<<< Full experiment listing


PXD031139 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHow do Protein Contaminants Influence DDA and DIA Proteomics?
DescriptionMass spectrometry-based proteomics is challenged by the presence of contaminant background signals. In particular, protein contaminants from reagents and sample handling are often abundant and almost impossible to avoid, reducing the sensitivity, specificity and reproducibility of protein identification and quantification. For data-dependent acquisition (DDA) proteomics, exclusion lists and a contaminant FASTA library can be used to reduce the influence of protein contaminants. However, protein contamination has not been evaluated and is rarely addressed in data-independent acquisition (DIA) proteomics. In this study, we established custom FASTA and spectral libraries for common protein contaminants in bottom-up proteomics, and evaluated the impact of protein contaminants on both DDA and DIA proteomics. We found that including our contaminant library can reduce false identifications, increase protein IDs, and modestly reduce quantification variations. We also compared various DIA and DDA data analysis platforms, and provided practical suggestions on how to best incorporate the contaminant library for different software platforms. Therefore, we recommend using our contaminant library for both DDA and DIA proteomics workflows. With the increasing popularity of DIA proteomics, our contaminant FASTA and spectral libraries can be an especially useful resource for the proteomics community.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterLing Hao
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationListOxidation; Acetyl; Carbamidomethyl
Instrumentinstrument model
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-01-21 07:21:08ID requested
12022-01-21 08:48:52announced
Publication List
no publication
Keyword List
submitter keyword: Protein Contaminant, Contamination, DIA, DDA, DIA-NN, Spectronaut, DirectDIA
Contact List
Ling Hao
contact affiliationThe George Washington University
contact emaillinghao@gwu.edu
lab head
Ling Hao
contact affiliationGeorge Washington University
contact emailhaolab.19@gmail.com
dataset submitter
Full Dataset Link List
MassIVE dataset URI
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://massive.ucsd.edu/MSV000088714/