PXD007656

PXD007656 is an original dataset announced via ProteomeXchange.

Title	SWATH-MS in quality control of biologicals: Towards confident label-free and non-targeted quantification with single injection? - An illustration with plasma residuals profiling in human immunoglobulin.
Description	By performing data-independent acquisition (DIA), SWATH-MS is expected to provide comprehensive and repeatable spectral data that can be perpetually interrogated by reference spectral libraries. In the context of biological sample quality control, a benchmark spectral library could index all the possible low-abundant contaminants that should be screened in the sample. Here, the case study concerns the profiling of plasma residuals in human immunoglobulin (Ig) preparations. Yet with such an application, a strong repeatability issue in protein quantification calls for a MS2-level data quality criterion. A MS device intrinsic relationship between MS2 quantification CV and peak area allows using peak area range instead of CV threshold as such a criterion, and by this flagging confident data from single injections. A Python script is provided to perform this flagging. Using such flagging becomes increasingly important as the library becomes more distant from the actual sample. Using appropriated sample fractionation, Ig residuals profiles based on flagged MS2-level quantifications are remarkably consistent with MS1-level quantifications based on classical shotgun (DDA) approach. Sensitivity, which is around three to four orders of magnitude in the concentration dynamic range with a TripleTOF5600 device, remains the main pitfall to gain confident quantification of proteins which were not identified with DDA in the sample and to fully benefit from the SWATH potential for QC applications: provide MS2 specific, comprehensive, label-free and non-targeted quantitative profiles with single injections.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:08:38.949.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-05 01:54:06	ID requested
1	2022-10-04 02:40:11	announced
⏵ 2	2023-11-14 08:08:39	announced	2023-11-14: Updated project metadata.

Limonier F, Willems S, Waeterloos G, Sneyers M, Dhaenens M, Deforce D, Estimating the Reliability of Low-Abundant Signals and Limited Replicate Measurements through MS2 Peak Area in SWATH. Proteomics, 18(24):e1800186(2018) [pubmed]

curator keyword: Technical, Biological

submitter keyword: single injection, Immunoglobulin, TripleTOF5600, biologicals,SWATH MS

Dieter Deforce
contact affiliation	Laboratory of Pharmaceutical Biotechnology. Department of Pharmaceutics, Ghent University, Belgium
contact email	Dieter.Deforce@UGent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
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/2022/10/PXD007656

PRIDE project URI

• PRIDE
  1. PXD007656
     1. Label: PRIDE project
     2. Name: SWATH-MS in quality control of biologicals: Towards confident label-free and non-targeted quantification with single injection? - An illustration with plasma residuals profiling in human immunoglobulin.