PXD024364

PXD024364 is an original dataset announced via ProteomeXchange.

Title	Deep Human Proteome Sequencing Enables Global Detection of Mutations and Alternative Splicing
Description	Mass spectrometry-based proteomics now routinely enables identification of over 10,000 human proteins from a single sample. However, proteins are typically identified by peptide sequences representing about 20% of all proteinogenic amino acids encoded in the transcriptome. Deeper protein sequencing - detection of all amino acids - is imperative for proteoform discovery and quantitative comparison. Here, we utilized six ENCODE cell lines, six proteases, and three tandem mass spectrometry (MS/MS) fragmentation methods to collect 2,491 raw MS data files. From these data we identified 17,717 protein groups with a median sequence coverage of 79.2%, confirming over eight million unique human amino acid residues. We compare our proteomics data with transcriptomics data and demonstrate how such deep proteome coverage can enable detection of over 7,000 proteoforms including 70.9 to 90.6% of all non-synonymous mutations and over 5,000 alternative splicing event junctions. Our dataset represents a valuable resource as the largest human proteome with the highest sequence coverage ever reported.
HostingRepository	MassIVE
AnnounceDate	2023-02-03
AnnouncementXML	Submission_2023-02-03_09:54:01.916.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dain Brademan
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; Oxidation
Instrument	Orbitrap Fusion; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-24 09:31:53	ID requested
⏵ 1	2023-02-03 09:54:02	announced

no publication

submitter keyword: single amino acid polymorphism, splice variant, deep sequencing, transcriptomics, proteomics, fractionation

Juergen Cox
contact affiliation	Max Planck Institute of Biochemistry
contact email	cox@biochem.mpg.de
lab head
Joshua Coon
contact affiliation	University of Wisconsin - Madison
contact email	jcoon@chem.wisc.edu
lab head
Dain Brademan
contact affiliation	Coon Laboratory
contact email	brademan@wisc.edu
dataset submitter

MassIVE dataset URI

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