From 47d77ddaed860042175b0f4e98138ea6d27fecf2 Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Mon, 18 Nov 2024 10:39:49 +0100 Subject: [PATCH 1/3] fix wrong modification mapping introduced in cdb1ddf --- alphabase/constants/const_files/psm_reader.yaml | 2 +- nbs_tests/psm_reader/dia_psm_reader.ipynb | 6 +++--- nbs_tests/psm_reader/maxquant_reader.ipynb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/alphabase/constants/const_files/psm_reader.yaml b/alphabase/constants/const_files/psm_reader.yaml index 03ce74ee..389f5626 100644 --- a/alphabase/constants/const_files/psm_reader.yaml +++ b/alphabase/constants/const_files/psm_reader.yaml @@ -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)' diff --git a/nbs_tests/psm_reader/dia_psm_reader.ipynb b/nbs_tests/psm_reader/dia_psm_reader.ipynb index 2d15c477..a008b7c4 100644 --- a/nbs_tests/psm_reader/dia_psm_reader.ipynb +++ b/nbs_tests/psm_reader/dia_psm_reader.ipynb @@ -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", diff --git a/nbs_tests/psm_reader/maxquant_reader.ipynb b/nbs_tests/psm_reader/maxquant_reader.ipynb index 16b5f745..e0c82301 100644 --- a/nbs_tests/psm_reader/maxquant_reader.ipynb +++ b/nbs_tests/psm_reader/maxquant_reader.ipynb @@ -155,9 +155,9 @@ "outputs": [], "source": [ "mq_tsv = io.StringIO('''Raw file\tScan number\tScan index\tSequence\tLength\tMissed cleavages\tModifications\tModified sequence\tOxidation (M) Probabilities\tOxidation (M) Score diffs\tAcetyl (Protein_N-term)\tOxidation (M)\tProteins\tCharge\tFragmentation\tMass analyzer\tType\tScan event number\tIsotope index\tm/z\tMass\tMass error [ppm]\tMass error [Da]\tSimple mass error [ppm]\tRetention time\tPEP\tScore\tDelta score\tScore diff\tLocalization prob\tCombinatorics\tPIF\tFraction of total spectrum\tBase peak fraction\tPrecursor full scan number\tPrecursor Intensity\tPrecursor apex fraction\tPrecursor apex offset\tPrecursor apex offset time\tMatches\tIntensities\tMass deviations [Da]\tMass deviations [ppm]\tMasses\tNumber of matches\tIntensity coverage\tPeak coverage\tNeutral loss level\tETD identification type\tReverse\tAll scores\tAll sequences\tAll modified sequences\tReporter PIF\tReporter fraction\tid\tProtein group IDs\tPeptide ID\tMod. peptide ID\tEvidence ID\tOxidation (M) site IDs\n", - "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t81358\t73979\tAAAAAAAAAPAAAATAPTTAATTAATAAQ\t29\t0\tUnmodified\t_(Acetyl (Protein_N-term))AAAAAAAAM(Oxidation (M))PAAAATAPTTAATTAATAAQ_\t\t\t0\t0\tsp|P37108|SRP14_HUMAN\t3\tHCD\tFTMS\tMULTI-MSMS\t13\t1\t790.07495\t2367.203\t0.35311\t0.00027898\t-0.061634807\t70.261\t0.012774\t41.423\t36.666\tNaN\tNaN\t1\t0\t0\t0\t81345\t10653955\t0.0338597821787898\t-11\t0.139877319335938\ty1;y2;y3;y4;y11;y1-NH3;y2-NH3;a2;b2;b3;b4;b5;b6;b7;b8;b9;b11;b12;b6(2+);b8(2+);b13(2+);b18(2+)\t2000000;2000000;300000;400000;200000;1000000;400000;300000;600000;1000000;2000000;3000000;3000000;3000000;3000000;2000000;600000;500000;1000000;2000000;300000;200000\t5.2861228709844E-06;-6.86980268369553E-05;-0.00238178789771837;0.000624715964988809;-0.0145624692099773;-0.000143471782706683;-0.000609501446461991;-0.000524972720768346;0.00010190530804266;5.8620815195809E-05;0.000229901232955854;-0.000108750048696038;-0.000229593152369034;0.00183148682538103;0.00276641182404092;0.000193118923334623;0.00200988580445483;0.000102216846016745;5.86208151389656E-05;0.000229901232955854;-0.00104559184393338;0.00525030008475369\t0.0359413365445091;-0.314964433555295;-8.23711898839045;1.60102421155213;-14.8975999917227;-1.10320467763838;-3.03102462870716;-4.56152475051625;0.712219104095465;0.273777366204575;0.806231096969562;-0.305312183824154;-0.537399178230218;3.67572664689217;4.85930954169285;0.301587577451224;2.48616190909398;0.116225745519871;0.273777365939099;0.806231096969562;-2.19774169175011;7.53961026980589\t147.076413378177;218.113601150127;289.153028027798;390.197699998035;977.50437775671;130.050013034583;201.087592852046;115.087114392821;143.081402136892;214.118559209185;285.155501716567;356.192954155649;427.230188786552;498.265241494374;569.301420357176;640.341107437877;808.429168310795;879.468189767554;214.118559209185;285.155501716567;475.757386711244;696.362265007215\t22\t0.262893575628735\t0.0826446280991736\tNone\tUnknown\t\t41.4230894199432;4.75668724862449;3.9515580701967\tAAAAAAAAAPAAAATAPTTAATTAATAAQ;FHRGPPDKDDMVSVTQILQGK;PVTLWITVTHMQADEVSVWR\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_FHRGPPDKDDMVSVTQILQGK_;_PVTLWITVTHMQADEVSVWR_\t\t\t0\t1443\t0\t0\t0\t\n", + "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t81358\t73979\tAAAAAAAAAPAAAATAPTTAATTAATAAQ\t29\t0\tUnmodified\t_(Acetyl (Protein N-term))AAAAAAAAM(Oxidation (M))PAAAATAPTTAATTAATAAQ_\t\t\t0\t0\tsp|P37108|SRP14_HUMAN\t3\tHCD\tFTMS\tMULTI-MSMS\t13\t1\t790.07495\t2367.203\t0.35311\t0.00027898\t-0.061634807\t70.261\t0.012774\t41.423\t36.666\tNaN\tNaN\t1\t0\t0\t0\t81345\t10653955\t0.0338597821787898\t-11\t0.139877319335938\ty1;y2;y3;y4;y11;y1-NH3;y2-NH3;a2;b2;b3;b4;b5;b6;b7;b8;b9;b11;b12;b6(2+);b8(2+);b13(2+);b18(2+)\t2000000;2000000;300000;400000;200000;1000000;400000;300000;600000;1000000;2000000;3000000;3000000;3000000;3000000;2000000;600000;500000;1000000;2000000;300000;200000\t5.2861228709844E-06;-6.86980268369553E-05;-0.00238178789771837;0.000624715964988809;-0.0145624692099773;-0.000143471782706683;-0.000609501446461991;-0.000524972720768346;0.00010190530804266;5.8620815195809E-05;0.000229901232955854;-0.000108750048696038;-0.000229593152369034;0.00183148682538103;0.00276641182404092;0.000193118923334623;0.00200988580445483;0.000102216846016745;5.86208151389656E-05;0.000229901232955854;-0.00104559184393338;0.00525030008475369\t0.0359413365445091;-0.314964433555295;-8.23711898839045;1.60102421155213;-14.8975999917227;-1.10320467763838;-3.03102462870716;-4.56152475051625;0.712219104095465;0.273777366204575;0.806231096969562;-0.305312183824154;-0.537399178230218;3.67572664689217;4.85930954169285;0.301587577451224;2.48616190909398;0.116225745519871;0.273777365939099;0.806231096969562;-2.19774169175011;7.53961026980589\t147.076413378177;218.113601150127;289.153028027798;390.197699998035;977.50437775671;130.050013034583;201.087592852046;115.087114392821;143.081402136892;214.118559209185;285.155501716567;356.192954155649;427.230188786552;498.265241494374;569.301420357176;640.341107437877;808.429168310795;879.468189767554;214.118559209185;285.155501716567;475.757386711244;696.362265007215\t22\t0.262893575628735\t0.0826446280991736\tNone\tUnknown\t\t41.4230894199432;4.75668724862449;3.9515580701967\tAAAAAAAAAPAAAATAPTTAATTAATAAQ;FHRGPPDKDDMVSVTQILQGK;PVTLWITVTHMQADEVSVWR\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_FHRGPPDKDDMVSVTQILQGK_;_PVTLWITVTHMQADEVSVWR_\t\t\t0\t1443\t0\t0\t0\t\n", "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t81391\t74010\tAAAAAAAAAAPAAAATAPTTAATTAATAAQ\t29\t0\tUnmodified\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_\t\t\t0\t0\tsp|P37108|SRP14_HUMAN\t2\tHCD\tFTMS\tMULTI-MSMS\t14\t0\t1184.6088\t2367.203\t0.037108\t4.3959E-05\t1.7026696\t70.287\t7.1474E-09\t118.21\t100.52\tNaN\tNaN\t1\t0\t0\t0\t81377\t9347701\t0.166790347889974\t-10\t0.12664794921875\ty1;y2;y3;y4;y5;y9;y12;y13;y14;y20;y13-H2O;y20-H2O;y1-NH3;y20-NH3;b3;b4;b5;b6;b7;b8;b9;b11;b12;b13;b14;b15;b16;b19;b15-H2O;b16-H2O\t500000;600000;200000;400000;200000;100000;200000;1000000;200000;300000;200000;100000;100000;70000;300000;900000;2000000;3000000;5000000;8000000;6000000;600000;800000;600000;200000;300000;200000;300000;300000;1000000\t-0.000194444760495571;0.000149986878682284;0.000774202587820128;-0.0002445094036716;0.000374520568641401;-0.00694293246522193;-0.0109837291331587;-0.0037745820627606;-0.000945546471939451;0.00152326440706929;0.00506054832726477;0.00996886361417637;6.25847393393997E-05;-0.024881067836759;-3.11821549132674E-05;-0.000183099230639527;0.000161332473453513;0.000265434980121881;0.000747070697229901;0.000975534518261156;0.00101513939785036;0.00651913000274362;0.0058584595163893;0.00579536744021425;0.00131097834105276;-0.0131378531671089;0.00472955218901916;-0.00161006322559842;-0.00201443239325272;0.0227149399370319\t-1.32206444236914;0.687655553213019;2.6775131607882;-0.626628140021726;0.811995006209331;-8.6203492854282;-10.1838066275079;-3.21078702288986;-0.758483069159249;0.881072738747222;4.37168212373889;5.82682888353564;0.481236695337485;-14.5343986203644;-0.145630261806375;-0.642102166533079;0.452935954800214;0.621293379181583;1.49934012872483;1.71355878380837;1.58531240493271;8.06399202403175;6.6614096214532;6.09718023739784;1.28333378040908;-11.7030234519348;3.96235146626144;-1.07856912288932;-1.82370619437775;19.3220953109188\t147.07661310906;218.113382465221;289.149872037312;390.198569223404;461.235063981231;805.411965958065;1078.54847749073;1175.59403219566;1246.62831694787;1728.87474561429;1157.57463237897;1710.85573532879;130.049806978061;1711.87460084504;214.118649012155;285.155914717031;356.192684073126;427.22969375842;498.266325910503;569.303211234482;640.340285417402;808.424659066597;879.462433524883;950.49961040476;1021.54120858166;1122.60333588727;1193.62258226971;1492.77704268533;1104.58164778019;1175.59403219566\t30\t0.474003002083763\t0.167630057803468\tNone\tUnknown\t\t118.209976573419;17.6937689289157;17.2534171481793\tAAAAAAAAAPAAAATAPTTAATTAATAAQ;SELKQEAMQSEQLQSVLYLK;VGSSVPSKASELVVMGDHDAARR\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_SELKQEAM(Oxidation (M))QSEQLQSVLYLK_;_VGSSVPSKASELVVMGDHDAARR_\t\t\t1\t1443\t0\t0\t1\t\n", - "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t107307\t98306\tAAAAAAAGDSDSWDADAFSVEDPVRK\t26\t1\tAcetyl (Protein_N-term)\t_(Acetyl (Protein_N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_\t\t\t1\t0\tsp|O75822|EIF3J_HUMAN\t3\tHCD\tFTMS\tMULTI-MSMS\t10\t2\t879.06841\t2634.1834\t-0.93926\t-0.00082567\t-3.2012471\t90.978\t2.1945E-12\t148.95\t141.24\tNaN\tNaN\t1\t0\t0\t0\t107297\t10193939\t0.267970762043589\t-8\t0.10211181640625\ty1;y2;y4;y5;y6;y7;y8;y9;y10;y11;y12;y13;y14;y15;y17;y18;y19;y20;y21;y23;y21-H2O;y1-NH3;y19-NH3;y14(2+);y16(2+);y22(2+);a2;b2;b3;b4;b5;b6;b7\t300000;200000;3000000;600000;1000000;500000;2000000;1000000;1000000;1000000;90000;1000000;400000;900000;1000000;400000;3000000;2000000;1000000;400000;100000;200000;200000;80000;100000;200000;200000;2000000;5000000;5000000;5000000;2000000;300000\t1.34859050149316E-07;-6.05140996867704E-06;2.27812602133781E-05;0.00128986659160546;-0.00934536073077652;0.000941953783126337;-0.00160424237344614;-0.00239257341399934;-0.00111053968612396;-0.00331340710044969;0.00330702864630439;0.000963683996815234;0.00596290290945944;-0.00662057038289277;-0.0117122701335575;0.00777853472800416;0.0021841542961738;0.000144322111736983;-0.00087403893667215;0.0197121595674616;-0.021204007680808;-0.000308954599830713;-0.026636719419912;-0.0137790992353075;0.00596067266928912;-0.0077053835773313;9.11402199221811E-06;-0.000142539300128419;-0.000251999832926231;1.90791054137662E-05;-0.00236430185879044;-9.54583337602344E-05;-0.000556959493223985\t0.000916705048437201;-0.0199575598103408;0.0456231928690862;2.09952637717462;-12.5708704058425;1.11808305811426;-1.72590731777249;-2.22239181008062;-0.967696370445928;-2.62418809422166;2.47964286628144;0.665205752892023;3.64753748704453;-3.84510115530963;-6.08782672045773;3.81508105974837;1.04209904973991;0.0666012719936656;-0.390545453668809;8.28224925531311;-9.55133250134922;-2.37499239179248;-12.8127653858411;-16.846761946123;6.48662354975264;-6.67117082062383;0.0580151981289049;-0.770098855873447;-0.983876895688683;0.0583162347158579;-5.93738717724506;-0.203431522818505;-1.03087538746314\t147.112804035741;303.21392125011;499.33507018564;614.360746132308;743.413974455831;842.472101057517;929.506675663573;1076.57587791081;1147.61170966489;1262.6408555643;1333.67134891635;1448.700635293;1634.77494902759;1721.81956091078;1923.88362405243;2038.89107627957;2095.9181343836;2166.95728800359;2237.99542015244;2380.04906152953;2220.00518543488;130.0865640237;2078.92040615582;817.907873297785;918.917619246831;1155.02717356753;157.097144992378;185.0922112678;256.129434516133;327.166277224995;398.205774393759;469.240619338034;540.278194626993\t33\t0.574496146107112\t0.14410480349345\tNone\tUnknown\t\t148.951235201399;7.71201258444522;7.36039532447559\tAAAAAAAGDSDSWDADAFSVEDPVRK;PSRQESELMWQWVDQRSDGER;HTLTSFWNFKAGCEEKCYSNR\t_(Acetyl (Protein_N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_;_PSRQESELM(Oxidation (M))WQWVDQRSDGER_;_HTLTSFWNFKAGCEEKCYSNR_\t\t\t2\t625\t1\t1\t2\t'''\n", + "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t107307\t98306\tAAAAAAAGDSDSWDADAFSVEDPVRK\t26\t1\tAcetyl (Protein_N-term)\t_(Acetyl (Protein N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_\t\t\t1\t0\tsp|O75822|EIF3J_HUMAN\t3\tHCD\tFTMS\tMULTI-MSMS\t10\t2\t879.06841\t2634.1834\t-0.93926\t-0.00082567\t-3.2012471\t90.978\t2.1945E-12\t148.95\t141.24\tNaN\tNaN\t1\t0\t0\t0\t107297\t10193939\t0.267970762043589\t-8\t0.10211181640625\ty1;y2;y4;y5;y6;y7;y8;y9;y10;y11;y12;y13;y14;y15;y17;y18;y19;y20;y21;y23;y21-H2O;y1-NH3;y19-NH3;y14(2+);y16(2+);y22(2+);a2;b2;b3;b4;b5;b6;b7\t300000;200000;3000000;600000;1000000;500000;2000000;1000000;1000000;1000000;90000;1000000;400000;900000;1000000;400000;3000000;2000000;1000000;400000;100000;200000;200000;80000;100000;200000;200000;2000000;5000000;5000000;5000000;2000000;300000\t1.34859050149316E-07;-6.05140996867704E-06;2.27812602133781E-05;0.00128986659160546;-0.00934536073077652;0.000941953783126337;-0.00160424237344614;-0.00239257341399934;-0.00111053968612396;-0.00331340710044969;0.00330702864630439;0.000963683996815234;0.00596290290945944;-0.00662057038289277;-0.0117122701335575;0.00777853472800416;0.0021841542961738;0.000144322111736983;-0.00087403893667215;0.0197121595674616;-0.021204007680808;-0.000308954599830713;-0.026636719419912;-0.0137790992353075;0.00596067266928912;-0.0077053835773313;9.11402199221811E-06;-0.000142539300128419;-0.000251999832926231;1.90791054137662E-05;-0.00236430185879044;-9.54583337602344E-05;-0.000556959493223985\t0.000916705048437201;-0.0199575598103408;0.0456231928690862;2.09952637717462;-12.5708704058425;1.11808305811426;-1.72590731777249;-2.22239181008062;-0.967696370445928;-2.62418809422166;2.47964286628144;0.665205752892023;3.64753748704453;-3.84510115530963;-6.08782672045773;3.81508105974837;1.04209904973991;0.0666012719936656;-0.390545453668809;8.28224925531311;-9.55133250134922;-2.37499239179248;-12.8127653858411;-16.846761946123;6.48662354975264;-6.67117082062383;0.0580151981289049;-0.770098855873447;-0.983876895688683;0.0583162347158579;-5.93738717724506;-0.203431522818505;-1.03087538746314\t147.112804035741;303.21392125011;499.33507018564;614.360746132308;743.413974455831;842.472101057517;929.506675663573;1076.57587791081;1147.61170966489;1262.6408555643;1333.67134891635;1448.700635293;1634.77494902759;1721.81956091078;1923.88362405243;2038.89107627957;2095.9181343836;2166.95728800359;2237.99542015244;2380.04906152953;2220.00518543488;130.0865640237;2078.92040615582;817.907873297785;918.917619246831;1155.02717356753;157.097144992378;185.0922112678;256.129434516133;327.166277224995;398.205774393759;469.240619338034;540.278194626993\t33\t0.574496146107112\t0.14410480349345\tNone\tUnknown\t\t148.951235201399;7.71201258444522;7.36039532447559\tAAAAAAAGDSDSWDADAFSVEDPVRK;PSRQESELMWQWVDQRSDGER;HTLTSFWNFKAGCEEKCYSNR\t_(Acetyl (Protein_N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_;_PSRQESELM(Oxidation (M))WQWVDQRSDGER_;_HTLTSFWNFKAGCEEKCYSNR_\t\t\t2\t625\t1\t1\t2\t'''\n", ")\n", "\n", "mq_reader = psm_reader_provider.get_reader('maxquant')\n", From a2a6eb8df1c31a1b94fddb984598b84e8c926429 Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Mon, 18 Nov 2024 10:44:31 +0100 Subject: [PATCH 2/3] revert changes to test data done in cdb1ddf --- nbs_tests/psm_reader/maxquant_reader.ipynb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nbs_tests/psm_reader/maxquant_reader.ipynb b/nbs_tests/psm_reader/maxquant_reader.ipynb index e0c82301..f1e63a2c 100644 --- a/nbs_tests/psm_reader/maxquant_reader.ipynb +++ b/nbs_tests/psm_reader/maxquant_reader.ipynb @@ -154,10 +154,10 @@ "metadata": {}, "outputs": [], "source": [ - "mq_tsv = io.StringIO('''Raw file\tScan number\tScan index\tSequence\tLength\tMissed cleavages\tModifications\tModified sequence\tOxidation (M) Probabilities\tOxidation (M) Score diffs\tAcetyl (Protein_N-term)\tOxidation (M)\tProteins\tCharge\tFragmentation\tMass analyzer\tType\tScan event number\tIsotope index\tm/z\tMass\tMass error [ppm]\tMass error [Da]\tSimple mass error [ppm]\tRetention time\tPEP\tScore\tDelta score\tScore diff\tLocalization prob\tCombinatorics\tPIF\tFraction of total spectrum\tBase peak fraction\tPrecursor full scan number\tPrecursor Intensity\tPrecursor apex fraction\tPrecursor apex offset\tPrecursor apex offset time\tMatches\tIntensities\tMass deviations [Da]\tMass deviations [ppm]\tMasses\tNumber of matches\tIntensity coverage\tPeak coverage\tNeutral loss level\tETD identification type\tReverse\tAll scores\tAll sequences\tAll modified sequences\tReporter PIF\tReporter fraction\tid\tProtein group IDs\tPeptide ID\tMod. peptide ID\tEvidence ID\tOxidation (M) site IDs\n", + "mq_tsv = io.StringIO('''Raw file\tScan number\tScan index\tSequence\tLength\tMissed cleavages\tModifications\tModified sequence\tOxidation (M) Probabilities\tOxidation (M) Score diffs\tAcetyl (Protein N-term)\tOxidation (M)\tProteins\tCharge\tFragmentation\tMass analyzer\tType\tScan event number\tIsotope index\tm/z\tMass\tMass error [ppm]\tMass error [Da]\tSimple mass error [ppm]\tRetention time\tPEP\tScore\tDelta score\tScore diff\tLocalization prob\tCombinatorics\tPIF\tFraction of total spectrum\tBase peak fraction\tPrecursor full scan number\tPrecursor Intensity\tPrecursor apex fraction\tPrecursor apex offset\tPrecursor apex offset time\tMatches\tIntensities\tMass deviations [Da]\tMass deviations [ppm]\tMasses\tNumber of matches\tIntensity coverage\tPeak coverage\tNeutral loss level\tETD identification type\tReverse\tAll scores\tAll sequences\tAll modified sequences\tReporter PIF\tReporter fraction\tid\tProtein group IDs\tPeptide ID\tMod. peptide ID\tEvidence ID\tOxidation (M) site IDs\n", "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t81358\t73979\tAAAAAAAAAPAAAATAPTTAATTAATAAQ\t29\t0\tUnmodified\t_(Acetyl (Protein N-term))AAAAAAAAM(Oxidation (M))PAAAATAPTTAATTAATAAQ_\t\t\t0\t0\tsp|P37108|SRP14_HUMAN\t3\tHCD\tFTMS\tMULTI-MSMS\t13\t1\t790.07495\t2367.203\t0.35311\t0.00027898\t-0.061634807\t70.261\t0.012774\t41.423\t36.666\tNaN\tNaN\t1\t0\t0\t0\t81345\t10653955\t0.0338597821787898\t-11\t0.139877319335938\ty1;y2;y3;y4;y11;y1-NH3;y2-NH3;a2;b2;b3;b4;b5;b6;b7;b8;b9;b11;b12;b6(2+);b8(2+);b13(2+);b18(2+)\t2000000;2000000;300000;400000;200000;1000000;400000;300000;600000;1000000;2000000;3000000;3000000;3000000;3000000;2000000;600000;500000;1000000;2000000;300000;200000\t5.2861228709844E-06;-6.86980268369553E-05;-0.00238178789771837;0.000624715964988809;-0.0145624692099773;-0.000143471782706683;-0.000609501446461991;-0.000524972720768346;0.00010190530804266;5.8620815195809E-05;0.000229901232955854;-0.000108750048696038;-0.000229593152369034;0.00183148682538103;0.00276641182404092;0.000193118923334623;0.00200988580445483;0.000102216846016745;5.86208151389656E-05;0.000229901232955854;-0.00104559184393338;0.00525030008475369\t0.0359413365445091;-0.314964433555295;-8.23711898839045;1.60102421155213;-14.8975999917227;-1.10320467763838;-3.03102462870716;-4.56152475051625;0.712219104095465;0.273777366204575;0.806231096969562;-0.305312183824154;-0.537399178230218;3.67572664689217;4.85930954169285;0.301587577451224;2.48616190909398;0.116225745519871;0.273777365939099;0.806231096969562;-2.19774169175011;7.53961026980589\t147.076413378177;218.113601150127;289.153028027798;390.197699998035;977.50437775671;130.050013034583;201.087592852046;115.087114392821;143.081402136892;214.118559209185;285.155501716567;356.192954155649;427.230188786552;498.265241494374;569.301420357176;640.341107437877;808.429168310795;879.468189767554;214.118559209185;285.155501716567;475.757386711244;696.362265007215\t22\t0.262893575628735\t0.0826446280991736\tNone\tUnknown\t\t41.4230894199432;4.75668724862449;3.9515580701967\tAAAAAAAAAPAAAATAPTTAATTAATAAQ;FHRGPPDKDDMVSVTQILQGK;PVTLWITVTHMQADEVSVWR\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_FHRGPPDKDDMVSVTQILQGK_;_PVTLWITVTHMQADEVSVWR_\t\t\t0\t1443\t0\t0\t0\t\n", "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t81391\t74010\tAAAAAAAAAAPAAAATAPTTAATTAATAAQ\t29\t0\tUnmodified\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_\t\t\t0\t0\tsp|P37108|SRP14_HUMAN\t2\tHCD\tFTMS\tMULTI-MSMS\t14\t0\t1184.6088\t2367.203\t0.037108\t4.3959E-05\t1.7026696\t70.287\t7.1474E-09\t118.21\t100.52\tNaN\tNaN\t1\t0\t0\t0\t81377\t9347701\t0.166790347889974\t-10\t0.12664794921875\ty1;y2;y3;y4;y5;y9;y12;y13;y14;y20;y13-H2O;y20-H2O;y1-NH3;y20-NH3;b3;b4;b5;b6;b7;b8;b9;b11;b12;b13;b14;b15;b16;b19;b15-H2O;b16-H2O\t500000;600000;200000;400000;200000;100000;200000;1000000;200000;300000;200000;100000;100000;70000;300000;900000;2000000;3000000;5000000;8000000;6000000;600000;800000;600000;200000;300000;200000;300000;300000;1000000\t-0.000194444760495571;0.000149986878682284;0.000774202587820128;-0.0002445094036716;0.000374520568641401;-0.00694293246522193;-0.0109837291331587;-0.0037745820627606;-0.000945546471939451;0.00152326440706929;0.00506054832726477;0.00996886361417637;6.25847393393997E-05;-0.024881067836759;-3.11821549132674E-05;-0.000183099230639527;0.000161332473453513;0.000265434980121881;0.000747070697229901;0.000975534518261156;0.00101513939785036;0.00651913000274362;0.0058584595163893;0.00579536744021425;0.00131097834105276;-0.0131378531671089;0.00472955218901916;-0.00161006322559842;-0.00201443239325272;0.0227149399370319\t-1.32206444236914;0.687655553213019;2.6775131607882;-0.626628140021726;0.811995006209331;-8.6203492854282;-10.1838066275079;-3.21078702288986;-0.758483069159249;0.881072738747222;4.37168212373889;5.82682888353564;0.481236695337485;-14.5343986203644;-0.145630261806375;-0.642102166533079;0.452935954800214;0.621293379181583;1.49934012872483;1.71355878380837;1.58531240493271;8.06399202403175;6.6614096214532;6.09718023739784;1.28333378040908;-11.7030234519348;3.96235146626144;-1.07856912288932;-1.82370619437775;19.3220953109188\t147.07661310906;218.113382465221;289.149872037312;390.198569223404;461.235063981231;805.411965958065;1078.54847749073;1175.59403219566;1246.62831694787;1728.87474561429;1157.57463237897;1710.85573532879;130.049806978061;1711.87460084504;214.118649012155;285.155914717031;356.192684073126;427.22969375842;498.266325910503;569.303211234482;640.340285417402;808.424659066597;879.462433524883;950.49961040476;1021.54120858166;1122.60333588727;1193.62258226971;1492.77704268533;1104.58164778019;1175.59403219566\t30\t0.474003002083763\t0.167630057803468\tNone\tUnknown\t\t118.209976573419;17.6937689289157;17.2534171481793\tAAAAAAAAAPAAAATAPTTAATTAATAAQ;SELKQEAMQSEQLQSVLYLK;VGSSVPSKASELVVMGDHDAARR\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_SELKQEAM(Oxidation (M))QSEQLQSVLYLK_;_VGSSVPSKASELVVMGDHDAARR_\t\t\t1\t1443\t0\t0\t1\t\n", - "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t107307\t98306\tAAAAAAAGDSDSWDADAFSVEDPVRK\t26\t1\tAcetyl (Protein_N-term)\t_(Acetyl (Protein N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_\t\t\t1\t0\tsp|O75822|EIF3J_HUMAN\t3\tHCD\tFTMS\tMULTI-MSMS\t10\t2\t879.06841\t2634.1834\t-0.93926\t-0.00082567\t-3.2012471\t90.978\t2.1945E-12\t148.95\t141.24\tNaN\tNaN\t1\t0\t0\t0\t107297\t10193939\t0.267970762043589\t-8\t0.10211181640625\ty1;y2;y4;y5;y6;y7;y8;y9;y10;y11;y12;y13;y14;y15;y17;y18;y19;y20;y21;y23;y21-H2O;y1-NH3;y19-NH3;y14(2+);y16(2+);y22(2+);a2;b2;b3;b4;b5;b6;b7\t300000;200000;3000000;600000;1000000;500000;2000000;1000000;1000000;1000000;90000;1000000;400000;900000;1000000;400000;3000000;2000000;1000000;400000;100000;200000;200000;80000;100000;200000;200000;2000000;5000000;5000000;5000000;2000000;300000\t1.34859050149316E-07;-6.05140996867704E-06;2.27812602133781E-05;0.00128986659160546;-0.00934536073077652;0.000941953783126337;-0.00160424237344614;-0.00239257341399934;-0.00111053968612396;-0.00331340710044969;0.00330702864630439;0.000963683996815234;0.00596290290945944;-0.00662057038289277;-0.0117122701335575;0.00777853472800416;0.0021841542961738;0.000144322111736983;-0.00087403893667215;0.0197121595674616;-0.021204007680808;-0.000308954599830713;-0.026636719419912;-0.0137790992353075;0.00596067266928912;-0.0077053835773313;9.11402199221811E-06;-0.000142539300128419;-0.000251999832926231;1.90791054137662E-05;-0.00236430185879044;-9.54583337602344E-05;-0.000556959493223985\t0.000916705048437201;-0.0199575598103408;0.0456231928690862;2.09952637717462;-12.5708704058425;1.11808305811426;-1.72590731777249;-2.22239181008062;-0.967696370445928;-2.62418809422166;2.47964286628144;0.665205752892023;3.64753748704453;-3.84510115530963;-6.08782672045773;3.81508105974837;1.04209904973991;0.0666012719936656;-0.390545453668809;8.28224925531311;-9.55133250134922;-2.37499239179248;-12.8127653858411;-16.846761946123;6.48662354975264;-6.67117082062383;0.0580151981289049;-0.770098855873447;-0.983876895688683;0.0583162347158579;-5.93738717724506;-0.203431522818505;-1.03087538746314\t147.112804035741;303.21392125011;499.33507018564;614.360746132308;743.413974455831;842.472101057517;929.506675663573;1076.57587791081;1147.61170966489;1262.6408555643;1333.67134891635;1448.700635293;1634.77494902759;1721.81956091078;1923.88362405243;2038.89107627957;2095.9181343836;2166.95728800359;2237.99542015244;2380.04906152953;2220.00518543488;130.0865640237;2078.92040615582;817.907873297785;918.917619246831;1155.02717356753;157.097144992378;185.0922112678;256.129434516133;327.166277224995;398.205774393759;469.240619338034;540.278194626993\t33\t0.574496146107112\t0.14410480349345\tNone\tUnknown\t\t148.951235201399;7.71201258444522;7.36039532447559\tAAAAAAAGDSDSWDADAFSVEDPVRK;PSRQESELMWQWVDQRSDGER;HTLTSFWNFKAGCEEKCYSNR\t_(Acetyl (Protein_N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_;_PSRQESELM(Oxidation (M))WQWVDQRSDGER_;_HTLTSFWNFKAGCEEKCYSNR_\t\t\t2\t625\t1\t1\t2\t'''\n", + "20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t107307\t98306\tAAAAAAAGDSDSWDADAFSVEDPVRK\t26\t1\tAcetyl (Protein N-term)\t_(Acetyl (Protein N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_\t\t\t1\t0\tsp|O75822|EIF3J_HUMAN\t3\tHCD\tFTMS\tMULTI-MSMS\t10\t2\t879.06841\t2634.1834\t-0.93926\t-0.00082567\t-3.2012471\t90.978\t2.1945E-12\t148.95\t141.24\tNaN\tNaN\t1\t0\t0\t0\t107297\t10193939\t0.267970762043589\t-8\t0.10211181640625\ty1;y2;y4;y5;y6;y7;y8;y9;y10;y11;y12;y13;y14;y15;y17;y18;y19;y20;y21;y23;y21-H2O;y1-NH3;y19-NH3;y14(2+);y16(2+);y22(2+);a2;b2;b3;b4;b5;b6;b7\t300000;200000;3000000;600000;1000000;500000;2000000;1000000;1000000;1000000;90000;1000000;400000;900000;1000000;400000;3000000;2000000;1000000;400000;100000;200000;200000;80000;100000;200000;200000;2000000;5000000;5000000;5000000;2000000;300000\t1.34859050149316E-07;-6.05140996867704E-06;2.27812602133781E-05;0.00128986659160546;-0.00934536073077652;0.000941953783126337;-0.00160424237344614;-0.00239257341399934;-0.00111053968612396;-0.00331340710044969;0.00330702864630439;0.000963683996815234;0.00596290290945944;-0.00662057038289277;-0.0117122701335575;0.00777853472800416;0.0021841542961738;0.000144322111736983;-0.00087403893667215;0.0197121595674616;-0.021204007680808;-0.000308954599830713;-0.026636719419912;-0.0137790992353075;0.00596067266928912;-0.0077053835773313;9.11402199221811E-06;-0.000142539300128419;-0.000251999832926231;1.90791054137662E-05;-0.00236430185879044;-9.54583337602344E-05;-0.000556959493223985\t0.000916705048437201;-0.0199575598103408;0.0456231928690862;2.09952637717462;-12.5708704058425;1.11808305811426;-1.72590731777249;-2.22239181008062;-0.967696370445928;-2.62418809422166;2.47964286628144;0.665205752892023;3.64753748704453;-3.84510115530963;-6.08782672045773;3.81508105974837;1.04209904973991;0.0666012719936656;-0.390545453668809;8.28224925531311;-9.55133250134922;-2.37499239179248;-12.8127653858411;-16.846761946123;6.48662354975264;-6.67117082062383;0.0580151981289049;-0.770098855873447;-0.983876895688683;0.0583162347158579;-5.93738717724506;-0.203431522818505;-1.03087538746314\t147.112804035741;303.21392125011;499.33507018564;614.360746132308;743.413974455831;842.472101057517;929.506675663573;1076.57587791081;1147.61170966489;1262.6408555643;1333.67134891635;1448.700635293;1634.77494902759;1721.81956091078;1923.88362405243;2038.89107627957;2095.9181343836;2166.95728800359;2237.99542015244;2380.04906152953;2220.00518543488;130.0865640237;2078.92040615582;817.907873297785;918.917619246831;1155.02717356753;157.097144992378;185.0922112678;256.129434516133;327.166277224995;398.205774393759;469.240619338034;540.278194626993\t33\t0.574496146107112\t0.14410480349345\tNone\tUnknown\t\t148.951235201399;7.71201258444522;7.36039532447559\tAAAAAAAGDSDSWDADAFSVEDPVRK;PSRQESELMWQWVDQRSDGER;HTLTSFWNFKAGCEEKCYSNR\t_(Acetyl (Protein N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_;_PSRQESELM(Oxidation (M))WQWVDQRSDGER_;_HTLTSFWNFKAGCEEKCYSNR_\t\t\t2\t625\t1\t1\t2\t'''\n", ")\n", "\n", "mq_reader = psm_reader_provider.get_reader('maxquant')\n", @@ -200,9 +200,9 @@ "import pytest\n", "\n", "mq_tsv = io.StringIO('''Sequence\tCharge\tRetention time\tModified sequence\tScan number\tScan index\tRaw file\tm/z\tScore\tProteins\tReverse\n", - "0\tAAAAAAAAAPAAAATAPTTAATTAATAAQ\t3\t70.261\t_(Acetyl (Protein_N-term))AAAAAAAAM(Oxidation (M))PAAAATAPTTAATTAATAAQ_\t81358\t73979\t20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t790.07495\t41.423\tsp|P37108|SRP14_HUMAN\tNaN\n", + "0\tAAAAAAAAAPAAAATAPTTAATTAATAAQ\t3\t70.261\t_(Acetyl (Protein N-term))AAAAAAAAM(Oxidation (M))PAAAATAPTTAATTAATAAQ_\t81358\t73979\t20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t790.07495\t41.423\tsp|P37108|SRP14_HUMAN\tNaN\n", "1\tAAAAAAAAAAPAAAATAPTTAATTAATAAQ\t2\t70.287\t_AAAAAAAAAPAAAATAPTTAATTAATAAQ_\t81391\t74010\t20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t1184.60880\t118.210\tsp|P37108|SRP14_HUMAN\tNaN\n", - "2\tAAAAAAAGDSDSWDADAFSVEDPVRK\t3\t90.978\t_(Acetyl (Protein_N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_\t107307\t98306\t20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t879.06841\t148.950\tsp|O75822|EIF3J_HUMAN\tNaN\n", + "2\tAAAAAAAGDSDSWDADAFSVEDPVRK\t3\t90.978\t_(Acetyl (Protein N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_\t107307\t98306\t20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t879.06841\t148.950\tsp|O75822|EIF3J_HUMAN\tNaN\n", "3\tAAAAAAAGDSDSWDADAFSVEDPVRK\t3\t90.978\t_(UnkownMod)AAAAAAAGDSDSWDADAFSVEDPVRK_\t107307\t98306\t20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t879.06841\t148.950\tsp|O75822|EIF3J_HUMAN\tNaN\n", "4\tAAAAAAAGDSDSWDADAFSVEDPVRK\t3\t90.978\t_(UniMod:3)AAAAAAAGDSDSWDADAFSVEDPVRK_\t107307\t98306\t20190402_QX1_SeVW_MA_HeLa_500ng_LC11\t879.06841\t148.950\tsp|O75822|EIF3J_HUMAN\tNaN\n", "''')\n", From 98059d5eccc293a29c8a45490a56654d93043bbf Mon Sep 17 00:00:00 2001 From: mschwoerer <82171591+mschwoer@users.noreply.github.com> Date: Mon, 18 Nov 2024 12:53:05 +0100 Subject: [PATCH 3/3] revert changes to test data done in cdb1ddf --- tests/integration/test_psm_readers.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/integration/test_psm_readers.py b/tests/integration/test_psm_readers.py index 2b4dfcd9..dbd33cff 100644 --- a/tests/integration/test_psm_readers.py +++ b/tests/integration/test_psm_readers.py @@ -68,10 +68,10 @@ def test_psm_reader_yaml() -> None: def test_maxquant_reader() -> None: """Test the MaxQuant reader.""" - input_data = io.StringIO("""Raw file Scan number Scan index Sequence Length Missed cleavages Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score diffs Acetyl (Protein_N-term) Oxidation (M) Proteins Charge Fragmentation Mass analyzer Type Scan event number Isotope index m/z Mass Mass error [ppm] Mass error [Da] Simple mass error [ppm] Retention time PEP Score Delta score Score diff Localization prob Combinatorics PIF Fraction of total spectrum Base peak fraction Precursor full scan number Precursor Intensity Precursor apex fraction Precursor apex offset Precursor apex offset time Matches Intensities Mass deviations [Da] Mass deviations [ppm] Masses Number of matches Intensity coverage Peak coverage Neutral loss level ETD identification type Reverse All scores All sequences All modified sequences Reporter PIF Reporter fraction id Protein group IDs Peptide ID Mod. peptide ID Evidence ID Oxidation (M) site IDs - 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 81358 73979 AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 0 Unmodified _(Acetyl (Protein_N-term))AAAAAAAAM(Oxidation (M))PAAAATAPTTAATTAATAAQ_ 0 0 sp|P37108|SRP14_HUMAN 3 HCD FTMS MULTI-MSMS 13 1 790.07495 2367.203 0.35311 0.00027898 -0.061634807 70.261 0.012774 41.423 36.666 NaN NaN 1 0 0 0 81345 10653955 0.0338597821787898 -11 0.139877319335938 y1;y2;y3;y4;y11;y1-NH3;y2-NH3;a2;b2;b3;b4;b5;b6;b7;b8;b9;b11;b12;b6(2+);b8(2+);b13(2+);b18(2+) 2000000;2000000;300000;400000;200000;1000000;400000;300000;600000;1000000;2000000;3000000;3000000;3000000;3000000;2000000;600000;500000;1000000;2000000;300000;200000 5.2861228709844E-06;-6.86980268369553E-05;-0.00238178789771837;0.000624715964988809;-0.0145624692099773;-0.000143471782706683;-0.000609501446461991;-0.000524972720768346;0.00010190530804266;5.8620815195809E-05;0.000229901232955854;-0.000108750048696038;-0.000229593152369034;0.00183148682538103;0.00276641182404092;0.000193118923334623;0.00200988580445483;0.000102216846016745;5.86208151389656E-05;0.000229901232955854;-0.00104559184393338;0.00525030008475369 0.0359413365445091;-0.314964433555295;-8.23711898839045;1.60102421155213;-14.8975999917227;-1.10320467763838;-3.03102462870716;-4.56152475051625;0.712219104095465;0.273777366204575;0.806231096969562;-0.305312183824154;-0.537399178230218;3.67572664689217;4.85930954169285;0.301587577451224;2.48616190909398;0.116225745519871;0.273777365939099;0.806231096969562;-2.19774169175011;7.53961026980589 147.076413378177;218.113601150127;289.153028027798;390.197699998035;977.50437775671;130.050013034583;201.087592852046;115.087114392821;143.081402136892;214.118559209185;285.155501716567;356.192954155649;427.230188786552;498.265241494374;569.301420357176;640.341107437877;808.429168310795;879.468189767554;214.118559209185;285.155501716567;475.757386711244;696.362265007215 22 0.262893575628735 0.0826446280991736 None Unknown 41.4230894199432;4.75668724862449;3.9515580701967 AAAAAAAAAPAAAATAPTTAATTAATAAQ;FHRGPPDKDDMVSVTQILQGK;PVTLWITVTHMQADEVSVWR _AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_FHRGPPDKDDMVSVTQILQGK_;_PVTLWITVTHMQADEVSVWR_ 0 1443 0 0 0 + input_data = io.StringIO("""Raw file Scan number Scan index Sequence Length Missed cleavages Modifications Modified sequence Oxidation (M) Probabilities Oxidation (M) Score diffs Acetyl (Protein N-term) Oxidation (M) Proteins Charge Fragmentation Mass analyzer Type Scan event number Isotope index m/z Mass Mass error [ppm] Mass error [Da] Simple mass error [ppm] Retention time PEP Score Delta score Score diff Localization prob Combinatorics PIF Fraction of total spectrum Base peak fraction Precursor full scan number Precursor Intensity Precursor apex fraction Precursor apex offset Precursor apex offset time Matches Intensities Mass deviations [Da] Mass deviations [ppm] Masses Number of matches Intensity coverage Peak coverage Neutral loss level ETD identification type Reverse All scores All sequences All modified sequences Reporter PIF Reporter fraction id Protein group IDs Peptide ID Mod. peptide ID Evidence ID Oxidation (M) site IDs + 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 81358 73979 AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 0 Unmodified _(Acetyl (Protein N-term))AAAAAAAAM(Oxidation (M))PAAAATAPTTAATTAATAAQ_ 0 0 sp|P37108|SRP14_HUMAN 3 HCD FTMS MULTI-MSMS 13 1 790.07495 2367.203 0.35311 0.00027898 -0.061634807 70.261 0.012774 41.423 36.666 NaN NaN 1 0 0 0 81345 10653955 0.0338597821787898 -11 0.139877319335938 y1;y2;y3;y4;y11;y1-NH3;y2-NH3;a2;b2;b3;b4;b5;b6;b7;b8;b9;b11;b12;b6(2+);b8(2+);b13(2+);b18(2+) 2000000;2000000;300000;400000;200000;1000000;400000;300000;600000;1000000;2000000;3000000;3000000;3000000;3000000;2000000;600000;500000;1000000;2000000;300000;200000 5.2861228709844E-06;-6.86980268369553E-05;-0.00238178789771837;0.000624715964988809;-0.0145624692099773;-0.000143471782706683;-0.000609501446461991;-0.000524972720768346;0.00010190530804266;5.8620815195809E-05;0.000229901232955854;-0.000108750048696038;-0.000229593152369034;0.00183148682538103;0.00276641182404092;0.000193118923334623;0.00200988580445483;0.000102216846016745;5.86208151389656E-05;0.000229901232955854;-0.00104559184393338;0.00525030008475369 0.0359413365445091;-0.314964433555295;-8.23711898839045;1.60102421155213;-14.8975999917227;-1.10320467763838;-3.03102462870716;-4.56152475051625;0.712219104095465;0.273777366204575;0.806231096969562;-0.305312183824154;-0.537399178230218;3.67572664689217;4.85930954169285;0.301587577451224;2.48616190909398;0.116225745519871;0.273777365939099;0.806231096969562;-2.19774169175011;7.53961026980589 147.076413378177;218.113601150127;289.153028027798;390.197699998035;977.50437775671;130.050013034583;201.087592852046;115.087114392821;143.081402136892;214.118559209185;285.155501716567;356.192954155649;427.230188786552;498.265241494374;569.301420357176;640.341107437877;808.429168310795;879.468189767554;214.118559209185;285.155501716567;475.757386711244;696.362265007215 22 0.262893575628735 0.0826446280991736 None Unknown 41.4230894199432;4.75668724862449;3.9515580701967 AAAAAAAAAPAAAATAPTTAATTAATAAQ;FHRGPPDKDDMVSVTQILQGK;PVTLWITVTHMQADEVSVWR _AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_FHRGPPDKDDMVSVTQILQGK_;_PVTLWITVTHMQADEVSVWR_ 0 1443 0 0 0 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 81391 74010 AAAAAAAAAAPAAAATAPTTAATTAATAAQ 29 0 Unmodified _AAAAAAAAAPAAAATAPTTAATTAATAAQ_ 0 0 sp|P37108|SRP14_HUMAN 2 HCD FTMS MULTI-MSMS 14 0 1184.6088 2367.203 0.037108 4.3959E-05 1.7026696 70.287 7.1474E-09 118.21 100.52 NaN NaN 1 0 0 0 81377 9347701 0.166790347889974 -10 0.12664794921875 y1;y2;y3;y4;y5;y9;y12;y13;y14;y20;y13-H2O;y20-H2O;y1-NH3;y20-NH3;b3;b4;b5;b6;b7;b8;b9;b11;b12;b13;b14;b15;b16;b19;b15-H2O;b16-H2O 500000;600000;200000;400000;200000;100000;200000;1000000;200000;300000;200000;100000;100000;70000;300000;900000;2000000;3000000;5000000;8000000;6000000;600000;800000;600000;200000;300000;200000;300000;300000;1000000 -0.000194444760495571;0.000149986878682284;0.000774202587820128;-0.0002445094036716;0.000374520568641401;-0.00694293246522193;-0.0109837291331587;-0.0037745820627606;-0.000945546471939451;0.00152326440706929;0.00506054832726477;0.00996886361417637;6.25847393393997E-05;-0.024881067836759;-3.11821549132674E-05;-0.000183099230639527;0.000161332473453513;0.000265434980121881;0.000747070697229901;0.000975534518261156;0.00101513939785036;0.00651913000274362;0.0058584595163893;0.00579536744021425;0.00131097834105276;-0.0131378531671089;0.00472955218901916;-0.00161006322559842;-0.00201443239325272;0.0227149399370319 -1.32206444236914;0.687655553213019;2.6775131607882;-0.626628140021726;0.811995006209331;-8.6203492854282;-10.1838066275079;-3.21078702288986;-0.758483069159249;0.881072738747222;4.37168212373889;5.82682888353564;0.481236695337485;-14.5343986203644;-0.145630261806375;-0.642102166533079;0.452935954800214;0.621293379181583;1.49934012872483;1.71355878380837;1.58531240493271;8.06399202403175;6.6614096214532;6.09718023739784;1.28333378040908;-11.7030234519348;3.96235146626144;-1.07856912288932;-1.82370619437775;19.3220953109188 147.07661310906;218.113382465221;289.149872037312;390.198569223404;461.235063981231;805.411965958065;1078.54847749073;1175.59403219566;1246.62831694787;1728.87474561429;1157.57463237897;1710.85573532879;130.049806978061;1711.87460084504;214.118649012155;285.155914717031;356.192684073126;427.22969375842;498.266325910503;569.303211234482;640.340285417402;808.424659066597;879.462433524883;950.49961040476;1021.54120858166;1122.60333588727;1193.62258226971;1492.77704268533;1104.58164778019;1175.59403219566 30 0.474003002083763 0.167630057803468 None Unknown 118.209976573419;17.6937689289157;17.2534171481793 AAAAAAAAAPAAAATAPTTAATTAATAAQ;SELKQEAMQSEQLQSVLYLK;VGSSVPSKASELVVMGDHDAARR _AAAAAAAAAPAAAATAPTTAATTAATAAQ_;_SELKQEAM(Oxidation (M))QSEQLQSVLYLK_;_VGSSVPSKASELVVMGDHDAARR_ 1 1443 0 0 1 - 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 107307 98306 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 Acetyl (Protein_N-term) _(Acetyl (Protein_N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_ 1 0 sp|O75822|EIF3J_HUMAN 3 HCD FTMS MULTI-MSMS 10 2 879.06841 2634.1834 -0.93926 -0.00082567 -3.2012471 90.978 2.1945E-12 148.95 141.24 NaN NaN 1 0 0 0 107297 10193939 0.267970762043589 -8 0.10211181640625 y1;y2;y4;y5;y6;y7;y8;y9;y10;y11;y12;y13;y14;y15;y17;y18;y19;y20;y21;y23;y21-H2O;y1-NH3;y19-NH3;y14(2+);y16(2+);y22(2+);a2;b2;b3;b4;b5;b6;b7 300000;200000;3000000;600000;1000000;500000;2000000;1000000;1000000;1000000;90000;1000000;400000;900000;1000000;400000;3000000;2000000;1000000;400000;100000;200000;200000;80000;100000;200000;200000;2000000;5000000;5000000;5000000;2000000;300000 1.34859050149316E-07;-6.05140996867704E-06;2.27812602133781E-05;0.00128986659160546;-0.00934536073077652;0.000941953783126337;-0.00160424237344614;-0.00239257341399934;-0.00111053968612396;-0.00331340710044969;0.00330702864630439;0.000963683996815234;0.00596290290945944;-0.00662057038289277;-0.0117122701335575;0.00777853472800416;0.0021841542961738;0.000144322111736983;-0.00087403893667215;0.0197121595674616;-0.021204007680808;-0.000308954599830713;-0.026636719419912;-0.0137790992353075;0.00596067266928912;-0.0077053835773313;9.11402199221811E-06;-0.000142539300128419;-0.000251999832926231;1.90791054137662E-05;-0.00236430185879044;-9.54583337602344E-05;-0.000556959493223985 0.000916705048437201;-0.0199575598103408;0.0456231928690862;2.09952637717462;-12.5708704058425;1.11808305811426;-1.72590731777249;-2.22239181008062;-0.967696370445928;-2.62418809422166;2.47964286628144;0.665205752892023;3.64753748704453;-3.84510115530963;-6.08782672045773;3.81508105974837;1.04209904973991;0.0666012719936656;-0.390545453668809;8.28224925531311;-9.55133250134922;-2.37499239179248;-12.8127653858411;-16.846761946123;6.48662354975264;-6.67117082062383;0.0580151981289049;-0.770098855873447;-0.983876895688683;0.0583162347158579;-5.93738717724506;-0.203431522818505;-1.03087538746314 147.112804035741;303.21392125011;499.33507018564;614.360746132308;743.413974455831;842.472101057517;929.506675663573;1076.57587791081;1147.61170966489;1262.6408555643;1333.67134891635;1448.700635293;1634.77494902759;1721.81956091078;1923.88362405243;2038.89107627957;2095.9181343836;2166.95728800359;2237.99542015244;2380.04906152953;2220.00518543488;130.0865640237;2078.92040615582;817.907873297785;918.917619246831;1155.02717356753;157.097144992378;185.0922112678;256.129434516133;327.166277224995;398.205774393759;469.240619338034;540.278194626993 33 0.574496146107112 0.14410480349345 None Unknown 148.951235201399;7.71201258444522;7.36039532447559 AAAAAAAGDSDSWDADAFSVEDPVRK;PSRQESELMWQWVDQRSDGER;HTLTSFWNFKAGCEEKCYSNR _(Acetyl (Protein_N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_;_PSRQESELM(Oxidation (M))WQWVDQRSDGER_;_HTLTSFWNFKAGCEEKCYSNR_ 2 625 1 1 2 """) + 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 107307 98306 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 Acetyl (Protein N-term) _(Acetyl (Protein N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_ 1 0 sp|O75822|EIF3J_HUMAN 3 HCD FTMS MULTI-MSMS 10 2 879.06841 2634.1834 -0.93926 -0.00082567 -3.2012471 90.978 2.1945E-12 148.95 141.24 NaN NaN 1 0 0 0 107297 10193939 0.267970762043589 -8 0.10211181640625 y1;y2;y4;y5;y6;y7;y8;y9;y10;y11;y12;y13;y14;y15;y17;y18;y19;y20;y21;y23;y21-H2O;y1-NH3;y19-NH3;y14(2+);y16(2+);y22(2+);a2;b2;b3;b4;b5;b6;b7 300000;200000;3000000;600000;1000000;500000;2000000;1000000;1000000;1000000;90000;1000000;400000;900000;1000000;400000;3000000;2000000;1000000;400000;100000;200000;200000;80000;100000;200000;200000;2000000;5000000;5000000;5000000;2000000;300000 1.34859050149316E-07;-6.05140996867704E-06;2.27812602133781E-05;0.00128986659160546;-0.00934536073077652;0.000941953783126337;-0.00160424237344614;-0.00239257341399934;-0.00111053968612396;-0.00331340710044969;0.00330702864630439;0.000963683996815234;0.00596290290945944;-0.00662057038289277;-0.0117122701335575;0.00777853472800416;0.0021841542961738;0.000144322111736983;-0.00087403893667215;0.0197121595674616;-0.021204007680808;-0.000308954599830713;-0.026636719419912;-0.0137790992353075;0.00596067266928912;-0.0077053835773313;9.11402199221811E-06;-0.000142539300128419;-0.000251999832926231;1.90791054137662E-05;-0.00236430185879044;-9.54583337602344E-05;-0.000556959493223985 0.000916705048437201;-0.0199575598103408;0.0456231928690862;2.09952637717462;-12.5708704058425;1.11808305811426;-1.72590731777249;-2.22239181008062;-0.967696370445928;-2.62418809422166;2.47964286628144;0.665205752892023;3.64753748704453;-3.84510115530963;-6.08782672045773;3.81508105974837;1.04209904973991;0.0666012719936656;-0.390545453668809;8.28224925531311;-9.55133250134922;-2.37499239179248;-12.8127653858411;-16.846761946123;6.48662354975264;-6.67117082062383;0.0580151981289049;-0.770098855873447;-0.983876895688683;0.0583162347158579;-5.93738717724506;-0.203431522818505;-1.03087538746314 147.112804035741;303.21392125011;499.33507018564;614.360746132308;743.413974455831;842.472101057517;929.506675663573;1076.57587791081;1147.61170966489;1262.6408555643;1333.67134891635;1448.700635293;1634.77494902759;1721.81956091078;1923.88362405243;2038.89107627957;2095.9181343836;2166.95728800359;2237.99542015244;2380.04906152953;2220.00518543488;130.0865640237;2078.92040615582;817.907873297785;918.917619246831;1155.02717356753;157.097144992378;185.0922112678;256.129434516133;327.166277224995;398.205774393759;469.240619338034;540.278194626993 33 0.574496146107112 0.14410480349345 None Unknown 148.951235201399;7.71201258444522;7.36039532447559 AAAAAAAGDSDSWDADAFSVEDPVRK;PSRQESELMWQWVDQRSDGER;HTLTSFWNFKAGCEEKCYSNR _(Acetyl (Protein N-term))AAAAAAAGDSDSWDADAFSVEDPVRK_;_PSRQESELM(Oxidation (M))WQWVDQRSDGER_;_HTLTSFWNFKAGCEEKCYSNR_ 2 625 1 1 2 """) reader = MaxQuantReader() reader.import_file(input_data) @@ -112,9 +112,9 @@ def test_spectronaut_reader() -> None: 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_100ug_test_S4-A1_1_25843 2 _ALVAT[+80]PGK_ True _ALVAT[Phospho (STY)]PGK_ ALVATPGK -5.032703 0.758 -5.032703 P19338 False _ALVAT[+80]PGK_ _ALVAT[Phospho (STY)]PGK_ 418.717511324722 0 10352 H3PO4 4 y 1 384.224142529733 26.31595 False sp P19338 P19338 NUCL_HUMAN Nucleolin Homo sapiens NCL 1 3 MCT_human_UP000005640_9606 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_100ug_test_S4-A1_1_25843 2 _TLT[+80]PCPLR_ True _TLT[Phospho (STY)]PC[Carbamidomethyl (C)]PLR_ TLTPCPLR 27.71659 0.818 27.71659 Q5T200 False _TLT[+80]PPLR_ _TLT[Phospho (STY)]PPLR_ 439.230785875227 0.000138389150379226 23117 noloss 3 b 1 396.153027901512 6.3264 False sp Q5T200 Q5T200 ZC3HD_HUMAN Zinc finger CCCH domain-containing protein 13 Homo sapiens ZC3H13 1 1 MCT_human_UP000005640_9606 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_100ug_test_S4-A1_1_25843 2 _TLT[+80]PCPLR_ True _TLT[Phospho (STY)]PC[Carbamidomethyl (C)]PLR_ TLTPCPLR 27.71659 0.818 27.71659 Q5T200 False _TLT[+80]PPLR_ _TLT[Phospho (STY)]PPLR_ 439.230785875227 0.000138389150379226 23117 noloss 3 y 1 385.255780000092 29.70625 False sp Q5T200 Q5T200 ZC3HD_HUMAN Zinc finger CCCH domain-containing protein 13 Homo sapiens ZC3H13 1 1 MCT_human_UP000005640_9606 - 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867 2 _LFVT[+80]PPEGSSR_ True _[Acetyl (Protein_N-term)]LFVS[Phospho (STY)]PPEGSSR_ LFVSPPEGSSR 38.05031 0.917 38.05031 Q14244;Q14244-6;Q14244-7 False _LFVT[+80]PPEGSSR_ _LFVT[Phospho (STY)]PPEGSSR_ 635.297385373987 0 14164 H3PO4 4 b 1 443.265279065723 12.24525 False sp Q14244;Q14244-6;Q14244-7 Q14244;Q14244-6;Q14244-7 MAP7_HUMAN Ensconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin Homo sapiens MAP7 1;; 1;; MCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional - 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867 2 _LFVT[+80]PPEGSSR_ True _[Acetyl (Protein_N-term)]LFVS[Phospho (STY)]PPEGSSR_ LFVSPPEGSSR 38.05031 0.917 38.05031 Q14244;Q14244-6;Q14244-7 False _LFVT[+80]PPEGSSR_ _LFVT[Phospho (STY)]PPEGSSR_ 635.297385373987 0 14164 noloss 6 y 1 632.299829640042 46.07855 False sp Q14244;Q14244-6;Q14244-7 Q14244;Q14244-6;Q14244-7 MAP7_HUMAN Ensconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin Homo sapiens MAP7 1;; 1;; MCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional - 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867 2 _LFVT[+80]PPEGSSR_ True _[Acetyl (Protein_N-term)]LFVS[Phospho (STY)]PPEGSSR_ LFVSPPEGSSR 38.05031 0.917 38.05031 Q14244;Q14244-6;Q14244-7 False _LFVT[+80]PPEGSSR_ _LFVT[Phospho (STY)]PPEGSSR_ 635.297385373987 0 14164 noloss 7 y 1 729.352593488892 100 False sp Q14244;Q14244-6;Q14244-7 Q14244;Q14244-6;Q14244-7 MAP7_HUMAN Ensconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin Homo sapiens MAP7 1;; 1;; MCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional + 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867 2 _LFVT[+80]PPEGSSR_ True _[Acetyl (Protein N-term)]LFVS[Phospho (STY)]PPEGSSR_ LFVSPPEGSSR 38.05031 0.917 38.05031 Q14244;Q14244-6;Q14244-7 False _LFVT[+80]PPEGSSR_ _LFVT[Phospho (STY)]PPEGSSR_ 635.297385373987 0 14164 H3PO4 4 b 1 443.265279065723 12.24525 False sp Q14244;Q14244-6;Q14244-7 Q14244;Q14244-6;Q14244-7 MAP7_HUMAN Ensconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin Homo sapiens MAP7 1;; 1;; MCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional + 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867 2 _LFVT[+80]PPEGSSR_ True _[Acetyl (Protein N-term)]LFVS[Phospho (STY)]PPEGSSR_ LFVSPPEGSSR 38.05031 0.917 38.05031 Q14244;Q14244-6;Q14244-7 False _LFVT[+80]PPEGSSR_ _LFVT[Phospho (STY)]PPEGSSR_ 635.297385373987 0 14164 noloss 6 y 1 632.299829640042 46.07855 False sp Q14244;Q14244-6;Q14244-7 Q14244;Q14244-6;Q14244-7 MAP7_HUMAN Ensconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin Homo sapiens MAP7 1;; 1;; MCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional + 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phospho_library25_S4-C1_1_25867 2 _LFVT[+80]PPEGSSR_ True _[Acetyl (Protein N-term)]LFVS[Phospho (STY)]PPEGSSR_ LFVSPPEGSSR 38.05031 0.917 38.05031 Q14244;Q14244-6;Q14244-7 False _LFVT[+80]PPEGSSR_ _LFVT[Phospho (STY)]PPEGSSR_ 635.297385373987 0 14164 noloss 7 y 1 729.352593488892 100 False sp Q14244;Q14244-6;Q14244-7 Q14244;Q14244-6;Q14244-7 MAP7_HUMAN Ensconsin;Isoform of Q14244, Isoform 6 of Ensconsin;Isoform of Q14244, Isoform 7 of Ensconsin Homo sapiens MAP7 1;; 1;; MCT_human_UP000005640_9606;MCT_human2_UP000005640_9606_additional;MCT_human2_UP000005640_9606_additional """) reader = SpectronautReader()