PXD000446

PXD000446 is an original dataset announced via ProteomeXchange.

Title	MSE quantified stroma proteome
Description	Label-free protein quantification has developed into an attractive alternative to isotopic labeling for the quantification of proteins by mass spectrometry. Recently, the suite of label-free quantification strategies was expanded by LC-MSE–based absolute and relative protein quantification. We report here a systematic evaluation of high definition (HD) MSE-based protein quantification and identification with the chloroplast stroma proteome. This proteome is of high complexity and comprises a wide dynamic range of protein concentrations. Our analysis identified many chloroplast proteins that were not previously identified in large-scale proteome analyses, suggesting HD-MSE as a suitable complementary tool for discovery proteomics. We find that HD-MSE tends to underestimate protein abundances at concentrations above 30 fmol, which is likely due to ion transmission loss and detector saturation. This limitation can be circumvented by combining HD-MSE and standard MSE scan types. The selection of peptides for protein quantification depends on sample characteristics; therefore different peptides may be used for the quantification of one protein in different replicates. This influences the robustness of protein quantification and requires critical scrutiny of quantification results. Based on the quantification of chloroplast stroma proteins we performed a meta-analysis and compared published quantitative data with our results, using a parts per million normalization scheme. Important pathways in the chloroplast stroma show quantitative stability against different experimental conditions and different quantification strategies.
HostingRepository	PRIDE
AnnounceDate	2016-04-14
AnnouncementXML	Submission_2016-04-14_05:16:51.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sacha Baginsky
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2013-09-03 12:15:28	ID requested
⏵ 1	2016-04-14 05:16:53	announced

Helm S, Dobritzsch D, R, ö, diger A, Agne B, Baginsky S, Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome. J Proteomics, 98():79-89(2014) [pubmed]

submitter keyword: arabidopsis thaliana, cloroplast stroma, quantitative LC-HDMSE, normalization, meta-analysis

Prof. Dr. Sacha Baginsky
contact affiliation	Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
contact email	sacha.baginsky@biochemtech.uni-halle.de
lab head
Sacha Baginsky
contact affiliation	Institut fuer Biochemie und Biotechnologie
contact email	pflanzen@biochemtech.uni-halle.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000446
     1. Label: PRIDE project
     2. Name: MSE quantified stroma proteome