PXD009265

PXD009265 is an original dataset announced via ProteomeXchange.

Title	Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2
Description	This project reanalzyes data from 4 other projects. Information about the samples can be found in the following four publications. The four samples used in this study include a ocean metaproteome sample, a human sample, a E. coli sample, and a Plamodium falciparum sample. B. N. Pease, E. L. Huttlin, M. P. Jedrychowski, E. Talevich, J. Harmon, T. Dillman, N. Kannan, C. Doerig, R. Chakrabarti, S. P. Gygi, and D. Chakrabarti. Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development. Journal of Proteome Research, 12:4028–4045, 2013. Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, and William S. Noble. An alignment-free metapeptide strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research, 15(8):2697–2705, 2016. PMID: 27396978. M. Kim, S. M. Pinto, D. Getnet, R. S. Nirujogi, S. S. Manda, R. Chaerkady, A. K. Madugundu, D. S. Kelkar, R. Isserlin, S. Jain, et al. A draft map of the human proteome. Nature, 509(7502):575–581, 2014. Hansjrg G ̋tzke, Claudio Muheim, A.F. Maarten Altelaar, Albert J.R. Heck, Gianluca Maddalo, and Daniel O. Daley. Identification of putative substrates for the periplasmic chaperone yfgm in Escherichia coli using quantitative proteomics. Molecular & Cellular Proteomics, 14(1):216–226, 2015.
HostingRepository	PRIDE
AnnounceDate	2018-09-19
AnnouncementXML	Submission_2018-09-19_05:40:05.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andy Lin
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Plasmodium falciparum (isolate 3D7); NCBI TaxID: 36329;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-20 06:45:32	ID requested
⏵ 1	2018-09-19 05:40:06	announced

Lin A, Howbert JJ, Noble WS, Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data. J Proteome Res, 17(11):3644-3656(2018) [pubmed]

curator keyword: Technical

submitter keyword: human, ocean, plasmodium, E. coli, score function

William Stafford Noble
contact affiliation	Department of Genome Sciences Department of Computer Science and Engineering University of Washington
contact email	william-noble@u.washington.edu
lab head
Andy Lin
contact affiliation	University of Washington
contact email	linandy@uw.edu
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/2018/09/PXD009265

PRIDE project URI

• PRIDE
  1. PXD009265
     1. Label: PRIDE project
     2. Name: Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2