PXD044032

PXD044032 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	HowDirty: An R package to evaluate molecular contaminants in LC-MS experiments
Description	Contaminants derived from consumables, reagents, and sample handling often negatively affect LC-MS data acquisition. In proteomics experiments, they can markedly reduce identification performance, reproducibility, and quantitative robustness. Here, we introduce a data analysis workflow combining MS1 feature extraction in Skyline with HowDirty, an R-markdown-based tool, that automatically generates an interactive report on the molecular contaminant level in LC-MS data sets. To facilitate the interpretation of the results, the HTML report is self-contained and self-explanatory, including plots that can be easily interpreted. The R package HowDirty is available from https://github.com/DavidGZ1/HowDirty. To demonstrate a showcase scenario for the application of HowDirty, we assessed the impact of ultrafiltration units from different providers on sample purity after filter-assisted sample preparation (FASP) digestion. This allowed us to select the filter units with the lowest contamination risk. Notably, the filter units with the lowest contaminant levels showed higher reproducibility regarding the number of peptides and proteins identified. Overall, HowDirty enables the efficient evaluation of sample quality covering a wide range of common contaminant groups that typically impair LC-MS analyses, facilitating taking corrective or preventive actions to minimize instrument downtime.
HostingRepository	jPOST
AnnounceDate	2023-10-12
AnnouncementXML	Submission_2023-10-11_08:00:06.568.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Gomez-Zepeda
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	Orbitrap Exploris 480

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-24 06:36:24	ID requested
⏵ 1	2023-10-11 08:00:07	announced

Publication List

Gomez-Zepeda D, Michna T, Ziesmann T, Distler U, Tenzer S, HowDirty: An R package to evaluate molecular contaminants in LC-MS experiments. Proteomics, 24(8):e2300134(2024) [pubmed]

Gomez-Zepeda D, Michna T, Ziesmann T, Distler U, Tenzer S, HowDirty: An R package to evaluate molecular contaminants in LC-MS experiments. Proteomics, 24(8):e2300134(2024) [pubmed]

Keyword List

submitter keyword: LC-MS, sample preparation, contamination, software

submitter keyword: LC-MS, sample preparation, contamination, software

Contact List

David Gomez-Zepeda, Stefan Tenzer
lab head
David Gomez-Zepeda
contact affiliation	HI-TRON, DKFZ
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST 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://ftp.jpostdb.org/JPST002256/