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PXD003881-1

PXD003881 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleQuantitative 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)
DescriptionTo 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.
HostingRepositoryPRIDE
AnnounceDate2018-05-16
AnnouncementXMLSubmission_2018-05-16_00:41:43.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD003881
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterXIAOMENG SHEN
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListOxidation; Acetyl; Carbamidomethyl
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-03-31 00:24:37ID requested
12018-05-16 00:41:44announced
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: Human, Ecoli, Orbitrap Fusion, Label-free, Benchmark, IonStar
Contact List
Jun Qu
contact affiliationUniversity at Buffalo
contact emailjunqu@buffalo.edu
lab head
XIAOMENG SHEN
contact affiliationUniversity at Buffalo
contact emailxiaomeng@buffalo.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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