Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABRF iPRG 2023 crosslinking study - Kojak COMPLETE results

ABSTRACT: The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year (2023) the iPRG group has put together a crosslinking study. The goal is to teach people how to analyze crosslinked samples with existing software and provide them with data sets that they can practice on. It is then hoped that more core labs will offer crosslinking analysis as a service to customers and collaborators. This particular submission provides the Kojak results in COMPLETE dataset format supporting mzIdentML 1.2.0 and it is used as a gold-standard for the new PRIDE Archive resource https://www.ebi.ac.uk/pride/archive/crosslinking

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Escherichia Coli

SUBMITTER: Yasset Perez-Riverol

LAB HEAD: Yasset Perez-Riverol

PROVIDER: PXD056910 | Pride | 2024-10-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	211026EWas01_E1.mzML	Mzml
	211026EWas01_E1.raw	Raw
	211026EWas02_F1.mzML	Mzml
	211026EWas02_F1.raw	Raw
	211026EWas03_F2.mzML	Mzml

Items per page:

1 - 5 of 9

Similar Datasets

ABRF iPRG 2023 crosslinking study - Mascot COMPLETE results

Project description:The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year (2023) the iPRG group has put together a crosslinking study. The goal is to teach people how to analyze crosslinked samples with existing software and provide them with data sets that they can practice on. It is then hoped that more core labs will offer crosslinking analysis as a service to customers and collaborators. This particular submission provides the Mascot results in COMPLETE dataset format supporting mzIdentML 1.2.0 and it is used as a gold-standard for the new PRIDE Archive resource https://www.ebi.ac.uk/pride/archive/crosslinking.

2024-08-08 | PXD054720 | 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

HipSci project pilot submission for 18 IPS cell lines

Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Raw data files for this study can be accessed from the PRIDE database at EMBL-EBI under accession number PXD003903: http://www.ebi.ac.uk/pride/archive/projects/PXD003903.

2016-06-22 | E-PROT-5 | biostudies-arrayexpress

PBC-DIGE - Serological comparative proteomics analysis of mitochondrial autoantibody-negative and -positive primary biliary cirrhosis

Project description:DIGE combined with MALDI-TOF-TOF MS/MS was applied to explore the differential expressed proteins between AMA positive and negative PBC.</br> NB <a href=" ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/11/PXD001397/extra_files.zip"> Extra peak files</a> are available on the FTP for this <a href=" ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/11/PXD001397">project</a> .

2014-11-27 | PXD001397 | Pride

Reanalysis of Cross-Linking Mass Spectrometry data from a ribisomal cellular fraction for benchmarking purposes

Project description:Reanalysis of a cross-linked ribosomal cellular fraction dataset, that is a subset of a fragmentation parameters optimization dataset (PRIDE project PXD006131). The HCD fragmented part of the dataset was searched with the Cross-Linking MS identification tools OpenPepXL, pLink2, Kojak and XiSearch.

2020-10-20 | PXD014520 | Pride

Tandem mass tag (TMT) quantification data from knee chondrocytes for 12 osteoarthritis patients, comparing disease tissue against control tissue in each individual

Project description:This data set is made up of 4 experiments (batches) analysing chondrocytes from healthy and diseased knees in 12 patients with osteoarthritis. There are 6 samples (from 3 patients) for each batch, where diseased and control samples were extracted from each patient and compared within patient. The batches were necessary due to the maximum sample capacity (6) of the mass spectrometer. The raw data files were deposited at EBI PRIDE database under accession number PXD002014 ( http://www.ebi.ac.uk/pride/archive/projects/PXD002014 ). This ArrayExpress record contains sample meta-data and processed data in the form of ratios and the log2 fold changes. The ratios were calculated for each patient as diseased vs control (the reference). Please note that one patient (number 52) was excluded from the fold change analysis as no proteins showed any significant change which suggests the samples were not correct or something went wrong with them. There is also the median and standard deviation across the patients.

2017-10-01 | E-PROT-4 | biostudies-arrayexpress

Mouse bone marrow derived neutrophils, LC-MSMS

Project description:Analysis of cell membrane-enriched proteins of mouse polymorphonuclear neutrophils. Further related data are present in project <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD002244">PXD002244</a>.

2015-10-09 | PXD003015 | Pride

Mouse bone marrow derived neutrophils, LC-MSMS

2015-07-20 | PXD002244 | Pride

MaxQuant Complete Submission: First Complete Submission in mzTab MaxQuant

Project description:This is the first MaxQuant Complete submission in mzTab and should be take as a reference for other softwares to export mzTab Complete Submissions into PRIDE Archive.

2018-09-28 | PXD011194 | Pride

In vitro crosslinking of PAX8 and PRDM3

Project description:MS crosslinking of PAX8 and PRDM3 using standard DSSO-based crosslinking

2021-03-09 | PXD021708 | Pride