raw_file
stringlengths 36
62
| scan_number
int64 371
92.9k
| retention_time
float64 0.44
60
| indexed_retention_time
float64 -78.47
206
| package
stringlengths 12
24
| modified_sequence
stringlengths 13
150
|
---|---|---|---|---|---|
02468b_BE9-TUM_mod_ubi_57_01_01-DDA-1h-R1 | 67,802 | 54.575 | 110.122323 | TUM_mod_ubi_57 | []-K[UNIMOD:121]MPLPLK[UNIMOD:121]LFEISDIVIK-[] |
01650b_BD1-TUM_first_pool_46_01_01-3xHCD-1h-R2 | 2,465 | 11.205 | -25.07929 | TUM_first_pool_46 | []-IHVSRSPTRPR-[] |
02445a_BE12-TUM_HLA_60_01_01-DDA-1h-R1 | 34,484 | 28.206 | 43.759981 | TUM_HLA_60_01 | []-FLEQQNKL-[] |
02523_BA1-TMT_TUM_mod_pY_1_01_01-TMT1-1h-R1 | 16,752 | 15.437 | 13.109216 | TMT_TUM_mod_pY | [UNIMOD:737]-SDY[UNIMOD:21]SEAAK[UNIMOD:737]-[] |
02445a_BG8-TUM_HLA_80_01_01-DDA-1h-R1 | 17,435 | 17.14 | -0.582486 | TUM_HLA_80_01 | []-EAENERL-[] |
03919_BA4-TMT_TUM_second_addon_4_01_01-TMT2-1h-R1 | 21,153 | 23.368 | 31.508017 | TMT_TUM_second_addon | [UNIMOD:737]-VC[UNIMOD:4]ASLC[UNIMOD:4]R-[] |
02468b_BE12-TUM_mod_ubi_60_01_01-2xIT_2xHCD-1h-R1 | 25,397 | 25.868 | 34.653574 | TUM_mod_ubi_60 | []-SSLK[UNIMOD:121]SDPEGENIHAGLLK-[] |
02208a_GD11-TUM_second_addon_47_01_01-3xHCD-1h-R1 | 31,048 | 50.496 | 128.927922 | TUM_second_addon_47 | []-M[UNIMOD:35]VNQSSTPGFLLLGFSEHPGLER-[] |
03924_GC5-TMT_TUM_HLA2_29_01_01-TMT1-1h-R1 | 15,313 | 20.753 | 23.764119 | TMT_TUM_HLA2_29 | [UNIMOD:737]-SSQRITSVAM[UNIMOD:35]K[UNIMOD:737]SGGT-[] |
02195a_GD5-TUM_mod_acetylated_41_01_01-2xIT_2xHCD-1h-R1 | 27,693 | 34.72 | 54.334022 | TUM_mod_acetylated_41 | []-TSAVPSPC[UNIMOD:4]GK[UNIMOD:1]YYTLNGSK-[] |
02527_BH1-TMT_TUM_HLA_85_01_01-TMT1-1h-R1 | 41,061 | 33.662 | 62.019407 | TMT_TUM_HLA_85 | [UNIMOD:737]-SYLERRLFSRL-[] |
02244b_GA8-TMT_Thermo_SRM_Pool_57_01_01-TMT1-1h-R2 | 38,624 | 36.299 | 68.622604 | TMT_Thermo_SRM_Pool | [UNIMOD:737]-K[UNIMOD:737]PGLAITFAK[UNIMOD:737]-[] |
02245b_BD3-TMT_TUM_isoform_39_01_01-TMT1-1h-R2 | 71,948 | 59.956 | 128.080468 | TMT_TUM_isoform_39 | [UNIMOD:737]-SFFEFLVLNK[UNIMOD:737]-[] |
02242_BD9-TMT_TUM_second_pool_45_01_01-TMT1-1h-R2 | 18,085 | 13.856 | 8.922344 | TMT_TUM_second_pool | [UNIMOD:737]-DSEDLQK[UNIMOD:737]THSPR-[] |
01709a_GF1-TUM_first_pool_104_01_01-DDA-1h-R1 | 33,474 | 40.434 | 85.874737 | TUM_first_pool_104 | []-LPEDDERPPEEYDQPWEWK-[] |
03035a_GB5-TUM_HLA2_17_01_01-DDA-1h-R1 | 11,296 | 14.078 | -14.191837 | TUM_HLA2_17_01 | []-APVSGGAAAAAKG-[] |
02445a_BH5-TUM_HLA_89_01_01-DDA-1h-R1 | 79,431 | 59.353 | 166.557325 | TUM_HLA_89_01 | []-LFDILVAGGM[UNIMOD:35]L-[] |
02446a_GE1-TUM_HLA_145_01_01-DDA-1h-R1 | 61,610 | 44.986 | 106.468255 | TUM_HLA_145_01 | []-IINSTSIF-[] |
02208a_GC1-TUM_second_addon_25_01_01-2xIT_2xHCD-1h-R1 | 18,168 | 17.276 | 2.643407 | TUM_second_addon_25 | []-ALAPDSPSASR-[] |
02446d_GG3-TUM_HLA_171_01_01-2xIT_2xHCD-1h-R4 | 38,621 | 31.082 | 58.300618 | TUM_HLA_171_01 | []-HFDVTVKM-[] |
02097a_BG4-TUM_isoform_76_01_01-DDA-1h-R3 | 49,668 | 43.314 | 103.844794 | TUM_isoform_76_01 | []-LLVYVTDDNLMSDR-[] |
02445d_BB2-TUM_HLA_14_01_01-2xIT_2xHCD-1h-R4 | 28,171 | 27.718 | 41.25706 | TUM_HLA_14_01 | []-LMYDGTKEV-[] |
03174_GE10-TUM_second_pool_113_01_01-DDA-1hnoincl-R1 | 35,122 | 33.783 | 63.484933 | TUM_second_pool_113 | []-LTDAAVGGDRTDIPSAIAAGPAR-[] |
02101a_GB2-TUM_proteo_TMT_14_01_01-2xIT_2xHCD-1h-R1 | 26,246 | 25.901 | 32.226475 | TUM_proteo_TMT_14 | []-QTDVGITHFR-[] |
03924_GA8-TMT_TUM_HLA2_8_01_01-TMT1-1h-R1 | 33,863 | 29.429 | 46.553088 | TMT_TUM_HLA2_8 | [UNIMOD:737]-EK[UNIMOD:737]PTTNSYL-[] |
02528_GB11-TMT_TUM_HLA_119_01_01-TMT2-1h-R1 | 53,936 | 45.177 | 90.236299 | TMT_TUM_HLA_119 | [UNIMOD:737]-ALSPYALEY-[] |
02446d_GC12-TUM_HLA_132_01_01-2xIT_2xHCD-1h-R4 | 52,064 | 40.815 | 97.966918 | TUM_HLA_132_01 | []-LTEIAGVSVSQY-[] |
02097a_BH4-TUM_isoform_88_01_01-3xHCD-1h-R3 | 29,187 | 32.447 | 66.331862 | TUM_isoform_88_01 | []-VPVGGM[UNIMOD:35]ADLNFKISK-[] |
02101a_GB11-TUM_proteo_TMT_23_01_01-3xHCD-1h-R1 | 63,239 | 59.884 | 167.901378 | TUM_proteo_TMT_23 | []-TQAFQVLLQPLAC[UNIMOD:4]VLK-[] |
02527_BA6-TMT_TUM_HLA_6_01_01-TMT1-1h-R1 | 35,013 | 27.547 | 44.809562 | TMT_TUM_HLA_6 | [UNIMOD:737]-LEERFRVA-[] |
03174_GD10-TUM_second_pool_101_01_01-2xIT_2xHCD-1hnoincl-R1 | 5,970 | 11.334 | -21.927178 | TUM_second_pool_101 | []-HQVIHTGEKPYK-[] |
02080d_GB4-TUM_isoform_112_01_01-2xIT_2xHCD-1h-R1 | 45,240 | 46.048 | 115.979947 | TUM_isoform_112_01 | []-ATHGPLPLADLGIHLPC[UNIMOD:4]VK-[] |
03036a_BB4-TUM_HLA2_112_01_01-DDA-1h-R1 | 21,142 | 22.157 | 16.305108 | TUM_HLA2_112_01 | []-DLVRAYHAM[UNIMOD:35]S-[] |
02080d_GB7-TUM_isoform_115_01_01-DDA-1h-R1 | 35,362 | 33.595 | 65.796843 | TUM_isoform_115_01 | []-GSLAPQLYLRPHETAHVPFK-[] |
03174_GF2-TUM_second_pool_117_01_01-DDA-1hnoincl-R1 | 36,888 | 35.314 | 70.342298 | TUM_second_pool_117 | []-LHAANVVLDQDTGHPYLFVSEDKR-[] |
02445d_BH12-TUM_HLA_96_01_01-2xIT_2xHCD-1h-R4 | 26,304 | 24.173 | 28.72083 | TUM_HLA_96_01 | []-LGYINTGKQE-[] |
03923_GD9-TMT_TUM_aspn_33_01_01-TMT2-1h-R1 | 50,465 | 45.187 | 88.521064 | TMT_TUM_aspn_33 | [UNIMOD:737]-DLIHIYK[UNIMOD:737]GFENVIH-[] |
02309a_GA5-TUM_mod_pY_5_01_01-DDA-1h-R1 | 9,280 | 15.287 | 5.673642 | TUM_mod_pY_5 | []-HY[UNIMOD:21]EELQAR-[] |
03174_GA2-TUM_first_pool_108_01_01-DDA-1hnoincl-R2 | 29,490 | 29.032 | 47.714492 | TUM_first_pool_108 | []-M[UNIMOD:35]EQVC[UNIMOD:4]GGDKPYIAPSDLER-[] |
02468b_BE9-TUM_mod_ubi_57_01_01-2xIT_2xHCD-1h-R1 | 42,076 | 37.207 | 64.57783 | TUM_mod_ubi_57 | []-DKDLNSKSASDLSEDLFK-[] |
02468b_BD5-TUM_mod_ubi_41_01_01-3xHCD-1h-R1 | 39,220 | 38.462 | 67.993132 | TUM_mod_ubi_41 | []-IGMVVK[UNIMOD:121]TGVVPQLVK-[] |
03035a_GH7-TUM_HLA2_91_01_01-DDA-1h-R1 | 52,091 | 45.761 | 108.514944 | TUM_HLA2_91_01 | []-FAALVASKVF-[] |
03922_GB11-TMT_TUM_lysn_23_01_01-TMT1-1h-R1 | 60,950 | 49.238 | 99.351675 | TMT_TUM_lysn_23 | [UNIMOD:737]-K[UNIMOD:737]SLARM[UNIMOD:35]LLNDFLNDQNRD-[] |
02445a_BC6-TUM_HLA_30_01_01-DDA-1h-R1 | 52,919 | 38.203 | 83.464719 | TUM_HLA_30_01 | []-ILSGGVFN-[] |
02445d_BH7-TUM_HLA_91_01_01-2xIT_2xHCD-1h-R4 | 50,084 | 39.741 | 90.143404 | TUM_HLA_91_01 | []-ALEVIPM[UNIMOD:35]A-[] |
02211a_BB1-TMT_TUM_proteo_TMT_13_01_01-DDA-1h-R1 | 36,599 | 38.129 | 82.608307 | TMT_TUM_proteo_TMT | [UNIMOD:737]-QLADAVAELK[UNIMOD:737]-[] |
03035a_GD4-TUM_HLA2_40_01_01-3xHCD-1h-R1 | 44,996 | 49.07 | 117.472331 | TUM_HLA2_40_01 | []-TPQNFLAVLRGDAEAVKG-[] |
02445a_BD4-TUM_HLA_40_01_01-DDA-1h-R1 | 24,567 | 20.475 | 14.884247 | TUM_HLA_40_01 | []-LYAATRATLK-[] |
03925_BB10-TMT_TUM_HLA2_118_01_01-TMT1-1h-R1 | 45,712 | 43.19 | 81.613298 | TMT_TUM_HLA2_118 | [UNIMOD:737]-LYEM[UNIMOD:35]DYLK[UNIMOD:737]EGI-[] |
03174_GF6-TUM_second_pool_121_01_01-DDA-1hnoincl-R1 | 8,813 | 13.978 | -13.168155 | TUM_second_pool_121 | []-PSPDPTRPPSR-[] |
02528_GG1-TMT_TUM_HLA_169_01_01-TMT1-1h-R1 | 52,160 | 37.273 | 66.311246 | TMT_TUM_HLA_169 | [UNIMOD:737]-LRPPIM[UNIMOD:35]IM[UNIMOD:35]-[] |
03035a_GB12-TUM_HLA2_24_01_01-DDA-1h-R1 | 35,183 | 31.94 | 53.873087 | TUM_HLA2_24_01 | []-IAKEGFEKISKGANPVEIRRGVM[UNIMOD:35]L-[] |
03174_GE12-TUM_second_pool_115_01_01-DDA-1hnoincl-R1 | 24,899 | 26.061 | 33.081174 | TUM_second_pool_115 | []-RILTAAGPSTSSEDENPAWHR-[] |
02243_GC1-TMT_TUM_second_pool_121_01_01-TMT1-1h-R2 | 50,772 | 37.542 | 80.293342 | TMT_TUM_second_pool | [UNIMOD:737]-GASGERGPSGLPGPVGPPGLIGLPGTK[UNIMOD:737]-[] |
03174_GA11-TUM_first_pool_117_01_01-DDA-1hnoincl-R1 | 21,407 | 23.06 | 25.806452 | TUM_first_pool_117 | []-LVSHVDGSVISR-[] |
02446a_GA5-TUM_HLA_101_01_01-DDA-1h-R1 | 45,547 | 34.364 | 66.412419 | TUM_HLA_101_01 | []-DVLDLRG-[] |
02529b_BA9-TUM_mod_imp_pSTY_9_01_02-2xIT_2xHCD-1h-R2 | 29,125 | 33.686 | 50.838566 | TUM_mod_imp_pSTY | []-GEPNVSY[UNIMOD:21]IC[UNIMOD:4]SRYYR-[] |
03174_GA4-TUM_first_pool_110_01_01-DDA-1hnoincl-R1 | 50,677 | 45.306 | 114.031342 | TUM_first_pool_110 | []-ALLLQDTSNLLK-[] |
02244_BA1-TMT_Thermo_SRM_Pool_1_01_01-TMT1-1h-R1 | 28,379 | 21.768 | 31.856308 | TMT_Thermo_SRM_Pool | [UNIMOD:737]-AMSSNETAAYK[UNIMOD:737]-[] |
03035a_GD10-TUM_HLA2_46_01_01-DDA-1h-R1 | 42,081 | 35.795 | 69.653202 | TUM_HLA2_46_01 | []-DLDRALLLH-[] |
02445a_BC4-TUM_HLA_28_01_01-DDA-1h-R1 | 21,709 | 18.46 | 7.158706 | TUM_HLA_28_01 | []-TPSVIRK-[] |
03035a_GD12-TUM_HLA2_48_01_01-DDA-1h-R1 | 4,447 | 9.0002 | -33.903121 | TUM_HLA2_48_01 | []-HKRGGSLPARHQV-[] |
02244b_GG10-TMT_Thermo_SRM_Pool_79_01_01-TMT2-1h-R2 | 30,030 | 31.362 | 55.110209 | TMT_Thermo_SRM_Pool | [UNIMOD:737]-HLLGFSAK[UNIMOD:737]-[] |
01790a_BA3-TUM_second_pool_83_01_01-2xIT_2xHCD-1h-R1 | 18,214 | 27.084 | 35.471431 | TUM_second_pool_83 | []-NM[UNIMOD:35]C[UNIMOD:4]NYQLVC[UNIMOD:4]DSDENLKNK-[] |
03919_BC4-TMT_TUM_second_addon_28_01_01-TMT1-1h-R1 | 39,505 | 34.573 | 61.134259 | TMT_TUM_second_addon | [UNIMOD:737]-IYGPPAEPLEPTR-[] |
02445a_BF11-TUM_HLA_71_01_01-DDA-1h-R1 | 27,104 | 23.06 | 24.853986 | TUM_HLA_71_01 | []-SPTGGAQL-[] |
02445a_BC10-TUM_HLA_34_01_01-DDA-1h-R1 | 37,942 | 28.657 | 46.944119 | TUM_HLA_34_01 | []-VEIAQDFK-[] |
03919_BA8-TMT_TUM_second_addon_8_01_01-TMT1-1h-R1 | 8,777 | 11.412 | -0.678757 | TMT_TUM_second_addon | [UNIMOD:737]-GPQGGAQR-[] |
01790a_BG2-TUM_second_pool_81_01_01-DDA-1h-R1 | 2,511 | 9.2016 | -38.4564 | TUM_second_pool_81 | []-SLQNHGRTHTGEKPC[UNIMOD:4]EC[UNIMOD:4]K-[] |
02527_BH4-TMT_TUM_HLA_88_01_01-TMT1-1h-R1 | 49,741 | 40.252 | 79.669682 | TMT_TUM_HLA_88 | [UNIMOD:737]-LPRALGSGFPHL-[] |
03174_GA11-TUM_first_pool_117_01_01-DDA-1hnoincl-R1 | 8,362 | 13.644 | -12.788458 | TUM_first_pool_117 | []-EGHDKPVFNGAGK-[] |
02527_BF9-TMT_TUM_HLA_69_01_01-TMT1-1h-R1 | 23,011 | 18.275 | 21.531216 | TMT_TUM_HLA_69 | [UNIMOD:737]-GPRSQDPSL-[] |
02588a_BA12-TUM_mod_pT_12_01_01-3xHCD-1h-R1 | 20,787 | 24.036 | 27.328469 | TUM_mod_pT_12 | []-T[UNIMOD:21]QPMTAQAASYR-[] |
03174_GE8-TUM_second_pool_111_01_01-DDA-1hnoincl-R1 | 61,238 | 53.977 | 146.58009 | TUM_second_pool_111 | []-KSALFEVSEVIPVMTNNYEENILK-[] |
03210a_BB3-TUM_lysn_15_01_01-DDA-1h-R1 | 30,824 | 23.344 | 23.866856 | TUM_lysn_15_01 | []-KQNSAYNM[UNIMOD:35]HSILSNTSAE-[] |
03174_GE1-TUM_second_pool_104_01_01-DDA-1hnoincl-R1 | 58,064 | 51.925 | 138.591203 | TUM_second_pool_104 | []-FFLVLGIDAAQK-[] |
02245b_BE2-TMT_TUM_isoform_50_01_01-TMT1-1h-R2 | 25,384 | 25.457 | 40.396239 | TMT_TUM_isoform_50 | [UNIMOD:737]-EVDLTPEEEAR-[] |
03924_GE5-TMT_TUM_HLA2_53_01_01-TMT2-1h-R1 | 53,858 | 48.078 | 90.950397 | TMT_TUM_HLA2_53 | [UNIMOD:737]-GRTYQFNALFLD-[] |
01790a_BC2-TUM_second_pool_77_01_01-DDA-1h-R1 | 36,066 | 39.059 | 81.591659 | TUM_second_pool_77 | []-WEANPEM[UNIMOD:35]FHKAEELFSK-[] |
03035a_GG2-TUM_HLA2_74_01_01-DDA-1h-R1 | 52,866 | 44.386 | 103.05973 | TUM_HLA2_74_01 | []-VPIAVGAALA-[] |
01748a_BC4-TUM_second_pool_61_01_01-DDA-1h-R1 | 40,795 | 42.688 | 101.602945 | TUM_second_pool_52 | []-LQNWVYNVLERPR-[] |
02446a_GC10-TUM_HLA_130_01_01-DDA-1h-R1 | 43,576 | 33.186 | 62.020706 | TUM_HLA_130_01 | []-FLDPASA-[] |
02528_GE7-TMT_TUM_HLA_151_01_01-TMT1-1h-R1 | 48,954 | 39.358 | 71.636059 | TMT_TUM_HLA_151 | [UNIMOD:737]-YSGTGFK[UNIMOD:737]F-[] |
02527_BE6-TMT_TUM_HLA_54_01_01-TMT1-1h-R1 | 56,883 | 42.813 | 84.350051 | TMT_TUM_HLA_54 | [UNIMOD:737]-LLNESPM[UNIMOD:35]L-[] |
02240_BD6-TMT_TUM_first_pool_42_01_01-TMT2-1h-R1 | 48,975 | 37.051 | 81.206868 | TMT_TUM_first_pool | [UNIMOD:737]-M[UNIMOD:35]SLLMISENVK[UNIMOD:737]-[] |
01709a_GH2-TUM_first_pool_114_01_01-DDA-1h-R1 | 38,421 | 45.388 | 104.435767 | TUM_first_pool_114 | []-VFIGINDLEKEGAFVYSDHSPM[UNIMOD:35]R-[] |
02080d_GE12-TUM_isoform_156_01_01-DDA-1h-R1 | 43,637 | 39.606 | 90.480413 | TUM_isoform_156_01 | []-LPASVSM[UNIMOD:35]FC[UNIMOD:4]VVHA-[] |
02528_GF3-TMT_TUM_HLA_159_01_01-TMT1-1h-R1 | 47,991 | 34.127 | 57.642263 | TMT_TUM_HLA_159 | [UNIMOD:737]-K[UNIMOD:737]VADFGLVR-[] |
01790a_BB3-TUM_second_pool_84_01_01-3xHCD-1h-R1 | 33,337 | 44.172 | 102.385827 | TUM_second_pool_84 | []-PNALSYLEERGEQWTTDR-[] |
02528_GG1-TMT_TUM_HLA_169_01_01-TMT1-1h-R1 | 28,034 | 21.023 | 25.423421 | TMT_TUM_HLA_169 | [UNIMOD:737]-AERPQEWAM[UNIMOD:35]-[] |
02446d_GF12-TUM_HLA_168_01_01-2xIT_2xHCD-1h-R4 | 12,602 | 16.852 | 2.949379 | TUM_HLA_168_01 | []-RPTPKNSLM-[] |
03919_BE3-TMT_TUM_second_addon_51_01_01-TMT1-1h-R1 | 45,543 | 48.764 | 99.185467 | TMT_TUM_second_addon | [UNIMOD:737]-VSTAFVADSEGDFYYGGAVFGGQVAR-[] |
03296a_BA12-TUM_mod_pyroGlu_12_01_01-DDA-1h-R1 | 27,717 | 26.394 | 36.346956 | TUM_mod_pyroGlu_12 | []-EDAPVIHQEM-[] |
03035a_GF12-TUM_HLA2_72_01_01-DDA-1h-R1 | 44,592 | 39.544 | 85.225523 | TUM_HLA2_72_01 | []-PYVEEGLHPQIIIRA-[] |
02244b_GB4-TMT_Thermo_SRM_Pool_26_01_01-TMT1-1h-R2 | 41,359 | 37.153 | 70.972914 | TMT_Thermo_SRM_Pool | [UNIMOD:737]-GISFEVGAQLEAR-[] |
03035a_GB4-TUM_HLA2_16_01_01-DDA-1h-R1 | 24,522 | 24.197 | 25.756735 | TUM_HLA2_10_01 | []-IKDGKIVHPTL-[] |
02468b_BF2-TUM_mod_ubi_62_01_01-2xIT_2xHCD-1h-R1 | 20,162 | 22.884 | 27.638474 | TUM_mod_ubi_62 | []-DVTHTC[UNIMOD:4]PSC[UNIMOD:4]KAYIYTYK[UNIMOD:121]R-[] |
02445d_BE5-TUM_HLA_53_01_01-2xIT_2xHCD-1h-R4 | 65,649 | 48.603 | 128.098028 | TUM_HLA_53_01 | []-YQIANIYEL-[] |
02528_GF2-TMT_TUM_HLA_158_01_01-TMT1-1h-R1 | 60,476 | 42.604 | 79.495072 | TMT_TUM_HLA_158 | [UNIMOD:737]-DIFSEVVGR-[] |
02446a_GE7-TUM_HLA_151_01_01-DDA-1h-R1 | 58,107 | 42.925 | 98.855737 | TUM_HLA_151_01 | []-LPLSIPREIG-[] |
PROSPECT PTMs - Retention Time Prediction
A mass-spectrometry dataset for applied machine learning in proteomics, processed and split for the task of retention time prediction.
Dataset Details
- Curated by: Wilhelmlab - Technical University of Munich - School of Life Sciences - Germany
- License: CC-BY4.0
Dataset Sources
The data is based on the PROSPECT PTMs datasets hosted in Zenodo.
- Repository: https://github.com/wilhelm-lab/PROSPECT
Uses
The dataset is intended to be used for retention time prediction given a peptide sequence. Optionally, addiional inputs can be used as features to encode PTMs or features describing the experimental setup.
Dataset Structure
The dataset has two configurations:
- default: this is the train/val/test data that is based on all the Zenodo PROSPECT PTMs datasets [3][4][5].
- holdout: this is the holdout datasets that can be eventually used to evaluate a model capable of processing PTMs. It is based on the PROSPECT Test-PTM dataset on Zenodo [6].
Use one of the following lines to load the respective configuration:
# main data for training and evaluation; contains train, val, tesst splits
main_dataset = load_dataset("Wilhelmlab/prospect-ptms-irt")
# holdout data for final benchmarking and model comparison; contains test split only
holdout_dataset = load_dataset("Wilhelmlab/prospect-ptms-irt", "holdout")
Dataset Creation
Curation Rationale
The dataset is intended to serve as a reference benchmark dataset for retention time prediction, processed, split, and ready-to-use for developing deep learning models for this specific task.
Source Data
The upstream source data is based on the ProteomeTools datasets available on PRIDE [1][2].
Data Collection and Processing
[More Information Needed]
Annotations
The indexed retention time was calculated based on the retention time measured during Liquid Chromotography.
Personal and Sensitive Information
The dataset does not contain any personal, sensitive, or private data.
Recommendations
We recommend using the holdout configuration for solely evaluation models at the end of the research iteration.
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References
[1] Daniel P Zolg, Mathias Wilhelm, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute, Bernard Delanghe, Derek J Bailey, Siegfried Gessulat, Hans-Christian Ehrlich, Maximilian Weininger, et al. Building proteometools based on a complete synthetic human proteome. Nature methods, 14(3):259–262, 2017.
[2] Daniel Paul Zolg, Mathias Wilhelm, Tobias Schmidt, Guillaume Médard, Johannes Zerweck, Tobias Knaute, Holger Wenschuh, Ulf Reimer, Karsten Schnatbaum, and Bernhard Kuster. Pro- teometools: Systematic characterization of 21 post-translational protein modifications by liquid chromatography tandem mass spectrometry (lc-ms/ms) using synthetic peptides. Molecular & Cellular Proteomics, 17(9):1850–1863, 2018.
[3] Wassim Gabriel, Omar Shouman, and Mathias Wilhelm. PROSPECT PTMs Dataset - Multi- PTM. DOI:https://doi.org/10.5281/zenodo.11472525, 2024.
[4] Wassim Gabriel, Omar Shouman, and Mathias Wilhelm. PROSPECT PTMs Dataset - TMT. DOI:https://doi.org/10.5281/zenodo.8221499, 2023.
[5] Wassim Gabriel, Omar Shouman, and Mathias Wilhelm. PROSPECT PTMs Dataset - TMT- PTM. DOI:https://doi.org/10.5281/zenodo.11474099, 2024.
[6] Wassim Gabriel, Omar Shouman, and Mathias Wilhelm. PROSPECT PTMs Dataset - Test-PTM. DOI:https://doi.org/10.5281/zenodo.11477731, 2024.
Dataset Card Contact
Wilhelmlab, TU Munich, School of Life Sciences, Germany.
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