PXD000125-1
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] |
Keyword List
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 |