PXD008425-3

PXD008425 is an original dataset announced via ProteomeXchange.

Title	A protein standard that emulates homology for the characterization of protein inference algorithms
Description	A natural way to benchmark the performance of an analytical experimental setup is to use samples of known content, and see to what degree one can correctly infer the content of such a sample from the data. For shotgun proteomics, one of the inherent problems of interpreting data is that the measured analytes are peptides and not the actual proteins themselves. As some proteins share proteolytic peptides, there might be more than one possible causative set of proteins resulting in a given set of peptides. Hence, there is a need for mechanisms that infer proteins from a list of detected peptides. Today's commercially available samples of known content do not expose these complications in protein inference, as their contained proteins deliberately are selected for producing tryptic peptides that are unique to a single protein. For a realistic benchmark of protein inference procedures, there is, therefore, a need for samples of known content where the present proteins share peptides with known absent proteins. Here, we present such a standard, based on E. coli expressed protein fragments.
HostingRepository	PRIDE
AnnounceDate	2017-12-13
AnnouncementXML	Submission_2018-04-12_08:58:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lukas Käll
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-12 06:11:49	ID requested
1	2017-12-12 07:18:19	announced
2	2017-12-12 23:34:02	announced	Updated project metadata.
⏵ 3	2018-04-12 08:58:44	announced	Updated project metadata.

The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsstr, ö, m B, K, ä, ll L, A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms. J Proteome Res, 17(5):1879-1886(2018) [pubmed]

curator keyword: Technical

submitter keyword: Protein Standard, LC-MS/MS, protein inference

Lukas Käll
contact affiliation	Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology
contact email	lukas.kall@scilifelab.se
lab head
Lukas Käll
contact affiliation	KTH
contact email	lukas.kall@scilifelab.se
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/2017/12/PXD008425

PRIDE project URI

• PRIDE
  1. PXD008425
     1. Label: PRIDE project
     2. Name: A protein standard that emulates homology for the characterization of protein inference algorithms