Dataset Information

Aplysia ganglion and memory formation

ABSTRACT: 2 DE plus ion-trap mass spectrum to identify unknown proteins from ganglion of aplysia californica

INSTRUMENT(S): Bruker Daltonics HCT Series, instrument model

ORGANISM(S): Aplysia Californica (california Sea Hare)

SUBMITTER: Gert Lubec

PROVIDER: PRD000283 | Pride | 2010-01-03

REPOSITORIES: Pride

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Publications

A first partial Aplysia californica proteome.

Sun Yanwei Y Monje Francisco J FJ Pollak Daniela D DD Lubec Gert G

Amino acids 20101111 4

Aplysia proteins have not been studied systematically and it was therefore the aim of the study to carry out protein profiling in ganglia from Aplysia californica (AC). AC ganglia were extirpated, proteins extracted and run on 2DE with subsequent in-gel digestion, followed by identification of proteins by nano-LC-ESI-MS/MS on an ion trap. Proteins were identified based upon a public Aplysia EST database. Out of 408 picked spots, 276 spots were identified corresponding to 172 ESTs and 118 individ ...[more]

PMID: 21069399

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Project 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.

Dataset Information

Aplysia ganglion and memory formation

Publications

A first partial Aplysia californica proteome.

Similar Datasets

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