Match to: SNAP-CDK2_human-FLAG Number of mass values searched: 65 Number of mass values matched: 8 Sequence Coverage: 22.4% Percentage of experimental masses matched (with background peaks): 12.3% 1     MKNDKDCEMK  RTTLDSPLGK   LELSGCEQGL    HRIIFLGKGT    SAADAVEVPA  PAAVLGGPEP  LMQATAWLNA YFHQPEAIEE 81    FPVPALHHPV     FQQESFTRQV   LWKLLKVVKF GEVISYSHLA   ALAGNPAATA  AVKTALSGNP VPILIPCHRV      VQGDLDVGGY  161 EGGLAVKEWL    LAHEGHRLGK  PGLGMENFQK VEKIGEGTYG  VVYKARNKLT GEVVALKKIR   LDTETEGVPS   TAIREISLLK 241 ELNHPNIVKL       LDVIHTENKL   YLVFEFLHQD   LKKFMDASAL TGIPLPLIKS      YLFQLLQGLA  FCHSHRVLHR DLKPQNLLIN 321 TEGAIKLADF       GLARAFGVPV  RTYTHEVVTL  WYRAPEILLG   CKYYSTAVDI   WSLGCIFAEM  VTRRALFPGD SEIDQLFRIF 401 RTLGTPDEVV      WPGVTSMPDY KPSFPKWARQ  DFSKVVPPLD   EDGRSLLSQM   LHYDPNKRIS   AKAALAHPFF QDVTKPVPHL 481 RLDYKDDDDK IDENTIFIED FRAGMENTS Range Theoretical Experimental DELTA Sequence [290-306] 2019.015 2019.148 0.133 SYLFQLLQGLAFCHSHR [311-326] 1765.994 1765.922 0.072 DLKPQNLLINTEGAIK [274-289] 1685.943 1685.995 0.052 FMDASALTGIPLPLIK [260-272] 1663.897 1663.991 0.094 LYLVFEFLHQDLK [191-204] 1540.814 1540.742 0.072 VEKIGEGTYGVVYK [221-234] 1487.747 1487.939 0.192 LDTETEGVPSTAIR [435-444] 1095.556 1095.571 0.015 VVPPLDEDGR [11- 20] 1086.603 1086.569 0.034 RTTLDSPLGK Match to: SNAP- p53 – FLAG Number of mass values searched: 62 Number of mass values matched: 3 Sequence Coverage: 6.3% Percentage of experimental masses matched: 4.8% 1     MKNDKDCEMK  RTTLDSPLGK    LELSGCEQGL    HRIIFLGKGT   SAADAVEVPA  PAAVLGGPEP  LMQATAWLNA  YFHQPEAIEE 81    FPVPALHHPV     FQQESFTRQV   LWKLLKVVKF  GEVISYSHLA  ALAGNPAATA  AVKTALSGNP  VPILIPCHRV     VQGDLDVGGY  161 EGGLAVKEWL   LAHEGHRLGK  PGLGMEEPQS   DPSVEPPLSQ   ETFSDLWKLL   PENNVLSPLP    SQAMDDLMLS PDDIEQWFTE 241 DPGPDEAPRM    PEAAPRVAPA   PAAPTPAAPA   PAPSWPLSSS   VPSQKTYQGS   YGFRLGFLHS   GTAKSVTCTY   SPALNKMFCQ 321 LAKTCPVQLW   VDSTPPPGTR   VRAMAIYKQS   QHMTEVVRRC PHHERCSDSD  GLAPPQHLIR    VEGNLRVEYL   DDRNTFRHSV 401 VVPYEPPEVG   SDCTTIHYNY    MCNSSCMGGM  NRRPILTIIT      LEDSSGNLLG   RNSFEVRVCA   CAGRDRRTEE  ENLRKKGEPH 481 HELPSGSTKR ALPNNTSSSP       QPKKKPLDGE    YFTLQIRGRE    RFEMFRELNE   ALELKDAQAG KEPGGSRAHS   SHLKSKKGQS 516 TSRHKKLMFK TEGPDSDLDY    KDDDDK  IDENTIFIED FRAGMENTS Range Theoretical Experimental DELTA Sequence [491-504] 1467.768 1467.817 0.049 ALPNNTSSSPQPKK [542-554] 1361.680 1361.786 0.106 EPGGSRAHSSHLK [ 11- 20] 1086.603 1086.663 0.060 RTTLDSPLGK

Table 4: Results of the matching of CDK2 and p53 samples experimental mass lists with the theoretical mass list obtained from the trypsin digestion of the sequence of native proteins plus SNAP tag and FLAG tag. After matching results there are reported the sequences of the chimera proteins: the peptides of SNAP tag are in black, those of native protein in red and those of FLAG tag in blue. The sequence coverage is calculated as the ratio between the number of residues matched and the total number of protein residues.