PXD000138
PXD000138 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Synthetic (Phospho)Peptide Library |
Description | The submitted dataset contains raw files from 96 synthetic peptide libraries, using either HCD or ETD as fragmentation technique. The synthesized 96 tryptic peptide libraries containing >100,000 unmodified peptides plus their corresponding >100,000 phosphorylated counterparts with precisely known sequences and modification sites. All these libraries were subjected to LC-MS/MS on an Orbitrap mass spectrometer using HCD and ETD fragmentation. The generated mass spectrometric data deposited in this database can be used in numerous ways to develop, evaluate and improve experimental and computational proteomic strategies. Raw MS data files were converted into Mascot generic format files (MGF) using Mascot Distiller (2.4.2.0, www.matrixscience.com). Important parameters included: i) signal to noise ratio of 20 for MS/MS and ii) time domain off (no merging of spectra of the same precursor). The MGF files were searched against human IPI v3.72 including the sequences of all 96 libraries,using the Mascot search engine (2.3.1, 24). Search settings: Decoy search using a randomized version of the human IPI v3.72 including the sequences of all 96 libraries was enabled; monoisotopic peptide mass (considering up to two 13C isotopes); trypsin/P as protease; a maximum of four missed cleavages; peptide charge +2 and +3; peptide tol. +/- 5 ppm; MS/MS tol. +/- 0.02 Da; instrument type ESI-Trap (for HCD data) or ETD-Trap (for ETD data) respectively; variable modifications: oxidation (M), phospho (ST), phospho (Y). The result files were exported to pepXML and Mascot XML with default options provided by Mascot. |
HostingRepository | PRIDE |
AnnounceDate | 2013-05-22 |
AnnouncementXML | Submission_2013-05-22_08:06:10.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Simone Lemeer |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2013-02-05 04:28:44 | ID requested | |
1 | 2013-05-05 12:42:10 | announced | |
1 | 2014-07-25 00:51:56 | announced | |
⏵ 2 | 2013-05-22 08:06:10 | announced | Add reference |
Publication List
Marx H, Lemeer S, Schliep JE, Matheron L, Mohammed S, Cox J, Mann M, Heck AJ, Kuster B, A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat Biotechnol, 31(6):557-64(2013) [pubmed] |
Keyword List
submitter keyword: Synthetic library, HCD, ETD |
Contact List
Simone Lemeer | |
---|---|
contact affiliation | Chair Proteomics and Bioanalytics |
contact email | simone.lemeer@tum.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/2013/05/PXD000138 |