PXD014003

PXD014003 is an original dataset announced via ProteomeXchange.

Title	YPIC challenge 2018: A case study in characterizing an unknown protein sample
Description	For the YPIC challenge 2018 contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in E. coli. We present how we analyzed this unknown sample using a tryptic digest with dynamic exclusion disabled to increase the signal-to-noise ratio of the measured molecules. Subsequently, spectral clustering was used to generate high-quality consensus spectra and condense the acquired MS/MS spectral data. De novo spectrum identification was used to determine the English questions encoded by the synthetic protein, and any post-translational modifications introduced by E. coli on the synthetic protein were detected using spectral networking. Although the synthetic protein sample for the YPIC challenge 2018 is not of biological interest, the experimental and computational strategy presented here can be directly used to analyze samples for which no protein sequence information is available. All software and code to perform the bioinformatics analysis is available as open source, and a self-contained Jupyter notebook is provided to fully recreate the analysis.
HostingRepository	PRIDE
AnnounceDate	2019-09-30
AnnouncementXML	Submission_2019-09-30_00:48:52.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wout Bittremieux
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-24 03:18:33	ID requested
1	2019-06-11 00:09:53	announced
⏵ 2	2019-09-30 00:48:54	announced	2019-09-30: Updated publication reference for PubMed record(s): 31556620.

Pino L, Lin A, Bittremieux W, 2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample. J Proteome Res, 18(11):3936-3943(2019) [pubmed]

submitter keyword: YPIC, synthetic protein, de novo, spectral clustering, spectral networking

William Stafford Noble
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA, USA
contact email	wnoble@uw.edu
lab head
Wout Bittremieux
contact affiliation	University of Antwerp
contact email	wout.bittremieux@uantwerpen.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD014003
     1. Label: PRIDE project
     2. Name: YPIC challenge 2018: A case study in characterizing an unknown protein sample