PXD052080-1

PXD052080 is an original dataset announced via ProteomeXchange.

Title	Combining data independent acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification )
Description	Data Independent Acquisition (DIA) is increasingly preferred over Data Dependent Acquisition (DDA) due to its higher throughput and fewer missing values. Whereas DDA often utilizes stable isotope labeling to improve quantification, DIA mostly relies on label-free approaches. Efforts to integrate DIA with isotope labeling include chemical methods like mTRAQ and dimethyl labeling, which, while effective, complicate sample preparation. Stable isotope labeling by amino acids in cell culture (SILAC) achieves high labeling efficiency through the metabolic incorporation of heavy labels into proteins in vivo. However, the need for metabolic incorporation limits the direct use in clinical scenarios. Spike-in SILAC methods utilize an externally generated heavy sample as an internal reference, enabling SILAC-based quantification even for samples that cannot be directly labeled. Here, we combine DIA with spike-in SILAC (DIA-SiS), leveraging the robust quantification of SILAC without the complexities associated with chemical labeling. We developed and rigorously validated DIA-SiS through a mixed-species benchmark to assess its performance in proteome coverage and quantification. We demonstrate that DIA-SiS significantly improves proteome coverage and quantification compared to label-free approaches and reduces the incidence of incorrectly quantified proteins. Additionally, DIA-SiS proves effective in analyzing proteins in low-input formalin-fixed paraffin-embedded (FFPE) tissue sections. DIA-SiS combines the precision of stable isotope-based quantification with the simplicity of label-free sample preparation, facilitating simple, accurate and comprehensive proteome profiling.
HostingRepository	PRIDE
AnnounceDate	2024-10-15
AnnouncementXML	Submission_2024-10-15_01:50:10.706.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Maximilian Gerwien
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480; timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-07 08:51:54	ID requested
⏵ 1	2024-10-15 01:50:12	announced

Welter AS, Gerwien M, Kerridge R, Alp KM, Mertins P, Selbach M, Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification. Mol Cell Proteomics, 23(10):100839(2024) [pubmed]

10.1016/j.mcpro.2024.100839;

submitter keyword: Multiplexing, DIA, PlexDIA,SILAC, Proteomics, Benchmark

Matthias Selbach
contact affiliation	Max Delbrück Center for Molecular Medicine Berlin and Charite Berlin
contact email	matthias.selbach@mdc-berlin.de
lab head
Maximilian Gerwien
contact affiliation	MDC Berlin
contact email	maximilian.gerwien@mdc-berlin.de
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/2024/10/PXD052080

PRIDE project URI

• PRIDE
  1. PXD052080
     1. Label: PRIDE project
     2. Name: Combining data independent acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification )