The Global Proteome Machine Organization
The Global Proteome Machine
The home of proteomics crowd-sourced "Big Data"
   QUACK: Quality Assurance & Control Knowledge base
Intro | Data sets | FTP site
The data sets on this site have been selected for the purposes of developing QA/QC algorithms for the diagnosis and rejection of flawed experimental results. Only data explicitly meant for algorithm development will be included on this site. No data associated with biological or biomedical experiments or associated publications will be permitted. If you would like to contribute some data, please contact Ron Beavis.
Data set 1 (2012/05/06)
This data set consists of 3 experiments, each containing 5 or 6 MudPit fractions. This data was introduced in a Commentary by John R Yates III, Sung Kyu Robin Park, Claire M Delahunty, Tao Xu, Jeffrey N Savas, Daniel Cociorva & Paulo Costa Carvalho in Nat Methods. 2012 9:455-6 (PubMed).
A preliminary peptide identification analysis of these experiments can be found here. Each experiment has been divided into all 14N and all 15N reports for the fractions as well as experimental summaries. The original raw data is available from either:
  1. the author's lab web site; or
  2. the HUBRIS Repository FTP site.
These three separate multidimensional chromatography experiments form a set to be used for protein and/or peptide-level quantitative measurement. The indivdual experiments — "1:1", "5:1" & "10:1" — refer the to ratio of all-14N to all-15N proteins from isotopically labeled S. cerevisiae cell cultures. Quantitative measurements are probably the sensitive to overall data quality of any common proteomics experiment. In this context, the data displays the following issues:
Severity Type Description
Chemical artifacts Excessive carbamylation and carboxamidomethylation of free amino groups.
Ion source stability Supression of peptides eluting during the low-organic portion of the gradient in "5:1": no similar signal suppression in the other two samples
Mass calibration Parent ion mass calibration is inconsistent between samples.
Protein contamination The "10:1" sample has molecular mass marker proteins present, which are absent in the other two samples.



Copyright © 2012, The Global Proteome Machine Organization. Privacy Statement