PXD001511 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Comparison of different sample preparation protocols reveals lysis buffer specific extraction biases in gram-negative bacteria and human cells |
Description | We evaluated different in-solution and FASP-based sample preparation strategies for absolute protein quantification. Label-free quantification (LFQ) was employed to compare different sample preparation strategies in the bacterium Pseudomonas aeruginosa and human embryonic kidney cells (HEK) and noted organismal specific differences in general performance and enrichment of specific protein classes. The original FASP protocol globally enriched for most proteins on the bacterial sample whereas the Sodium deoxycholate in-solution strategy was more efficient on HEK cells. Although detergents were found highly suited for global proteome analysis higher intensities were obtained for high abundant nucleic acid associated protein complexes, like the ribosome and histone proteins using guanidine hydrochloride. Importantly, we show for the first time that the observable total proteome mass of a sample strongly depends on the sample preparation protocol with some protocols resulting in significant underestimation of protein mass due to incomplete protein extraction of biased protein groups |
HostingRepository | PRIDE |
AnnounceDate | 2018-02-14 |
AnnouncementXML | Submission_2018-02-14_02:00:57.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD001511 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Timo Glatter |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Pseudomonas aeruginosa PAO1; NCBI TaxID: 208964; |
ModificationList | Oxidation; Carbamidomethyl |
Instrument | LTQ Orbitrap Velos; LTQ Orbitrap Elite |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2014-11-18 07:43:35 | ID requested | |
1 | 2015-10-06 00:10:39 | announced | |
⏵ 2 | 2018-02-14 02:00:58 | announced | Updated project metadata. |
Publication List
Glatter T, Ahrn, é E, Schmidt A, Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. J Proteome Res, 14(11):4472-85(2015) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: HEK293, Pseudomonas aeruginosa |
Contact List
Alexander Schmidt |
contact affiliation | Proteomics Core Facility Biozentrum University of Basel |
contact email | alex.schmidt@unibas.ch |
lab head | |
Timo Glatter |
contact affiliation | Biozentrum Basel |
contact email | timo.glatter@unibas.ch |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD001511
- Label: PRIDE project
- Name: Comparison of different sample preparation protocols reveals lysis buffer specific extraction biases in gram-negative bacteria and human cells