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PXD018152

PXD018152 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleproteiNorm – A user-friendly tool for normalization and analysis of TMT and label-free protein quantification
DescriptionThe technological advances in mass spectrometry allow us to collect more comprehensive data with higher quality and increasing speed. With the rapidly increasing amount of data generated, the need for streamlining analyses becomes more apparent. Proteomic data is known to be often affected by systemic bias from unknown sources, and failing to adequately normalize the data can lead to erroneous conclusions. To allow researchers to easily evaluate and compare different normalization methods via a user-friendly interface, we have developed “proteiNorm”. The current implementation of proteiNorm accommodates preliminary filter on peptide and sample level, followed by an evaluation of several popular normalization methods and visualization of missing value. The user then selects an adequate normalization method and one of several imputation methods used for the subsequent comparison of different differential abundance/expression methods and estimation of statistical power. The application of proteiNorm and interpretation of its results is demonstrated on a Tandem Mass Tag mass spectrometry example data set, where the proteome of three different breast cancer cell lines was profiled with and without hydroxyurea treatment. With proteiNorm, we provide a user-friendly tool to identify an adequate normalization method and to select an appropriate method for a differential abundance/expression analysis.
HostingRepositoryPRIDE
AnnounceDate2021-09-09
AnnouncementXMLSubmission_2021-09-08_18:38:58.787.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD018152
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterStephanie Byrum
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Eclipse
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-03-23 09:14:23ID requested
12021-09-08 18:38:59announced
Publication List
Graw S, Tang J, Zafar MK, Byrd AK, Bolden C, Peterson EC, Byrum SD, proteiNorm - A User-Friendly Tool for Normalization and Analysis of TMT and Label-Free Protein Quantification. ACS Omega, 5(40):25625-25633(2020) [pubmed]
Keyword List
submitter keyword: Proteomics, Normalization, Differential analysis
Contact List
Stephanie Diane Byrum
contact affiliation1. Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 2. Arkansas Children's Research Institute
contact emailsbyrum@uams.edu
lab head
Stephanie Byrum
contact affiliationUAMS
contact emailsbyrum@uams.edu
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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