PXD014556

PXD014556 is an original dataset announced via ProteomeXchange.

Title	Automated sample preparation with SP3 for low-input clinical proteomics
Description	High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety of sources, including frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format, performing unbiased protein purification and digestion delivering peptides that can be directly analyzed by LCMS. AutoSP3 eliminates hands-on time and minimizes the risk of error, and we show it reduces the protein quantification variability, and improves longitudinal performance and reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low-input samples, reproducibly quantifying 500-1000 proteins from 100-1000 cells (<100 ng protein). Furthermore we applied it to process a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples, and recapitulate their separation into known histological growth patterns based on proteome profiles. Collectively, autoSP3 provides a generic, scalable, and cost-effective pipeline for routine and standardized proteomic sample processing that should enable reproducible proteomics in broad range of clinical and non-clinical applications.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:27.010.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Torsten Mueller
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-10 03:37:29	ID requested
1	2020-01-10 08:09:27	announced
2	2020-02-17 03:00:24	announced	2020-02-17: Updated publication reference for DOI(s): 10.15252/msb.20199111.
3	2020-09-22 07:36:52	announced	2020-02-17: Updated publication reference for DOI(s): 10.15252/msb.20199111. 2020-09-22: Updated publication reference for PubMed record(s): 32129943. 2020-09-22: Updated publication reference for DOI(s): 10.15252/msb.20199111.
⏵ 4	2023-11-14 08:50:30	announced	2023-11-14: Updated project metadata.

M, ü, ller T, Kalxdorf M, Longuesp, é, e R, Kazdal DN, Stenzinger A, Krijgsveld J, Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol, 16(1):e9111(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: SP3, clinical proteomics, pulmonary adenocarcinoma, sample preparation, low-input, high-throughput, automation

Jeroen Krijgsveld
contact affiliation	Division of Proteomics of Stem Cells and Cancer German Cancer Research Center (DKFZ)
contact email	j.krijgsveld@dkfz.de
lab head
Torsten Mueller
contact affiliation	DKFZ
contact email	torsten.mueller84@googlemail.com
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/2020/01/PXD014556

PRIDE project URI

• PRIDE
  1. PXD014556
     1. Label: PRIDE project
     2. Name: Automated sample preparation with SP3 for low-input clinical proteomics