PXD017201

PXD017201 is an original dataset announced via ProteomeXchange.

Title	In-depth plasma proteomics in patients with metastatic cutaneous melanoma treated with immune checkpoint inhibitors or MAPK-inhibitors
Description	Recent development of new therapies with immune checkpoint inhibitors (ICIs) and MAPK-inhibitors (MAPKis) have significantly improved the outcome in metastatic cutaneous melanoma (CM). However, therapy response is limited to subgroups of patients and clinically useful predictive biomarkers for treatment outcome are lacking. To discover treatment-related systemic changes in plasma and potential biomarkers associated with treatment outcomes, we analysed 45 plasma samples from 24 patients with metastatic (stage IV) CM, using HiRIEF LC-MS/MS, collected before (pre-trm) and during treatment (trm). Of these, 27 samples were taken from 15 metastatic CM patients treated with ICIs (13 pre-trm and 14 trm samples; 12 matched) and 9 patients treated with MAPKis (9 matched). Matched samples were trm and pre-trm samples taken from the same individual before treatment and after the first cycle of treatment (before the second cycle). We have analysed the change in the plasma protein levels during treatment by comparing the plasma levels in the trm samples to the pre-trm samples, to detect treatment-induced alterations in the plasma proteome. We have analysed the patients treated with ICIs separately from the patients treated with MAPKis, to detect treatment-specific changes for both.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:08:47.316.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Haris Babačić
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-20 06:03:30	ID requested
1	2020-05-05 22:42:48	announced
⏵ 2	2024-10-22 05:08:50	announced	2024-10-22: Updated project metadata.

10.1136/jitc-2019-000204;

Baba, č, i, ć H, Lehti, ö J, Pico de Coa, ñ, a Y, Pernemalm M, Eriksson H, In-depth plasma proteomics reveals increase in circulating PD-1 during anti-PD-1 immunotherapy in patients with metastatic cutaneous melanoma. J Immunother Cancer, 8(1):(2020) [pubmed]

submitter keyword: ipilimumab, MAPK-inhibitors,metastatic, plasma, MAPK, trametinib, programmed cell death protein 1, HiRIEF, immune checkpoint inhibitors, LC-MS/MS, nivolumab, dabrafenib, melanoma, vemurafenib, biomarkers

Janne Lehtiö
contact affiliation	Department of Oncology and Pathology, Karolinska Institute; Science for Life Laboratory, Stockholm, Sweden
contact email	janne.lehtio@ki.se
lab head
Haris Babačić
contact affiliation	1. Department of Oncology-Pathology, Karolinska Institute, Stockholm; 2. Proteogenomics Facility, Science for Life Laboratory
contact email	haris.babacic@ki.se
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/2020/07/PXD017201

PRIDE project URI

• PRIDE
  1. PXD017201
     1. Label: PRIDE project
     2. Name: In-depth plasma proteomics in patients with metastatic cutaneous melanoma treated with immune checkpoint inhibitors or MAPK-inhibitors