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Merge pull request #241 from MannLabs/fix_modifications_bug
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Fix modifications bug
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@mschwoer
mschwoer authored Nov 19, 2024
2 parents 7cf2f55 + 98059d5 commit 9478da3
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Showing 4 changed files with 15 additions and 15 deletions.
2 changes: 1 addition & 1 deletion alphabase/constants/const_files/psm_reader.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ maxquant:
'Dimethyl@Any_N-term':
- '(Dimethyl)'
'Acetyl@Protein_N-term':
- '_(Acetyl (Protein_N-term))'
- '_(Acetyl (Protein N-term))'
- '_(ac)'
'Acetyl@K':
- 'K(ac)'
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6 changes: 3 additions & 3 deletions nbs_tests/psm_reader/dia_psm_reader.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -438,9 +438,9 @@
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_100ug_test_S4-A1_1_25843\t2\t\t_ALVAT[+80]PGK_\t\tTrue\t_ALVAT[Phospho (STY)]PGK_\tALVATPGK\t-5.032703\t0.758\t-5.032703\tP19338\tFalse\t_ALVAT[+80]PGK_\t_ALVAT[Phospho (STY)]PGK_\t418.717511324722\t0\t10352\tH3PO4\t4\ty\t1\t384.224142529733\t26.31595\tFalse\tsp\tP19338\tP19338\tNUCL_HUMAN\tNucleolin\tHomo sapiens\t\tNCL\t1\t3\tMCT_human_UP000005640_9606\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_100ug_test_S4-A1_1_25843\t2\t\t_TLT[+80]PCPLR_\t\tTrue\t_TLT[Phospho (STY)]PC[Carbamidomethyl (C)]PLR_\tTLTPCPLR\t27.71659\t0.818\t27.71659\tQ5T200\tFalse\t_TLT[+80]PPLR_\t_TLT[Phospho (STY)]PPLR_\t439.230785875227\t0.000138389150379226\t23117\tnoloss\t3\tb\t1\t396.153027901512\t6.3264\tFalse\tsp\tQ5T200\tQ5T200\tZC3HD_HUMAN\tZinc finger CCCH domain-containing protein 13\tHomo sapiens\t\tZC3H13\t1\t1\tMCT_human_UP000005640_9606\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_100ug_test_S4-A1_1_25843\t2\t\t_TLT[+80]PCPLR_\t\tTrue\t_TLT[Phospho (STY)]PC[Carbamidomethyl (C)]PLR_\tTLTPCPLR\t27.71659\t0.818\t27.71659\tQ5T200\tFalse\t_TLT[+80]PPLR_\t_TLT[Phospho (STY)]PPLR_\t439.230785875227\t0.000138389150379226\t23117\tnoloss\t3\ty\t1\t385.255780000092\t29.70625\tFalse\tsp\tQ5T200\tQ5T200\tZC3HD_HUMAN\tZinc finger CCCH domain-containing protein 13\tHomo sapiens\t\tZC3H13\t1\t1\tMCT_human_UP000005640_9606\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867\t2\t\t_LFVT[+80]PPEGSSR_\t\tTrue\t_[Acetyl (Protein_N-term)]LFVS[Phospho (STY)]PPEGSSR_\tLFVSPPEGSSR\t38.05031\t0.917\t38.05031\tQ14244;Q14244-6;Q14244-7\tFalse\t_LFVT[+80]PPEGSSR_\t_LFVT[Phospho (STY)]PPEGSSR_\t635.297385373987\t0\t14164\tH3PO4\t4\tb\t1\t443.265279065723\t12.24525\tFalse\tsp\tQ14244;Q14244-6;Q14244-7\tQ14244;Q14244-6;Q14244-7\tMAP7_HUMAN\tEnsconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin\tHomo sapiens\t\tMAP7\t1;;\t1;;\tMCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867\t2\t\t_LFVT[+80]PPEGSSR_\t\tTrue\t_[Acetyl (Protein_N-term)]LFVS[Phospho (STY)]PPEGSSR_\tLFVSPPEGSSR\t38.05031\t0.917\t38.05031\tQ14244;Q14244-6;Q14244-7\tFalse\t_LFVT[+80]PPEGSSR_\t_LFVT[Phospho (STY)]PPEGSSR_\t635.297385373987\t0\t14164\tnoloss\t6\ty\t1\t632.299829640042\t46.07855\tFalse\tsp\tQ14244;Q14244-6;Q14244-7\tQ14244;Q14244-6;Q14244-7\tMAP7_HUMAN\tEnsconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin\tHomo sapiens\t\tMAP7\t1;;\t1;;\tMCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867\t2\t\t_LFVT[+80]PPEGSSR_\t\tTrue\t_[Acetyl (Protein_N-term)]LFVS[Phospho (STY)]PPEGSSR_\tLFVSPPEGSSR\t38.05031\t0.917\t38.05031\tQ14244;Q14244-6;Q14244-7\tFalse\t_LFVT[+80]PPEGSSR_\t_LFVT[Phospho (STY)]PPEGSSR_\t635.297385373987\t0\t14164\tnoloss\t7\ty\t1\t729.352593488892\t100\tFalse\tsp\tQ14244;Q14244-6;Q14244-7\tQ14244;Q14244-6;Q14244-7\tMAP7_HUMAN\tEnsconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin\tHomo sapiens\t\tMAP7\t1;;\t1;;\tMCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867\t2\t\t_LFVT[+80]PPEGSSR_\t\tTrue\t_[Acetyl (Protein N-term)]LFVS[Phospho (STY)]PPEGSSR_\tLFVSPPEGSSR\t38.05031\t0.917\t38.05031\tQ14244;Q14244-6;Q14244-7\tFalse\t_LFVT[+80]PPEGSSR_\t_LFVT[Phospho (STY)]PPEGSSR_\t635.297385373987\t0\t14164\tH3PO4\t4\tb\t1\t443.265279065723\t12.24525\tFalse\tsp\tQ14244;Q14244-6;Q14244-7\tQ14244;Q14244-6;Q14244-7\tMAP7_HUMAN\tEnsconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin\tHomo sapiens\t\tMAP7\t1;;\t1;;\tMCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867\t2\t\t_LFVT[+80]PPEGSSR_\t\tTrue\t_[Acetyl (Protein N-term)]LFVS[Phospho (STY)]PPEGSSR_\tLFVSPPEGSSR\t38.05031\t0.917\t38.05031\tQ14244;Q14244-6;Q14244-7\tFalse\t_LFVT[+80]PPEGSSR_\t_LFVT[Phospho (STY)]PPEGSSR_\t635.297385373987\t0\t14164\tnoloss\t6\ty\t1\t632.299829640042\t46.07855\tFalse\tsp\tQ14244;Q14244-6;Q14244-7\tQ14244;Q14244-6;Q14244-7\tMAP7_HUMAN\tEnsconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin\tHomo sapiens\t\tMAP7\t1;;\t1;;\tMCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional\n",
"202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867\t2\t\t_LFVT[+80]PPEGSSR_\t\tTrue\t_[Acetyl (Protein N-term)]LFVS[Phospho (STY)]PPEGSSR_\tLFVSPPEGSSR\t38.05031\t0.917\t38.05031\tQ14244;Q14244-6;Q14244-7\tFalse\t_LFVT[+80]PPEGSSR_\t_LFVT[Phospho (STY)]PPEGSSR_\t635.297385373987\t0\t14164\tnoloss\t7\ty\t1\t729.352593488892\t100\tFalse\tsp\tQ14244;Q14244-6;Q14244-7\tQ14244;Q14244-6;Q14244-7\tMAP7_HUMAN\tEnsconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin\tHomo sapiens\t\tMAP7\t1;;\t1;;\tMCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional\n",
"''')\n",
"\n",
"spn_reader = psm_reader_provider.get_reader('spectronaut')\n",
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