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Sample GSM304323 Query DataSets for GSM304323
Status Public on Sep 01, 2009
Title Proteins from vacuoles of Cyanidioschyzon merolae strain 10D
Sample type protein
Source name vacuoles
Organism Cyanidioschyzon merolae strain 10D
Characteristics organelle: vacuoles of C. merolae synchronized at interphase
Extracted molecule protein
Extraction protocol The vacuoles of C. merolae synchronized at interphase were isolated by differential and iodixanol-gradient ultracentrifugation. The supernatant (5 ug of protein) were subjected to SDS-PAGE, cut into 69 slices without staining, and subjected to automatic sample preparation for MALDI-TOF-MS by a robot Xcise (Shimadzu). Alternatively, the vacuolar fraction protein (15.8 ug) was alkylated with 5% (w/v) acrylamide, subjected to SDS-PAGE, and stained with Imperial Protein Stain (Pierce). The gel slices of 58 visible bands were destained and digested as described previously (PMID: 11507753). After the digestion, the peptide fragments were extracted from the gel pieces with 5% (v/v) formic acid in 50% (v/v) CH3CN. Extracts were dried in a vacuum concentrator. The dried peptides were dissolved in 0.1% (v/v) trichloroacetic acid (TFA), desalted using uC18-Zip Tip microcolumns (Millipore) and spotted onto a 384-well plate (KRATOS Analytical). After completely drying the samples, 0.5% (w/v) alpha-cyano-4-hydroxycinnamic acid in 50% (v/v) CH3CN and 0.1% (v/v) TFA were spotted on the peptide spots and allowed to dry.
Label protocol *
Hybridization protocol *
Scan protocol *
Description Identification of proteins from vacuoles of red algae [Cyanidioschyzon merolae strain 10D (Eukaryota; Rhodophyta; Bangiophyceae; Cyanidiales; Cyanidiaceae)] synchronized at interphase, using MALDI-TOF.
Data processing The samples were analyzed by peptide mass fingerprinting (PMF) using a mass spectrometer (AXIMA-TOF2; Shimadzu) in the reflectron mode. When samples could not be identified by PMF, several peptide peaks were further analyzed by post source decay (PSD)-MS/MS. Database searches were performed using the software program MASCOT v2.2.01 (Matrix Science) running on a local database built from the FASTA files of 5014 open reading frames in the C. merolae genome database ( The peptide tolerance was set to 0.1-0.2 Da. Cysteine carbamidomethylation (for samples prepared by Xcise) or propionamidation (for manually prepared samples) was included as a fixed modification and methionine oxidation was included as a variable modification. The identification threshold was set to p < 0.05. As a result, 46 proteins were identified.
Submission date Jul 08, 2008
Last update date May 27, 2009
Contact name Fumi Yagisawa
Organization name Rikkyo (St. Paul's) University
Department Research Information Center for Extremophiles
Street address 3-34-1
City Nishiikebukuro
State/province Tokyo
ZIP/Postal code 171-8501
Country Japan
Platform ID GPL7033
Series (1)
GSE12042 Identification of proteins from vacuoles of red algae

Data table header descriptions
ID_REF protein locus name
MASCOT file(s) corresponding MASCOT output file(s) (available for download in supplementary file section below)
Spectrum file(s) corresponding Spectrum file(s) (available for download in supplementary file section below)

Data table
ID_REF MASCOT file(s) Spectrum file(s)
CMP249C F009131.dat J3ms0001.mzData
CMG087C F008918.dat K2ms0001.mzData
CMT279C F009222.dat H4ms0001.mzData
CMR432C F009102.dat G3ms0001.mzData
CMD095C F009166.dat M3ms0001.mzData
CMO102C F009168.dat P3ms0002.mzData
CMS342C F009199.dat D4ms0001.mzData
CMF058C F008914.dat J2ms0001.mzData
CMS401C F008941.dat M2ms0001.mzData
CMC151C F008918.dat K2ms0001.mzData
CMO274C F008952.dat P2ms0001.mzData
CMT466C F008987.dat C3ms0001.mzData
CMQ010C F008992.dat E3ms0001.mzData
CMQ323C F008805.dat, F008803.dat C2a0001.mzData, C2b0001.mzData
CMH200C F008812.dat D2ms0001.mzData
CMQ375C F008943.dat N2ms0001.mzData
CMJ056C F008535.dat A1ms0001.mzData
CMD062C F008998.dat D1ms0001.mzData
CMQ074C F008691.dat M1ms0001.mzData
CMQ198C F009003.dat I1ms0001.mzData

Total number of rows: 46

Table truncated, full table size 1 Kbytes.

Supplementary file Size Download File type/resource 1.0 Mb (ftp)(http) ZIP 504.1 Kb (ftp)(http) ZIP
Processed data provided as supplementary file

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