PXD000125

PXD000125 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Comprehensive identification of proteins from MALDI imaging
Description	MALDI imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic and prognostic value. One main challenge is that the molecular identity of such potential biomarkers mostly remains unknown. We introduce a method that removes this issue by systematically identifying the proteins embedded in the MALDI matrix using a combination of bottom-up and top-down proteomics. The analyses of ten human tissues lead to the identification of 1,400 abundant and soluble proteins constituting the set of proteins detectable by MALDI IMS including >90% of all IMS biomarkers reported in the literature. Top-down analysis of the matrix proteome identified 124 mostly N- and C-terminally fragmented proteins indicating considerable protein processing activity in tissues. This work presents a generic method and near complete list of MALDI IMS biomarkers that will become a valuable resource for the IMS community. Detailed description of the bioinformatics pipeline can be found in pipeline.txt. Briefly, different Mascot Distiller, Mascot and Scaffold versions have been used for the bottom-up and top-down data.
HostingRepository	PRIDE
AnnounceDate	2013-07-03
AnnouncementXML	Submission_2013-07-03_05:44:12.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stefan K Maier
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue; deamidated residue; monohydroxylated residue; acetylated residue
Instrument	LTQ Orbitrap; LTQ Orbitrap Elite

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2013-01-18 03:04:05	ID requested
1	2013-07-03 01:44:59	announced
1	2014-07-25 00:50:18	announced
⏵ 2	2013-07-03 05:44:12	announced	Add reference

Publication List

Maier SK, Hahne H, Gholami AM, Balluff B, Meding S, Schoene C, Walch AK, Kuster B, Comprehensive identification of proteins from MALDI imaging. Mol Cell Proteomics, 12(10):2901-10(2013) [pubmed]

Maier SK, Hahne H, Gholami AM, Balluff B, Meding S, Schoene C, Walch AK, Kuster B, Comprehensive identification of proteins from MALDI imaging. Mol Cell Proteomics, 12(10):2901-10(2013) [pubmed]

Keyword List

submitter keyword: Matrix and Tissue Proteome

submitter keyword: Matrix and Tissue Proteome

Contact List

Stefan K Maier
contact affiliation	Chair of Proteomics and Bioanalytics
contact email	stefan.maier@helmholtz-muenchen.de

Full Dataset Link List

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/2013/07/PXD000125

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/2013/07/PXD000125