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Proteogenomic analysis of Human acute myeloid leukemia

ABSTRACT: Here, we used OpenCustomDB, a web-based tool that uses both sample-specific RNAseq data to identify genomic variants and the OpenProt resource that annotates alternative proteins in addition to canonical proteins. We tested OpenCustomDB with a cohort of 17 patients with acute myeloid leukemia and detected 3026 peptides from alternative proteins, including 208 variants in LC-MS/MS.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Blood

DISEASE(S): Acute Leukemia

SUBMITTER: Noé Guilloy

LAB HEAD: Xavier Roucou

PROVIDER: PXD029240 | Pride | 2023-05-10

REPOSITORIES: Pride

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			Action	DRS
	AML_P01_G1_F1.raw	Raw
	AML_P01_G1_F2.raw	Raw
	AML_P01_G1_F3.raw	Raw
	AML_P01_G1_F4.raw	Raw
	AML_P01_G2_F1.raw	Raw

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Publications

OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.

Guilloy Noé N Brunet Marie A MA Leblanc Sébastien S Jacques Jean-François JF Hardy Marie-Pierre MP Ehx Grégory G Lanoix Joël J Thibault Pierre P Perreault Claude C Roucou Xavier X

Journal of proteome research 20230324 5

Proteomic diversity in biological samples can be characterized by mass spectrometry (MS)-based proteomics using customized protein databases generated from sets of transcripts previously detected by RNA-seq. This diversity has only been increased by the recent discovery that many translated alternative open reading frames rest unannotated at unsuspected locations of mRNAs and ncRNAs. These novel protein products, termed alternative proteins, have been left out of all previous custom database gen ...[more]

PMID: 36961377

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