment strategy followed by PNGase catalyzed deglycosylation reaction was employed to assign potential N-linked glycosylation sites.

2015-11-25 | PXD002849 | Pride

Detection of Five Solid Carcinomas Using Blood Circulating Proteins

Project description:When diagnosed in a metastatic stage cancer is mostly incurable making its early detection via biomarkers of immense clinical interest. Proteins circulating in blood are a preferred source of biomarkers for a wide range of cancers due to the ease and non-invasiveness of collection. Our approach to cancer biomarker discovery is based on the observation that proteomic changes in tumor tissue are remotely detectable as changes in the protein composition of blood plasma. To determine whether these changes in the plasma of patients are specific for their specific cancer or represent a response to cancer in general we performed a cross-tumor plasma proteomic study. Using a proteomic serum/plasma workflow consisting of the combined use of N-glycosite enrichment and SWATH mass spectrometry (SWATH-MS), we investigated 155 blood samples derived from cohorts of patients with carcinomas at a localized or locally advanced clinical stage, or from a matched control group. A quantitative comparison of the resulting N-glycosite profiles indicated that some biomarkers are common to several cancers, while others are highly specific for one cancer type.

2018-08-09 | PXD004998 | 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