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]

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

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

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