Table I. The six cancer related studies that were analysed by PQPQ. Sample pools denotes iTRAQ/TMT sets in this table.
| Study | Samples | Replicates | Sample pools | Labeling | Σ no samples | MS instrument | Peptide data |
|---|---|---|---|---|---|---|---|
| I | Human Lung Cancer samples | 1 | 3 | 8-plex iTRAQ | 24 | MALDIa Q-TOFb Orbitrap | Protein Pilot Spectrum Mill Proteome Discoverer |
| II | Colon cell line | 1 | 1 | 8-plex iTRAQ | 8 | MALDIa | Protein Pilot |
| Fibroplast cell line | 1 | 1 | 8 | ||||
| III | Human Breast Cancer samples | 1 | 4 | 8-plex iTRAQ | 32 | Orbitrap | Proteome Discoverer |
| IV | Cell line: A549 | 1 | 1 | 8-plex iTRAQ | 8 | MALDIa Q-TOFb Orbitrap | Protein Pilot Spectrum Mill Proteome Discoverer |
| V | Cell line: MCF7 Spike in proteins | 1 | 1 | 8-plex iTRAQ 6-plex TMT | 14 | Orbitrap | Proteome Discoverer |
| VI | Cell line: MCF7 (cytosol fraction) | 3 | 1 | 4-plex iTRAQ | 12 | MALDIa Q-TOFb | Protein Pilot Spectrum Mill |
| Cell line: LCC 2 (cytosol fraction) | |||||||
| Cell line: MCF7 (DNA fraction) | 3 | 1 | |||||
| Cell line: LCC 2 (DNA fraction) | |||||||
| VII | Human Vulvar Cancer samples | 1 | 2 | 8-plex iTRAQ | 16 | Orbitrap | Proteome Discoverer |
a Matrix-assisted laser desorption/ionization.
b Quadrupole time-of-flight.