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PXD030406

PXD030406 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleComparative analysis of MS sample preparation methods
DescriptionWe compare the most commonly used proteomic sample preparation strategies such as classical in solution digest protocols, SPEED, FASP, STrap, SP3, as well as the commercially available kits iST (PreOmics) and EasyPep (Thermo Scientific) in their efficacy to extract proteomes from HeLa cells. We find a remarkably good performance of the majority of the protocols with high reproducibility, little method dependencies and low levels of artifact formation. Despite these similarities we observe significant differences in the recovery of specific sets of proteins in a k-means cluster analysis.
HostingRepositoryPRIDE
AnnounceDate2022-09-06
AnnouncementXMLSubmission_2022-09-06_06:21:20.421.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD030406
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterWolfgang Reiter
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive HF-X
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-12-14 10:01:29ID requested
12022-09-06 06:21:21announced
Publication List
Varnavides G, Madern M, Anrather D, Hartl N, Reiter W, Hartl M, In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods. J Proteome Res, 21(10):2397-2411(2022) [pubmed]
Keyword List
submitter keyword: HeLa, Human, sample preparation, LC-MS/MS
Contact List
Markus Hartl
contact affiliationMass Spectrometry Facility, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
contact emailmarkus.hartl@univie.ac.at
lab head
Wolfgang Reiter
contact affiliationMAX F. PERUTZ LABORATORIES - University of Vienna
contact emailwolfgang.l.reiter@univie.ac.at
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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