PXD009376

PXD009376 is an original dataset announced via ProteomeXchange.

Title	Identification of Poly Ethylene Glycol (PEG) and PEG-based Detergents Using Peptide Search Engines
Description	Polyethylene glycol (PEG) is one of the most common polymer contaminations in MS samples. At present, the detection of PEG and other polymers relies largely on manual inspection of raw data which is laborious and frequently difficult due to sample complexity and retention characteristics of polymer species in reversed phase chromatography. We developed a new strategy for the automated identification of PEG molecules from MSMS data using protein identification algorithms in combination with a database containing “PEG-proteins”. Through definition of variable modifications, we extend the approach for the identification of commonly used PEG-based detergents. We exemplify the identification of different types of polymers by static nanoESI-MSMS analysis of pure detergent solutions and data analysis using Mascot. Analysis of LC-MSMS runs of a PEG contaminated sample by Mascot identified 806 PEG-spectra originating from four PEG species using a defined set of modifications covering PEG and common PEG-based detergents. Further characterization of the sample for unidentified PEG species using error tolerant and mass tolerant searches resulted in identification of 3409 and 3187 PEG related MSMS spectra, respectively. We further demonstrate the applicability of the strategy for Protein Pilot and MaxQuant.
HostingRepository	PRIDE
AnnounceDate	2018-05-28
AnnouncementXML	Submission_2018-05-28_02:05:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shiva Ahmadi
SpeciesList	scientific name: Rattus rattus (Black rat); NCBI TaxID: 10117;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-03 08:13:28	ID requested
⏵ 1	2018-05-28 02:05:04	announced

Ahmadi S, Winter D, Identification of Poly(ethylene glycol) and Poly(ethylene glycol)-Based Detergents Using Peptide Search Engines. Anal Chem, 90(11):6594-6600(2018) [pubmed]

curator keyword: Technical

submitter keyword: Poly Ethylene Glycol, PEG, Automated, Polymer, Peptide search engine, Mass Spectrometry

Dominic Winter
contact affiliation	Institute for Biochemistry and Molecular Biology, University of Bonn, 53115 Bonn, Germany
contact email	dwin@uni-bonn.de
lab head
Shiva Ahmadi
contact affiliation	Researcher
contact email	sheeva.ahmadi@gmail.com
dataset submitter

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/pride/data/archive/2018/05/PXD009376

PRIDE project URI

• PRIDE
  1. PXD009376
     1. Label: PRIDE project
     2. Name: Identification of Poly Ethylene Glycol (PEG) and PEG-based Detergents Using Peptide Search Engines