PXD001511-1

PXD001511 is an original dataset announced via ProteomeXchange.

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	2015-10-06
AnnouncementXML	Submission_2015-10-06_00:10:38.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

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.

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]

curator keyword: Technical

submitter keyword: HEK293, Pseudomonas aeruginosa

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

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PRIDE project URI

• PRIDE
  1. PXD001511
     1. Label: PRIDE project
     2. Name: Comparison of different sample preparation protocols reveals lysis buffer specific extraction biases in gram-negative bacteria and human cells