PXD018152 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | proteiNorm – A user-friendly tool for normalization and analysis of TMT and label-free protein quantification |
Description | The 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. |
HostingRepository | PRIDE |
AnnounceDate | 2021-09-09 |
AnnouncementXML | Submission_2021-09-08_18:38:58.787.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD018152 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Stephanie Byrum |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Eclipse |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-03-23 09:14:23 | ID requested | |
⏵ 1 | 2021-09-08 18:38:59 | announced | |
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 affiliation | 1. Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 2. Arkansas Children's Research Institute |
contact email | sbyrum@uams.edu |
lab head | |
Stephanie Byrum |
contact affiliation | UAMS |
contact email | sbyrum@uams.edu |
dataset submitter | |
Full Dataset Link List
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/2021/09/PXD018152 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD018152
- Label: PRIDE project
- Name: proteiNorm – A user-friendly tool for normalization and analysis of TMT and label-free protein quantification