PXD030406 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Comparative analysis of MS sample preparation methods |
Description | We 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. |
HostingRepository | PRIDE |
AnnounceDate | 2022-09-06 |
AnnouncementXML | Submission_2022-09-06_06:21:20.421.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD030406 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Wolfgang Reiter |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF-X |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-12-14 10:01:29 | ID requested | |
⏵ 1 | 2022-09-06 06:21:21 | announced | |
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 affiliation | Mass Spectrometry Facility, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria |
contact email | markus.hartl@univie.ac.at |
lab head | |
Wolfgang Reiter |
contact affiliation | MAX F. PERUTZ LABORATORIES - University of Vienna |
contact email | wolfgang.l.reiter@univie.ac.at |
dataset submitter | |
Full Dataset Link List
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/2022/09/PXD030406 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD030406
- Label: PRIDE project
- Name: Comparative analysis of MS sample preparation methods