PXD043014

PXD043014 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Secretome Processing for Proteomics: A Methods Comparison
Description	The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: 1. Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); 2. Acetone protein precipitation coupled to IGD; 3. MWCO filter-based protein concentration followed by to in-solution digestion (ISD); 4. Acetone protein precipitation coupled to ISD; 5. Direct ISD; 6. Secretome lyophilization and ISD. To this end, we assessed workflow triplicates in terms of total number of protein identifications, unique identifications, reproducibility of protein identification and quantification and detectability of small proteins with important functions in cancer biology such as cytokines, chemokines and growth factors.
HostingRepository	PRIDE
AnnounceDate	2024-02-12
AnnouncementXML	Submission_2024-02-12_05:16:40.191.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thang Pham
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-15 05:01:18	ID requested
⏵ 1	2024-02-12 05:16:41	announced

Publication List

Almeida-Marques C, Rolfs F, Piersma SR, Bijnsdorp IV, Pham TV, Knol JC, Jimenez CR, Secretome processing for proteomics: A methods comparison. Proteomics, 24(7):e2300262(2024) [pubmed]
10.1002/pmic.202300262;

Almeida-Marques C, Rolfs F, Piersma SR, Bijnsdorp IV, Pham TV, Knol JC, Jimenez CR, Secretome processing for proteomics: A methods comparison. Proteomics, 24(7):e2300262(2024) [pubmed]

10.1002/pmic.202300262;

Keyword List

submitter keyword: Proteomics
In-solution digestion
Single-shot
Secretome
Biomarker

submitter keyword: Proteomics

In-solution digestion

Single-shot

Secretome

Biomarker

Contact List

Connie Jimenez
contact affiliation	Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
contact email	c.jimenez@amsterdamumc.nl
lab head
Thang Pham
contact affiliation	Amsterdam UMC
contact email	t.pham@amsterdamumc.nl
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/2024/02/PXD043014
PRIDE project URI

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/2024/02/PXD043014

PRIDE project URI

Repository Record List

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