PXD011175

PXD011175 is an original dataset announced via ProteomeXchange.

Title	AUTOMATED PHOSPHOPEPTIDE ENRICHMENT FROM MINUTE QUANTITIES OF FROZEN MALIGNANT MELANOMA TISSUE
Description	To acquire a deeper understanding of malignant melanoma (MM), it is essential to study the proteome of patient tissues. In particular, phosphoproteomics of MM has become of significant importance because of the central role that phosphorylation plays in the development of MM. Investigating clinical samples, however, is an extremely challenging task as there is usually only very limited quantities of material available to perform targeted enrichment approaches. Here, an automated phosphopeptide enrichment protocol using the AssayMap Bravo platform was applied to MM tissues and assessed for performance. The strategy proved to be highly-sensitive, less prone to variability, less laborious than existing techniques and adequate for starting quantities at the microgram level. An Fe(III)-NTA-IMAC-based enrichment workflow was applied to a dilution series of MM tissue lysates. The workflow was efficient in terms of sensitivity, reproducibility and phosphosite localization; and from only 12.5 µg of sample, more than 1,000 phosphopeptides were identified. In addition, from 60 µg of protein material the number of identified phosphoproteins from individual MM samples was comparable to previous reports that used extensive fractionation methods. Our data set included key pathways that are involved in MM progression; such as MAPK, melanocyte development and integrin signaling. Moreover, tissue-specific immunological proteins were identified, that have not been previously observed in the proteome of MM-derived cell lines. In conclusion, this workflow is suitable to study large cohorts of clinical samples that demand automatic and careful handling.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:14:23.817.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	JIMMY RODRIGUEZ
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-24 05:58:16	ID requested
1	2018-11-23 06:57:26	announced
2	2019-05-29 04:06:01	announced	Updated publication reference for PubMed record(s): 30532160.
⏵ 3	2024-10-22 04:14:24	announced	2024-10-22: Updated project metadata.

10.1371/journal.pone.0208562;

Murillo JR, Kuras M, Rezeli M, Miliotis T, Betancourt L, Marko-Varga G, Automated phosphopeptide enrichment from minute quantities of frozen malignant melanoma tissue. PLoS One, 13(12):e0208562(2018) [pubmed]

submitter keyword: Bravo AssayMap, sensitivity, Fe(III)-IMAC., malignant melanoma phosphoproteomics,Phosphopeptide enrichment

Gyorgy Marko-Varga
contact affiliation	Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund), Department of Biomedical Engineering, Lund University, Lund, Sweden.
contact email	gyorgy.marko-varga@bme.lth.se
lab head
JIMMY RODRIGUEZ
contact affiliation	Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
contact email	esneider007@gmail.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/2018/11/PXD011175

PRIDE project URI

• PRIDE
  1. PXD011175
     1. Label: PRIDE project
     2. Name: AUTOMATED PHOSPHOPEPTIDE ENRICHMENT FROM MINUTE QUANTITIES OF FROZEN MALIGNANT MELANOMA TISSUE