What data can be used? - EBI-Metabolights/SAFERnmr GitHub Wiki
SAFER was designed primarily for most standard 1H1D NMR spectra like noesypr1d, cpmg, proton-detected 13C (such as hsqcetgpsisp), zg, and similar experiments should also work with it. The important thing is that these experiements produce at least some of the peaks one would detect in a proton 1D experiment. Typically the number of points will be 65-130K and range between [-1, 11] ppm. pJRES are not recommended, as multiplet shapes are collapsed into single peaks. However, you may get really nice results by rotating a subset of peak slices (e.g. selected by STOCSY) back onto the 1H ∂ axis and re-convoluting the peaks. Such signatures could be valuable as queries in SAFER, and we are exploring this.
SAFER is not limited to a particular sample type or field strength, but a few factors are important to keep in mind:
- your reference library should be “close enough” to the field strenth at which it was collected. We round to the nearest 100 MHz when using GISSMO slices
- if lineshapes or field strength differ much between the two datasets, you may need to reduce your correlation threshold (going too low will lower the quality of the results and potentially lead to instability). We are exploring these limits, and are eager to hear any feedback if you’ve tried this.
- you could easily add your own reference library of PCRSs or near-pure reference spectra. more details @ [link]
Distinct 1H1D NMR experiment types we were able to convert from Metabolights:
| no. | pulse_program | spectra |
|---|---|---|
| 1 | cpmgpr1d | 4730 |
| 2 | noesypr1d | 2231 |
| 3 | pulsecal | 1970 |
| 4 | noesygppr1d | 1901 |
| 5 | cpmgpr1d.comp | 1453 |
| 6 | NA | 876 |
| 7 | noesygppr1d.comp | 638 |
| 8 | ledbpgppr2s1d.comp | 476 |
| 9 | zgpr | 409 |
| 10 | zg | 244 |
| 11 | noesygppr1dQ.ayp | 236 |
| 12 | pulProg_missing | 132 |
| 13 | zg30 | 76 |
| 14 | K_cpmgpr1d | 68 |
| 15 | zgesgp | 63 |
| 16 | noesyesgpph | 54 |
| 17 | zgpg | 47 |
| 18 | ledbpgppr2s1d | 38 |
| 19 | doublefilter.sc | 24 |
| 20 | noesygppr1d.ayp | 8 |
| 21 | zgpr.ayp | 4 |
| 22 | c12filternoesygpc13cpd | 3 |
| 23 | c12c13filternoesygpc13cpd | 3 |
| 24 | c12c13filteresgp.2 | 1 |
| 25 | c12filteresgp.2 | 1 |
These can be grouped into comparable experiment types. Those appropriate for annotation using SAFER are indicated: experiment type names description number of spectra