PXD000280

PXD000280 is an original dataset announced via ProteomeXchange.

Title	Arabidopsis thaliana Cytochrome c Novel Partners Identification by LTQ
Description	Programmed cell death is an event displayed by many different organisms along the evolutionary scale. In plants, it is necessary for development and for the hypersensitive response to stress or pathogenic infection. A common feature to programmed cell death among organisms is the mitochondria-to-cytosol translocation of cytochrome c. To understand the role of cytochrome c in the onset of plant programmed cell death, a proteomic approach based on affinity chromatography has been developed, using Arabidopsis cytochrome c as bait. Eleven putative, new cytochrome c partners have been identified. Nine of them bind the heme protein in plant protoplasts and in human cells, as a heterologous system, according to Bimolecular Fluorescence Complementation. The binding affinities and the kinetic rate constants of three cytochrome c - target complexes have been estimated by Surface Plasmon Resonance. Our data suggest that the role of cytochrome c as a programmed cell death-signaling messenger could be evolutionarily well-conserved. Data Processing & data analysis: Peptides were analyzed using a nanoliquid chromatography-MS/MS on an LTQ linear ion trap mass spectrometer (Thermo Electron San Jose, CA, USA).  The mass spectrometer was operated in the data-dependent mode to automatically switch between full MS and MS/MS acquisition. The parameters for ion scanning were the following: Full-scan MS(400-1800 m/z) plus top seven peaks Zoom/MS/MS (isolation width 2 m/z), normalized collision energy 35%. The scanning was performed using a dynamic exclusion list (120s exclusion list size of 50). Peak lists from all MS/MS spectra were extracted from the  Xcalibur  RAW  files  using  a  freely  available  program  DTAsupercharge  v.1.19 (http://msquant.sourceforge.net/). MASCOT 2.1 was used to search the Uniprot_Arabidopsis protein database 100323  (90895 sequences). Database search parameters used were the following: trypsin as enzyme; peptide tolerance, 300ppm; fragment ion tolerance, 0.6 Da; missed cleavage sites,1; fixed modification, carbamidomethyl cysteine and variable modifications, methionine oxidation. In all protein identifications the probability scores were greater than the score fixed by MASCOT (30) as  significant with a p-value <0.05.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:39:18.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000280
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jonathan Martinez Fabregas
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	instrument model: LTQ; LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2013-06-10 03:32:38	ID requested
1	2013-11-11 02:47:58	announced
1	2013-11-11 06:34:17	announced
⏵ 2	2014-07-28 00:39:18	announced	Updated project metadata.

Dataset with its publication pending

submitter keyword: Arabidopsis thaliana, H2O2, Programmed cell death, Protein-Protein Interactions, Cytochrome c

Jonathan Martinez Fabregas
contact affiliation	Cell Signaling and Immunology
contact email	jmartinezfabregas@dundee.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000280
     1. Label: PRIDE project
     2. Name: Arabidopsis thaliana Cytochrome c Novel Partners Identification by LTQ