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Comparison of the depletion and enrichment approaches to combinatorial peptidomics |
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| Depletion approach |
Enrichment approach |
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| 1. Individual steps per each "filtering" stage |
1 step process, i.e. bind to beads (beads discarded) |
3 step process, i.e. bind to beads, wash and elute |
| 2. Number of combinations using 6 amino acid filters |
63 |
63 |
| 3. Range of suitable peptide lengths |
Longer peptides require less "filtering" stages (i.e. 10 or more amino acid residues preferred) |
Shorter peptides require less "filtering" stages (i.e. 10 or less amino acid residues preferred) |
| 4. Complexity of peptide mixtures |
Decreased |
Decreased |
| 5. Amino acid compositional complexity of the remaining peptides |
Decreased (by the number of "filters" used) |
Not changed (20 amino acids) |
| 6. Quantitative analysis |
A single-stage depletion is more straightforward and quantitative than a triple-stage enrichment |
Enrichment approach is less straightforward and robust than the depletion |
| 7. Scaling up |
Possible (larger "filters" or consecutive stages) |
Possible (larger "filters" or parallel reactions) |
| 8. Scaling down |
Possible (low fmol level MS sensitivity requires high pmol filter binding capacities) |
Especially suitable : low fmol level MS sensitivity requires fmol binding capacities |
| 9A. Limitations (overloading) |
Large binding capacity of the "filters" is crucial – overloading will allow all peptides to pass the "filter" |
Overloading of the "filters" is not an issue, excess of sample may be applied |
| 9A. Limitations (incompletely digestion) |
Products of incomplete digestion will be mostly eliminated |
Products of incomplete digestion will be mostly retained and may interfere with the downstream purification and analysis steps |
| 10. Nano-applications |
Problematic due to limitation (see above) – excess of binding sites required to maintain efficient separation. Suitable for micro-fluidic applications |
Suitable for nano-applications, since smaller number of binding sites required (compared to depletion strategy) |
Soloviev et al. Journal of Nanobiotechnology 2003 1:4 doi:10.1186/1477-3155-1-4 |
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