PXD003881-1

PXD003881 is an original dataset announced via ProteomeXchange.

Title	Quantitative Proteomics Benchmark Dataset to evaluate label-free quantitative methods- LC/Orbitrap Fusion MS analysis of E coli proteomes spiked-in Human proteins at 5 different levels (N=20)
Description	To unbiasedly evaluate the quantitative performance of different quantitative methods, and compare different popular proteomics data processing workflows, we prepared a benchmark dataset where the various levels of spikeed-in E. Coli proteome that true fold change (i.e. 1 fold, 1.5 fold, 2 fold, 2.5 fold and 3 fold) and true identities of positives/negatives (i.e. E.Coli proteins are true positives while Human proteins are true negatives) are known. To best mimic the proteomics application in comparison of multiple replicates, each fold change group contains 4 replicates, so there are 20 LC-MS/MS analysis in this benchmark dataset. To our knowledge, this spike-in benchmark dataset is largest-scale ever that encompasses 5 different spike level, >500 true positive proteins, and >3000 true negative proteins (2peptide criteria, 1% protein FDR), with a wide concentration dynamic range. The dataset is ideal to test quantitative accuracy, precision, false-positive biomarker discovery and missing data level.
HostingRepository	PRIDE
AnnounceDate	2018-05-16
AnnouncementXML	Submission_2018-05-16_00:41:43.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD003881
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	XIAOMENG SHEN
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Acetyl; Carbamidomethyl
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-31 00:24:37	ID requested
⏵ 1	2018-05-16 00:41:44	announced

Shen X, Shen S, Li J, Hu Q, Nie L, Tu C, Wang X, Poulsen DJ, Orsburn BC, Wang J, Qu J, IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts. Proc Natl Acad Sci U S A, 115(21):E4767-E4776(2018) [pubmed]

curator keyword: Technical

submitter keyword: Human, Ecoli, Orbitrap Fusion, Label-free, Benchmark, IonStar

Jun Qu
contact affiliation	University at Buffalo
contact email	junqu@buffalo.edu
lab head
XIAOMENG SHEN
contact affiliation	University at Buffalo
contact email	xiaomeng@buffalo.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003881
     1. Label: PRIDE project
     2. Name: Quantitative Proteomics Benchmark Dataset to evaluate label-free quantitative methods- LC/Orbitrap Fusion MS analysis of E coli proteomes spiked-in Human proteins at 5 different levels (N=20)