PXD028700

PXD028700 is an original dataset announced via ProteomeXchange.

Title	Individualized proteogenomics reveals mutational landscape of melanoma patients in response to immunotherapy
Description	Immune checkpoint inhibitors are used to restore or augment antitumor immune response and show great promise in treatment of melanoma and other types of cancers. However, only a relatively small percentage of patients are fully responsive to immune checkpoint inhibition, mostly due to tumor heterogeneity and primary resistance to therapy. Both of these features are largely driven by accumulation of patient-specific mutations, pointing to the need for personalized approaches in diagnostics and immunotherapy. Proteogenomics integrates patient-specific genomic and proteomic data to study cancer development and resistance mechanisms, as well as tumor heterogeneity in individual patients. Here, we use a proteogenomic approach to characterize the mutational landscape of samples derived from four clinical melanoma patients at the genomic, proteomic and phosphoproteomic level. Integration of datasets enabled identification and quantification of an extensive number of sample-specific amino acid variants, among them many were not previously reported in melanoma. We detected a disproportional number of alternate peptides between treated and untreated (naïve) samples with a high potential to influence signal transduction. This is one of the first proteogenomic study designed to study the mutational landscape of patient-derived melanoma tissue samples in response to immunotherapy.
HostingRepository	PRIDE
AnnounceDate	2022-02-16
AnnouncementXML	Submission_2022-02-16_13:27:03.313.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-22 12:06:11	ID requested
⏵ 1	2022-02-16 13:27:04	announced

Schmitt M, Sinnberg T, Niessner H, Forschner A, Garbe C, Macek B, Nalpas NC, Individualized Proteogenomics Reveals the Mutational Landscape of Melanoma Patients in Response to Immunotherapy. Cancers (Basel), 13(21):(2021) [pubmed]

submitter keyword: Proteogenomics, Melanoma, Mass Spectrometry, Immunotherapy, Whole Exome Sequencing

Prof. Dr. Boris Macek
contact affiliation	Chair Quantitative Proteomics Director Proteome Center Tuebingen Interfaculty Institute for Cell Biology University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen Germany
contact email	boris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliation	Tuebingen University
contact email	nalpas.nicolas@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028700
     1. Label: PRIDE project
     2. Name: Individualized proteogenomics reveals mutational landscape of melanoma patients in response to immunotherapy