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Identify and analyze PTMs in large-scale
(a) identify new or existing PTMs, (using MODa software)
(b) list peptides and proteins that carry these PTMs.
1. List of modified and unmodified peptides with mass-shifts
Identify modified peptides along with the unmodified counterparts.
- Deliverables:
- reports generated by MODa (mass-shifts and peptide-spectral matches)
- Tools Used:
- MODa: (Na S et. al. ) used to identify mass-shifts on given peptides
2. Mapping mass-shifts to post-translational modifications and substitutions
Mapping the mass-shifts identified in step 1. to actual post-translational modifications and/or substitutions
- Deliverables:
- Mass-shift to PTM mapping
- Tools Used:
- ABRF delta mass: (Nesvhizskii et. al. ) used to identify PTMs mapping to mass-shifts identified above (i.e., 80 Dalton mass-shift on Serine indicates phosphorylation)
- ABRF delta mass: (Nesvhizskii et. al. ) used to identify PTMs mapping to mass-shifts identified above (i.e., 80 Dalton mass-shift on Serine indicates phosphorylation)
3. Comprehensive list of all modified peptides
List of all peptides mapped to proteins along with the site of modification (i.e., Serine phosphorylation)
- Deliverables:
- Excel file that has list of all modified peptide-spectral matches