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; |
Keyword List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD036799
- Label: PRIDE project
- Name: InterBatch Benchmarking Experiment for Isobaric Proteomics