Table 1 Summary of database contents. A summary of the data sets included in the initial release of PEDRo. The database provides more detailed descriptions of sample generation, sample processing, mass spectrometry and in silico analyses, populating the model described in [2].
From: PEDRo: A database for storing, searching and disseminating experimental proteomics data
1 | Organism | Saccharomyces cerevisiae | Sample Generation | Whole cell extracts (bead beating) |
| Â | Experimenter | Al Brown et al. | Sample Processing | 2D gel |
| Â | Description | GCN4-dependent proteins that respond to amino acid starvation | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT, MS-Fit) |
2 | Organism | Candida albicans | Sample Generation | Whole cell extracts (bead beating) |
| Â | Experimenter | Al Brown et al. | Sample Processing | 2D gel |
| Â | Description | GCN4-dependent proteins that respond to amino acid starvation | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT, MS-Fit) |
3 | Organism | Candida glabrata | Sample Generation | Whole cell extracts (bead beating) |
| Â | Experimenter | Ken Haynes et al. | Sample Processing | 2D gel |
| Â | Description | Proteins that respond to the inactivation of ACE2 | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT, MS-Fit) |
4 | Organism | Streptomyces coelicolor | Sample Generation | Whole cell extracts (sonication) |
| Â | Experimenter | Andrew Hesketh | Sample Processing | 2D gel |
| Â | Description | Changes in the proteome of strain M600 during growth and antibiotic production in liquid medium | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT) |
5 | Organism | Mus Musculus BALB/C | Sample Generation | Exfoliated jejunal epithelium prepared as per Bjerknes & Cheng, Anat Rec 1981, 199, 565. |
| Â | Experimenter | Alan Pemberton, Pamela Knight | Sample Processing | 2D gel |
| Â | Description | Trichinella spiralis infection in mice induces alterations in the proteome of the small mucosal epithelium | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT, MS-FIT) |
6 | Organism | Homo sapiens | Sample Generation | Gel image analysis data from 12 patients, used to assign spot picks from a preparative 2D gel |
| Â | Experimenter | Tony Whetton, Caroline Evans | Sample Processing | 2D gel |
| Â | Description | Proteomics can identify prognostic markers in CLL disease progression | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT) |
7 | Organism | Saccharomyces cerevisiae | Sample Generation | Saccharomyces cerevisiae, strain YMK36, butanol – and butanol + |
| Â | Experimenter | Kathleen Carroll | Sample Processing | 2D gel |
| Â | Description | Effect of butanol stress on yeast | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT) |
8 | Organism | Saccharomyces cerevisiae | Sample Generation | Â |
| Â | Experimenter | Kathleen Carroll | Sample Processing | 2D gel |
| Â | Description | Mapping Heat shock proteins in Saccharomyces cerevisiae | Mass Spectrometry | MALDI-ToF |
| Â | Â | Â | In Silico Analysis | Peptide mass fingerprint searches (MASCOT) |
9 | Organism | T. bruceii | Sample Generation | Gel pieces |
| Â | Experimenter | Sarah Hart | Sample Processing | Bands from 1D gel |
| Â | Description | Trypanosome Flagella | Mass Spectrometry | MALDI-ToF, LC MS/MS |
| Â | Â | Â | In Silico Analysis | Mascot MS/MS |