PXD004555 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | An optimized version of the Secretome protein enrichment with click sugars (SPECS) method leads to enhanced coverage of the secretome |
Description | The secretome, the entirety of all soluble proteins either being secreted or proteolytically released by a cell, plays a key role in intercellular communication of multicellular organisms. Pathological alterations contribute to diseases such as hypertension, cancer, autoimmune disorders or neurodegenerative diseases. Hence, studying disease related perturbations of the secretome and the secretome itself covers an important aspect of cellular physiology. We recently developed the Secretome Protein Enrichment with Click Sugars (SPECS) method which enables the analysis of secretomes of in vitro cell cultures even in the presence of fetal calf serum with mass spectrometry and thus far enabled the identification of protease substrates of BACE1, SPPL3 and ADAM10. Though, the SPECS method has already enabled deep insights into secretome biology, we aimed to improve the SPECS protocol to obtain even more information from mass spectrometry based secretome analysis and reduce the amount of input material. Here, we optimized pH and the reaction buffer and replaced DBCO-PEG12-Biotin with the more water soluble variant DBCO-Sulfo-Biotin to finally provide an optimized protocol of the recently published SPECS protocol which increases the number of quantified glycoproteins 1.6-fold and their sequence coverage 2.4-fold and thus allows to reduce the input material by half without losing information. These improvements make the SPECS method more sensitive and more universal applicable to low abundant cell types. |
HostingRepository | PRIDE |
AnnounceDate | 2017-11-24 |
AnnouncementXML | Submission_2017-11-24_01:40:32.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Stephan Mueller |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; acetylated residue; iodoacetic acid derivatized residue |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2016-07-11 23:35:00 | ID requested | |
⏵ 1 | 2017-11-24 01:40:33 | announced | |
Publication List
Serdaroglu A, M, ü, ller SA, Schepers U, Br, ä, se S, Weichert W, Lichtenthaler SF, Kuhn PH, An optimised version of the secretome protein enrichment with click sugars (SPECS) method leads to enhanced coverage of the secretome. Proteomics, 17(5):(2017) [pubmed] |
Keyword List
curator keyword: Technical, Biological |
submitter keyword: SPECS, label-free quantification, glycoprotein, glycocapture |
Contact List
Peer-Hendrik Kuhn |
contact affiliation | Institut für Allgemeine Pathologie und Pathologische Anatomie Institute for Advanced Study Technische Universität München Trogerstr. 18 81675 Munich Germany |
contact email | peer.kuhn@tum.de |
lab head | |
Stephan Mueller |
contact affiliation | DZNE Munich Neuroproteomics |
contact email | stephan.mueller@dzne.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD004555
- Label: PRIDE project
- Name: An optimized version of the Secretome protein enrichment with click sugars (SPECS) method leads to enhanced coverage of the secretome