PXD036799-2

PXD036799 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	InterBatch Benchmarking Experiment for Isobaric Proteomics
Description	We developed a unique multi-batch benchmarking dataset. The design is based on a standard two-species dilution model3,18,19 with mouse plasma used to create a background of potentially interfering peptides at 1:1 ratios while yeast cultures are mixed across a range of known ratios. For the purposes of investigating how best to combine isobaric batches the experiment is designed with two main goals. First, we needed multiple batches of data containing a wide range of known changes, with some large enough to test the dynamic range of our instrument, and others small enough to probe our capacity for detecting small perturbations. Second, we need a wide variety of batch compositions to better reflect the full set of patterns that we might observe when studying a random assortment of genetically diverse samples. To this end, yeast proteomes were diluted at eleven different levels of known changes with a maximum dilution of 1/32 by the use of an automated liquid handler. To generate a diversity of batch compositions across the proteome, we cultured yeast in various carbon and nitrogen source combinations known to substantially alter the yeast proteome20. Both media groups and dilution levels were randomly assigned throughout six batches of TMT-labeled samples
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:33:55.030.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jonathon O'Brien
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-17 04:01:12	ID requested
1	2024-03-18 08:34:59	announced
⏵ 2	2024-10-22 06:33:56	announced	2024-10-22: Updated project metadata.

Publication List

O'Brien JJ, Raj A, Gaun A, Waite A, Li W, Hendrickson DG, Olsson N, McAllister FE, A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments. Nat Methods, 21(2):290-300(2024) [pubmed]
10.1038/s41592-023-02120-6;

O'Brien JJ, Raj A, Gaun A, Waite A, Li W, Hendrickson DG, Olsson N, McAllister FE, A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments. Nat Methods, 21(2):290-300(2024) [pubmed]

10.1038/s41592-023-02120-6;

Keyword List

submitter keyword: Isobaric, Yeast, two-species interference model, Mouse,TMT

submitter keyword: Isobaric, Yeast, two-species interference model, Mouse,TMT

Contact List

Fiona McAllister
contact affiliation	Calico Life Sciences
contact email	fiona@calicolabs.com
lab head
Jonathon O'Brien
contact affiliation	Calico Life Sciences
contact email	obrien@calicolabs.com
dataset submitter

Full Dataset Link List

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/03/PXD036799
PRIDE project URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/03/PXD036799

PRIDE project URI

Repository Record List

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