PXD015153

PXD015153 is an original dataset announced via ProteomeXchange.

Title	A serial sample processing strategy with improved performance for in-depth quantitative analysis of type III secretion events in Pseudomonas aeruginosa
Description	Bacterial pathogens have the ability to secrete effector proteins to promote host cell invasion. The efficient analysis of the secretomes in close to wildtype cell systems is important to study the mechanisms of bacterial secretion efficiently at different levels. In particular the secretome analysis of bacteria that rely on rich media for optimal secretion may hamper analysis via modern sample preparation shotgun proteomics workflows due to higher degree of sample impurities. This is may be a reason for the low number of quantitative secretome investigations in such cells. We assessed the efficiency of different workflows and their amenability for secretome analysis including precipitation, SP3 and a combined, serial workflow. Using the model organism Pseudomonas aeruginosa, we found that, the combined TCA-SP3 strategy outperforms the other tested methods on all levels and proofed most efficient in the recovery of proteins related to the type III secretion system (T3SS), including all known effector proteins and secretion machinery components. Moreover, the serial workflows resulted in improved quantification accuracy using MS1 label-free quantification. Finally by monitoring the compositional changes of secretome samples over time we observed strong increase of the fraction made up by T3SS related proteins with parallel decrease of proteins not linked to T3SS. Our study shows how combining sample preparation procedures can lead to orthogonality in depleting impurities that result in better chromatographic peptide separation, and more efficient MS detection with improved quantification parameters.
HostingRepository	PRIDE
AnnounceDate	2019-12-11
AnnouncementXML	Submission_2019-12-11_02:36:31.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD015153
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Timo Glatter
SpeciesList	scientific name: Pseudomonas aeruginosa PAO1; NCBI TaxID: 208964;
ModificationList	Deamidated; Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-26 00:36:01	ID requested
⏵ 1	2019-12-11 02:36:33	announced

Lampaki D, Diepold A, Glatter T, . J Proteome Res, 19(1):543-553(2020) [pubmed]

curator keyword: Technical, Biological

submitter keyword: SP3, Protein precipitation, Secretome, Pseudomonas aeruginosa

Timo Glatter
contact affiliation	Facility for Mass Spectrometry and bacterial Proteomics Max Planck Institute for Terrestrial Microbiology Marburg, Germany
contact email	glatter@mpi-marburg.mpg.de
lab head
Timo Glatter
contact affiliation	MPI Marburg
contact email	glatter@mpi-marburg.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015153
     1. Label: PRIDE project
     2. Name: A serial sample processing strategy with improved performance for in-depth quantitative analysis of type III secretion events in Pseudomonas aeruginosa