PXD005869

PXD005869 is an original dataset announced via ProteomeXchange.

Title	Scanning quadrupole DIA - Scanning Quadrupole Data Independent Acquisition - Part A
Description	A scanning quadrupole data independent acquisition (DIA) method is described and characterised for the qualitative and quantitative label free proteomic analysis of complex biological samples. The principle of the scanning quadrupole DIA is discussed and the effect of the optimization of analytical instrument characteristics, such as acquisition speed, sample complexity, and scan/integration time in relation to sample complexity for a number of different model proteomes of various complexity and dynamic range, including plasma, human cell lines, and bacteria samples, discussed. In addition, its technological merits from an acquisition neutral perspective are reviewed. The qualitative and semi-quantitative performance of the method is illustrated and contrasted for the analysis of a well-characterised human cell line sample using untargeted and targeted search strategies. The application of the method is demonstrated for the analysis of the calcineurin-dependent proteome of drug treated Aspergillus fumigatus. The design of these experiments afforded assessment of the precision and accuracy of scanning quadrupole data independent acquisition (DIA) method as will be demonstrated by peptide and protein centric analysis of the study pool QC samples of the study. Moreover, novel and specific interactors in response to drug treatment that are indicative of the role of calcineurin role in regulating these effectors have been identified.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:35:40.261.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005869
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Hans Vissers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Xevo G2-S QTof

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-07 06:30:58	ID requested
1	2017-09-14 05:44:34	announced
⏵ 2	2024-10-22 04:35:46	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.7b00464;

10.6019/PXD005869;

Moseley MA, Hughes CJ, Juvvadi PR, Soderblom EJ, Lennon S, Perkins SR, Thompson JW, Steinbach WJ, Geromanos SJ, Wildgoose J, Langridge JI, Richardson K, Vissers JPC, Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. J Proteome Res, 17(2):770-779(2018) [pubmed]

curator keyword: Technical, Biological

submitter keyword: DIA

JPC Vissers
contact affiliation	Waters Corporation
contact email	hans_vissers@waters.com
lab head
Hans Vissers
contact affiliation	Waters Corporation
contact email	hans_vissers@waters.com
dataset submitter

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/2017/09/PXD005869

PRIDE project URI

• PRIDE
  1. PXD005869
     1. Label: PRIDE project
     2. Name: Scanning quadrupole DIA - Scanning Quadrupole Data Independent Acquisition - Part A