PXD005408-1

PXD005408 is an original dataset announced via ProteomeXchange.

Title	A novel tool, Multiple Marker Abundance Profiling, uses Selected Reaction Monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples.
Description	Methods were investigated that would deliver rapid and semi-quantitative analysis of the subcellular composition of Arabidopsis samples, as the standard technique for this i.e. immunoblotting is difficult to quantify and relies on a very few protein targets, whose responses to developmental or environmental cues are often not known. Spectral counts from shotgun analysis of different Arabidopsis tissues, cells or growth stages were compared to selected reaction monitoring (SRM) analyses of the same samples. Results were further compared to a novel protein abundance scoring method, MASCP Gator scoring, described in this study for the first time. The latter is reliant on previously collated public proteomics data and so provides an estimate of protein abundance even in the absence of de-novo experimentation. This scoring method is presented as an online tool, Multiple Marker Abundance Profiling (MMAP), available at http:SUBA.live. This submission comprises the shotgun data from this study. SRM results are available in a separate submission: http://www.peptideatlas.org/PASS/PASS00906
HostingRepository	PRIDE
AnnounceDate	2018-10-26
AnnouncementXML	Submission_2018-10-26_12:51:40.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005408
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Harriet Parsons
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-21 05:23:35	ID requested
⏵ 1	2018-10-26 12:51:41	announced

Hooper CM, Stevens TJ, Saukkonen A, Castleden IR, Singh P, Mann GW, Fabre B, Ito J, Deery MJ, Lilley KS, Petzold CJ, Millar AH, Heazlewood JL, Parsons HT, Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. Plant J, 92(6):1202-1217(2017) [pubmed]

curator keyword: Technical

submitter keyword: Arabidopsis, organelle, subcellular proteomics, quantitation, shotgun, SRM

Harriet Parsons
contact affiliation	Dept. Biochemistry, Cambridge University, UK
contact email	tempeparsons@gmail.com
lab head
Harriet Parsons
contact affiliation	Cambridge University
contact email	tempeparsons@gmail.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/2018/10/PXD005408

PRIDE project URI

• PRIDE
  1. PXD005408
     1. Label: PRIDE project
     2. Name: A novel tool, Multiple Marker Abundance Profiling, uses Selected Reaction Monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples.