Replace sequence with sequences within convention
replace_sequences.RdThe original peptide sequences are replaced with the peptide convention - described in the get_sequence_bonds function. Moreover the maximal uptake value is calculated based on the number of exchangeable bonds according to the convention. Function from prepHaDeX.
Examples
replace_sequences(alpha_dat)
#> Sequence Start End Protein Modification MHP State
#> <char> <num> <num> <char> <char> <num> <char>
#> 1: gfGDLKSpAGL 1 11 db_eEF1Ba 1061.5626 ALPHA_Gamma
#> 2: gfGDLKSpAGL 1 11 db_eEF1Ba 1061.5626 ALPHA_Gamma
#> 3: gfGDLKSpAGL 1 11 db_eEF1Ba 1061.5626 ALPHA_Gamma
#> 4: gfGDLKSpAGL 1 11 db_eEF1Ba 1061.5626 ALPHA_Gamma
#> 5: gfGDLKSpAGL 1 11 db_eEF1Ba 1061.5626 ALPHA_Gamma
#> ---
#> 9600: dvAAF 217 221 db_eEF1Ba 522.2558 Alpha_KSCN
#> 9601: dvAAF 217 221 db_eEF1Ba 522.2558 Alpha_KSCN
#> 9602: dvAAF 217 221 db_eEF1Ba 522.2558 Alpha_KSCN
#> 9603: dvAAF 217 221 db_eEF1Ba 522.2558 Alpha_KSCN
#> 9604: dvAAF 217 221 db_eEF1Ba 522.2558 Alpha_KSCN
#> Exposure File z Inten Center
#> <num> <char> <int> <num> <num>
#> 1: 0.000 Tania_161112_eEF1Ba_KSCN_IMS_seq1 1 138844 1062.1913
#> 2: 0.000 Tania_161112_eEF1Ba_KSCN_IMS_seq1 2 728218 531.6754
#> 3: 0.167 Tania_161109_1eEF1Bag_KSCN_10sec 1 41100 1064.0150
#> 4: 0.167 Tania_161109_1eEF1Bag_KSCN_10sec 2 393115 532.4975
#> 5: 0.167 Tania_161109_2eEF1Bag_KSCN_10sec 1 46642 1063.9682
#> ---
#> 9600: 150.000 Tania_161111_2eEF1Ba_KSCN_2_5h 1 1359937 524.7925
#> 9601: 150.000 Tania_161111_3eEF1Ba_KSCN_2_5h 1 1294714 524.7521
#> 9602: 1440.000 Tania_161111_1eEF1Ba_KSCN_out 1 1420195 524.7612
#> 9603: 1440.000 Tania_161112_2eEF1Ba_KSCN_out 1 1385283 524.7661
#> 9604: 1440.000 Tania_161112_3eEF1Ba_KSCN_out 1 1191113 524.7790
#> MaxUptake
#> <int>
#> 1: 8
#> 2: 8
#> 3: 8
#> 4: 8
#> 5: 8
#> ---
#> 9600: 3
#> 9601: 3
#> 9602: 3
#> 9603: 3
#> 9604: 3