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Title: Qian Plasma alkylated samples      
description:
Qian Plasma alkylated samples Weijun Qian's paper (Qian et. al., Molecular and Cellular Proteomics 2005, 4, 700-709) was compiled from 461 data files, totalling 9.0 GB. The files from the Qian paper are mainly global, trypsinized plasma. The WQ-PLAS files were all analyzed with static iodoacetimide on C while the remaining files (plasma12, plasmaJK, & plasmaJon) were not alkylated and therefore were not analyzed with any modifications enabled.
privacy:
not applicable
aggregation:
instance of dataset
ID:
PAe000169
refinement:
curated
availability:
available
types:
mass spectrometry
strain:
Adult, Human plasma
name:
Human
description:
Treatment: Aliquots of 200µl each of the control and LPS-treated plasma samples were diluted and denatured using 8M urea, 50mM NH₄HCO₃, pH 8.2 for 1 h at 37°C and reduced with 10mM DTT for 30 min at 37°C. Protein cysteinyl residues were alkylated with 40mM iodoacetamide for 90 min at room temperature, and samples were desalted using a prepacked PD-10 column containing Sephadex G-25 (Amersham Biosciences). The protein concentrations for the desalted samples were measured using a BCA protein assay (Pierce) that gave total protein amounts of 15.0 and 13.9mg for the control and LPS-treated plasma samples, respectively.; Growth: ; Digestion: The samples were digested into peptides using sequencing grade trypsin (Promega, Madison, WI) overnight at 37°C with a 1:50 (w/w) trypsin-to-protein ratio. Tryptic activity of residual trypsin was quenched by boiling the samples for 10 min and immediately placing the samples on ice.; Extraction: ; Separation: The ¹⁶O/¹⁸O-labeled peptide samples from the control and LPS-treated plasma samples were fractionated by Strong Cation Exchange (SCX) Fractionation. The lyophilized sample was resuspended in 1.5ml of 10mM ammonium formate, 25% acetonitrile, pH 3.0 and injected onto a 10 × 4.6-mm guard column attached to a polysulfoethyl A 200 × 4.6-mm (5-µm, 300-Å) column (Poly LC, Columbia, MD). The mobile phases consisted of solvent A (10mM ammonium formate, 25% acetonitrile, pH 3.0) and solvent B (500mM ammonium formate, 25% acetonitrile, pH 6.8). After sample loading, the separation was isocratic for 10 min with 100% solvent A with a flow rate of 1ml/min. Peptides were eluted using sequential linear gradients from 100% solvent A to 50% solvent B over 40 min and from 50% solvent B to 100% solvent B over another 10 min. The mobile phase was held at 100% solvent B for another 15 min. 1-ml fractions (1 min/fraction) were collected after the start of the gradient using a Shimadzu FRC-10A fraction collector (Kyoto, Japan) and combined into 30 fractions. Each fraction was lyophilized and analyzed by reversed-phase LC-FTICR.
name:
LCQ Duo
accessURL: ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000169/
storedIn:
Peptide Atlas
qualifier:
gzip compressed
format:
XML
accessType:
download
authentication:
none
authorization:
none
abbreviation:
ISB
homePage: http://www.systemsbiology.org/
ID:
SCR:011305
name:
Institute for Systems Biology
homePage: http://www.peptideatlas.org/
ID:
SCR:006783
name:
PeptideAtlas

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