PXD003278-1

PXD003278 is an original dataset announced via ProteomeXchange.

Title	Impact of alternative splicing on the human proteome
Description	Alternative splicing is a critical determinant of genome complexity and by implication, is assumed to engender proteomic diversity. This notion has not been experimentally tested in a targeted, quantitative manner. Here, we have developed an integrative approach to ask whether dynamic perturbations in mRNA splicing patterns that follow depletion of the core spliceosome factor PRPF8 alter the composition of the proteome. We integrate RNA-sequencing (to comprehensively report intron retention, differential transcript usage and gene expression) with a newly developed data-independent acquisition (DIA) method, SWATH-MS (Sequential Window Acquisition of all THeoretical spectra – mass spectrometry), to capture an unbiased and quantitative snapshot of constitutive and alternative splicing events at the protein level. Whereas intron retention is accompanied by decreased protein abundance, dynamic alterations in differential transcript usage and gene expression alter protein abundance proportionally to transcript levels. Our findings exemplify how RNA splicing exerts a pervasive effect linking isoform expression in the human transcriptome with proteomic diversity, and provide a toolkit for studying its perturbation in human diseases.
HostingRepository	PRIDE
AnnounceDate	2017-08-02
AnnouncementXML	Submission_2017-08-02_10:04:40.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yansheng Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2015-12-03 23:58:31	ID requested
⏵ 1	2017-08-02 10:04:40	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Alternative splicing, Proteome, PRPF8, SWATH

Ruedi Aebersold
contact affiliation	Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Yansheng Liu
contact affiliation	Institute of Molecular Systems Biology, ETH Zurich
contact email	liu@imsb.biol.ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003278
     1. Label: PRIDE project
     2. Name: Impact of alternative splicing on the human proteome