PXD031139-1

PXD031139 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	How do Protein Contaminants Influence DDA and DIA Proteomics?
Description	Mass 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.
HostingRepository	MassIVE
AnnounceDate	2022-01-21
AnnouncementXML	Submission_2022-01-21_08:48:52.312.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ling Hao
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Oxidation; Acetyl; Carbamidomethyl
Instrument	instrument model

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-21 07:21:08	ID requested
⏵ 1	2022-01-21 08:48:52	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Protein Contaminant, Contamination, DIA, DDA, DIA-NN, Spectronaut, DirectDIA

submitter keyword: Protein Contaminant, Contamination, DIA, DDA, DIA-NN, Spectronaut, DirectDIA

Contact List

Ling Hao
contact affiliation	The George Washington University
contact email	linghao@gwu.edu
lab head
Ling Hao
contact affiliation	George Washington University
contact email	haolab.19@gmail.com
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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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/