PXD006026

PXD006026 is an original dataset announced via ProteomeXchange.

Title	Identification of alternative splice variants using unique isoform-specific tryptic peptide sequences for database searches
Description	Alternative splicing is a mechanism in eukaryotes by which different forms of messenger RNAs (mRNAs) are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database which contains only proteotypic tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to the peptide sequences that matches the unique amino acid sequence of splice variants to MS data. Furthermore, we combined this database without isoform 1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa), and phosphoproteomics studies were analyzed using these two databases. Several non-isoform 1-specific peptides were found in both cell lines, some of them seemed to be cell line specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several non-isoform 1-specific peptides and some of them showed clear quantitative differences between the two states.
HostingRepository	PRIDE
AnnounceDate	2017-05-19
AnnouncementXML	Submission_2017-05-19_01:02:45.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Koehler
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-06 01:48:33	ID requested
⏵ 1	2017-05-19 01:02:46	announced

Tran TT, Bollineni RC, Strozynski M, Koehler CJ, Thiede B, Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches. J Proteome Res, 16(7):2571-2578(2017) [pubmed]

curator keyword: Technical, Biological

submitter keyword: alternative splicing, isoforms, mass spectrometry, phosphorylation, protein species, proteoform, proteomics

Bernd Thiede
contact affiliation	University of Oslo Department of Biosciences
contact email	bernd.thiede@ibv.uio.no
lab head
Christian Koehler
contact affiliation	University of Oslo
contact email	christian.koehler@ibv.uio.no
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/2017/05/PXD006026

PRIDE project URI

• PRIDE
  1. PXD006026
     1. Label: PRIDE project
     2. Name: Identification of alternative splice variants using unique isoform-specific tryptic peptide sequences for database searches