PXD045958

PXD045958 is an original dataset announced via ProteomeXchange.

Title	Optimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples
Description	Data independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be easily optimised to minimise the occurrence of false positives across different samples. Using an immunological model system to demonstrate the impact of adjusting search settings we analysed mouse macrophages and compared their proteome to macrophages spiked with Candida albicans. This experimental system enabled the identification of ‘false positives’ since Candida albicans peptides and proteins should not be present in the mouse only samples. We show that adjusting the search parameters reduced ‘false positive’ identifications by up 89% at the peptide and protein level, thereby considerably increasing the quality of the data. We also show that these optimised parameters incur a moderate cost, only reducing the overall number of ‘true positive’ identifications across each biological replicate by less than 6.7% at both the peptide and protein level. We believe the value of our updated search parameters extends beyond a two-organism analysis and would be of great value to any experiment analysing heterogenous populations of cell types or tissues.
HostingRepository	PRIDE
AnnounceDate	2023-10-16
AnnouncementXML	Submission_2023-10-16_07:58:29.648.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	AlejandroBrenes
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Candida albicans (Yeast); NCBI TaxID: 5476;
ModificationList	oxidation; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-07 17:54:46	ID requested
1	2023-10-11 14:51:17	announced
⏵ 2	2023-10-16 07:58:30	announced	2023-10-16: Updated project metadata.

Dataset with its publication pending

submitter keyword: data quality, Spectronaut, false positives, immunology, C. albicans, mouse, infection,DIA, XIC, multi-species

SimonArthur
contact affiliation	Cell Signalling & Immunology, University of Dundee
contact email	j.s.c.arthur@dundee.ac.uk
lab head
AlejandroBrenes
contact affiliation	Cell Signalling & Immunology, University of Dundee
contact email	ajbrenesmurillo@dundee.ac.uk
dataset submitter

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/2023/10/PXD045958

PRIDE project URI

• PRIDE
  1. PXD045958
     1. Label: PRIDE project
     2. Name: Optimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples