PXD000874

PXD000874 is an original dataset announced via ProteomeXchange.

Title	Cardiac myofilament isoforms
Description	Purpose: The identification of protein isoforms in complex biological samples is challenging. We, therefore, used a mass spectrometry (MS) approach to unambiguously identify cardiac myofilament protein isoforms based on the observation of a tryptic peptide consisting of a sequence unique to a particular isoform. Experimental design: Three different workflows were used to isolate and fractionate the rat cardiac myofilament subproteomes. All fractions were analyzed on an LTQ-Orbitrap MS, proteins were identified using various search engines (Mascot, X!Tandem, X!Tandem Kscore and OMSSA) with results combined via PepArML Meta-Search Engine, and a post-search analysis performed by MASPECTRAS. Results: The combination of multiple workflows and search engines resulted in a larger number of non-redundant proteins identified than individual methods. A total of 461 proteins were observed overlapping in two or three of the workflows. Literature search for myofilament presence with manual validation of the MS spectra was carried out for unambiguous identification: 10 cardiac myofilament and 17 cardiac myofilament-associated proteins were confirmed to have multiple isoforms or sub-isoforms. Conclusion and clinical relevance: We have identified multiple isoforms of myofilament proteins that are present in cardiac tissue using unique tryptic peptides. Changes of distribution of these protein isoforms under pathological conditions could ultimately allow for clinical diagnostics or as therapeutic targets.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_03:08:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vidya Venkatraman
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	2-pyrrolidone-5-carboxylic acid (Glu); monohydroxylated residue; iodoacetamide derivatized residue; phosphorylated residue; (R)-5-oxo-1: 4-tetrahydrothiazine-3-carboxylic acid; 2-pyrrolidone-5-carboxylic acid (Gln)
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-03 07:14:02	ID requested
1	2014-08-28 05:41:34	announced
2	2014-08-29 00:30:47	announced	Updated project metadata.
⏵ 3	2014-10-23 03:08:09	announced	Updated project metadata.

Kooij V, Venkatraman V, Kirk JA, Ubaida-Mohien C, Graham DR, Faber MJ, Van Eyk JE, Identification of cardiac myofilament protein isoforms using multiple mass spectrometry based approaches. Proteomics Clin Appl, 8(7-8):578-589(2014) [pubmed]

curator keyword: Biological, Technical, Cardiovascular

submitter keyword: Rat Cardiac Tissue, cardiomyocyte, LC-MS/MS, myofilament proteome, sarcomere, protein isoforms, protein sub-isoforms, Multiple Search Engines, Bioinformatics

Dr. Jennifer E Van Eyk
contact affiliation	Cedars-Sinai Medical Center Advanced Clinical Biosystems Research Institute Advanced Health Science Pavillion, Room A9307 8700 Beverly Blvd. Los Angeles, CA 90048
contact email	jennifer.vaneyk@cshs.org
lab head
Vidya Venkatraman
contact affiliation	Cedar-Sinai Medical Center
contact email	Vidya.Venkatraman@cshs.org
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/2014/08/PXD000874

PRIDE project URI

• PRIDE
  1. PXD000874
     1. Label: PRIDE project
     2. Name: Cardiac myofilament isoforms