| #1 |
Mass spectra in Thermo RAW format |
Amino
acid property in any format |
(i) Use operation peptide identification;
(ii) Use operation Target-Decoy; (iii) Use operation retention time prediction; (iv) Do not use operation Protein identification
|
| #2 |
Mass spectra in Thermo RAW format |
Pathway or network in any
format |
(i) Use operation peptide identification operation;
(ii) Use operation enrichment analysis; (iii) Use
operation enrichment analysis only after peptide identification operation; (iv) Use tool ProteinProphet only after PeptideProphet
|
| #3 |
Mass spectra in Thermo RAW format |
Protein
identification in any format |
(i) Use operation PTM identification; (ii)
Use operation PTM identification only after operation Target-Decoy; (iii) Use operation Target-Decoy only after operation peptide database search; (iv)
Do not use operation Target-Decoy more than once |
| #4 |
Mass spectra in Thermo RAW format |
Expression data in any format |
(i) Use operation iTRAQ; (ii) Use operation iTRAQ only after operation Target-Decoy
|
