PXD022996

PXD022996 is an original dataset announced via ProteomeXchange.

Title	Pilot data for Imputation, LC-MS/MS
Description	Missing values in proteomic data sets have real consequences on downstream data analysis and reproducibility. Although several imputation methods exist to handle missing values, no single imputation method is best suited for a diverse range of data sets, and no clear strategy exists for evaluating imputation methods for large-scale DIA-MS data sets, especially at different levels of protein quantification. To navigate through the different imputation strategies available in the literature, we have established a workflow to assess imputation methods on large-scale label-free DIA-MS data sets. We used three DIA-MS data sets with real missing values to evaluate eight different imputation methods with multiple parameters at different levels of protein quantification; dilution series data set, a small pilot data set, and a larger proteomic data set.
HostingRepository	PRIDE
AnnounceDate	2021-05-07
AnnouncementXML	Submission_2021-05-07_01:00:46.533.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kruttika Dabke
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-08 06:43:23	ID requested
⏵ 1	2021-05-07 01:00:47	announced

Dabke K, Kreimer S, Jones MR, Parker SJ, A Simple Optimization Workflow to Enable Precise and Accurate Imputation of Missing Values in Proteomic Data Sets. J Proteome Res, 20(6):3214-3229(2021) [pubmed]

submitter keyword: Imputation, Ovarian cancer, DIA-MS

Sarah Parker
contact affiliation	Cedars-Sinai Medical Center
contact email	sarah.parker@cshs.org
lab head
Kruttika Dabke
contact affiliation	Cedars-Sinai Medical Center
contact email	kruttika.dabke@cshs.org
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/2021/05/PXD022996

PRIDE project URI

• PRIDE
  1. PXD022996
     1. Label: PRIDE project
     2. Name: Pilot data for Imputation, LC-MS/MS