PSM readers#
[1]:
%reload_ext autoreload
%autoreload 2
[2]:
from alphabase.io.psm_reader import psm_reader_provider
alphabase.io.psm_reader.psm_reader_provider has registered some basic reader classes for the following search engine results:
[3]:
psm_reader_provider.reader_dict
[3]:
{'alphapept': alphabase.psm_reader.alphapept_reader.AlphaPeptReader,
'maxquant': alphabase.psm_reader.maxquant_reader.MaxQuantReader,
'spectronaut': alphabase.psm_reader.dia_psm_reader.SpectronautReader,
'openswath': alphabase.psm_reader.dia_psm_reader.SwathReader,
'swath': alphabase.psm_reader.dia_psm_reader.SwathReader,
'diann': alphabase.psm_reader.dia_psm_reader.DiannReader,
'spectronaut_report': alphabase.psm_reader.dia_psm_reader.SpectronautReportReader,
'pfind': alphabase.psm_reader.pfind_reader.pFindReader,
'msfragger_psm_tsv': alphabase.psm_reader.msfragger_reader.MSFragger_PSM_TSV_Reader,
'msfragger': alphabase.psm_reader.msfragger_reader.MSFragger_PSM_TSV_Reader,
'msfragger_pepxml': alphabase.psm_reader.msfragger_reader.MSFraggerPepXML}
We can then use psm_reader_provider.get_reader to get a reader and then import_file.
MaxQaunt msms.txt:
[4]:
import io
import numpy as np
msms_txt = 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 '''
)
mq_reader = psm_reader_provider.get_reader('maxquant')
mq_reader.import_file(msms_txt)
[4]:
| sequence | charge | rt | scan_num | raw_name | precursor_mz | score | proteins | decoy | spec_idx | mods | mod_sites | nAA | rt_norm | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | AAAAAAAGDSDSWDADAFSVEDPVRK | 3 | 90.978 | 107307 | 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 | 879.06841 | 148.950 | sp|O75822|EIF3J_HUMAN | 0 | 107306 | Acetyl@Protein N-term | 0 | 26 | 1.000000 |
| 1 | AAAAAAAAAPAAAATAPTTAATTAATAAQ | 3 | 70.261 | 81358 | 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 | 790.07495 | 41.423 | sp|P37108|SRP14_HUMAN | 0 | 81357 | Acetyl@Protein N-term;Oxidation@M | 0;9 | 29 | 0.772286 |
| 2 | AAAAAAAAAAPAAAATAPTTAATTAATAAQ | 2 | 70.287 | 81391 | 20190402_QX1_SeVW_MA_HeLa_500ng_LC11 | 1184.60880 | 118.210 | sp|P37108|SRP14_HUMAN | 0 | 81390 | 30 | 0.772571 |
pFind pfind.spectra file at 1% FDR by default:
[5]:
from io import StringIO
txt = StringIO("""File_Name Scan_No Exp.MH+ Charge Q-value Sequence Calc.MH+ Mass_Shift(Exp.-Calc.) Raw_Score Final_Score Modification Specificity Proteins Positions Label Target/Decoy Miss.Clv.Sites Avg.Frag.Mass.Shift Others
Ecoli-1to1to1-un-C13-N15-10mM-20150823.30507.30507.2.0.dta 30507 2074.030369 2 0 AMIEAGAAAVHFEDQLASVK 2074.027271 0.003098 35.299588 5.15726e-013 2,Oxidation[M]; 3 gi|16131841|ref|NP_418439.1|/ 173,K,K/ 1|0| target 0 0.948977 131070 0 0 0 262143 0 0 0 32
Ecoli-1to1to1-un-C13-N15-150mM-20150823.41501.41501.3.0.dta 41501 2712.197421 3 0 EGDNYVVLSDILGDEDHLGDMDFK 2712.198013 -0.000592 27.073978 9.82619e-010 21,Unknown[M]; 3 gi|145698316|ref|NP_417633.4|/ 470,K,V/ 1|0| target 0 0.814438 65596 0 0 0 4194288 0 0 0 36
XXX.25802.25802.4.0.dta 25802 2388.339186 4 0.0032066 SVFLIKGDKVWVYPPEKKEK 2388.332468 0.006718 17.822784 0.100787 21,Didehydro[AnyC-termK]; 0 sp|P02790|HEMO_HUMAN/ 106,N,G/ 1|0| target 0 0.704714 36
""")
psm_reader_provider.get_reader('pfind').import_file(txt)
/Users/zengwenfeng/opt/anaconda3/lib/python3.8/site-packages/pandas/util/_decorators.py:311: ParserWarning: Length of header or names does not match length of data. This leads to a loss of data with index_col=False.
return func(*args, **kwargs)
[5]:
| sequence | charge | raw_name | query_id | scan_num | score | proteins | uniprot_ids | fdr | decoy | spec_idx | mods | mod_sites | nAA | precursor_mz | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | AMIEAGAAAVHFEDQLASVK | 2 | Ecoli-1to1to1-un-C13-N15-10mM-20150823 | Ecoli-1to1to1-un-C13-N15-10mM-20150823.30507.3... | 30507 | 28.293201 | gi|16131841|ref|NP_418439.1| | gi|16131841|ref|NP_418439.1| | 0.000000 | 0 | 30506 | Oxidation@M | 2 | 20 | 1037.517322 |
| 1 | SVFLIKGDKVWVYPPEKKEK | 4 | XXX | XXX.25802.25802.4.0.dta | 25802 | 2.294746 | sp|P02790|HEMO_HUMAN | sp|P02790|HEMO_HUMAN | 0.003207 | 0 | 25801 | Didehydro@K^Any C-term | -1 | 20 | 597.838602 |
Diann TSV report:
[6]:
from io import StringIO
tsv = StringIO('''File.Name Run Protein.Group Protein.Ids Protein.Names Genes PG.Quantity PG.Normalised PG.MaxLFQ Genes.Quantity Genes.Normalised Genes.MaxLFQ Genes.MaxLFQ.Unique Modified.Sequence Stripped.Sequence Precursor.Id Precursor.Charge Q.Value Global.Q.Value Protein.Q.Value PG.Q.Value Global.PG.Q.Value GG.Q.Value Translated.Q.Value Proteotypic Precursor.Quantity Precursor.Normalised Precursor.Translated Quantity.Quality RT RT.Start RT.Stop iRT Predicted.RT Predicted.iRT Lib.Q.Value Ms1.Profile.Corr Ms1.Area Evidence Spectrum.Similarity Mass.Evidence CScore Decoy.Evidence Decoy.CScore Fragment.Quant.Raw Fragment.Quant.Corrected Fragment.Correlations MS2.Scan IM iIM Predicted.IM Predicted.iIM
F:\XXX\20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-A2_1_22636.d 20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-A2_1_22636 Q9UH36 Q9UH36 SRRD 3296.49 3428.89 3428.89 3296.49 3428.89 3428.89 3428.89 (UniMod:1)AAAAAAALESWQAAAPR AAAAAAALESWQAAAPR (UniMod:1)AAAAAAALESWQAAAPR2 2 3.99074e-05 1.96448e-05 0.000159821 0.000159821 0.000146135 0.000161212 0 1 3296.49 3428.89 3296.49 0.852479 19.9208 19.8731 19.9685 123.9 19.8266 128.292 0 0.960106 5308.05 1.96902 0.683134 0.362287 0.999997 1.23691 3.43242e-05 1212.01;2178.03;1390.01;1020.01;714.008;778.008; 1212.01;1351.73;887.591;432.92;216.728;732.751; 0.956668;0.757581;0.670497;0.592489;0.47072;0.855203; 30053 1.19708 1.19328 1.19453 1.19469
F:\XXX\20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-A8_1_22642.d 20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-A8_1_22642 Q9UH36 Q9UH36 SRRD 2365 2334.05 2334.05 2365 2334.05 2334.05 2334.05 (UniMod:1)AAAAAAALESWQAAAPR AAAAAAALESWQAAAPR (UniMod:1)AAAAAAALESWQAAAPR2 2 0.000184434 1.96448e-05 0.000596659 0.000596659 0.000146135 0.000604961 0 1 2365 2334.05 2365 0.922581 19.905 19.8573 19.9527 123.9 19.782 128.535 0 0.940191 4594.04 1.31068 0.758988 0 0.995505 0.28633 2.12584e-06 1209.02;1210.02;1414.02;1051.01;236.003;130.002; 1209.02;1109.89;732.154;735.384;0;46.0967; 0.919244;0.937624;0.436748;0.639369;0.296736;0.647924; 30029 1.195 1.19328 1.19381 1.19339
F:\XXX\20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-B2_1_22648.d 20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-B2_1_22648 Q9UH36 Q9UH36 SRRD 1664.51 1635.46 1635.47 1664.51 1635.46 1635.47 1635.47 (UniMod:1)AAAAAAALESWQAAAPR AAAAAAALESWQAAAPR (UniMod:1)AAAAAAALESWQAAAPR2 2 0.000185123 1.96448e-05 0.000307409 0.000307409 0.000146135 0.000311332 0 1 1664.51 1635.46 1664.51 0.811147 19.8893 19.8416 19.937 123.9 19.7567 128.896 0 0.458773 6614.06 1.7503 0.491071 0.00111683 0.997286 1.92753 2.80543e-05 744.01;1708.02;1630.02;1475.02;0;533.006; 322.907;808.594;577.15;536.033;0;533.006; 0.760181;0.764072;0.542005;0.415779;0;0.913438; 30005 1.19409 1.19328 1.19323 1.19308
''')
psm_reader_provider.get_reader('diann').import_file(tsv)
[6]:
| raw_name | sequence | charge | rt | mobility | proteins | uniprot_ids | genes | scan_num | score | fdr | spec_idx | mods | mod_sites | nAA | rt_norm | precursor_mz | ccs | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_sp... | AAAAAAALESWQAAAPR | 2 | 19.9208 | 1.19708 | NaN | Q9UH36 | SRRD | 30053 | 0.999997 | 0.000040 | 30052 | Acetyl@Any N-term | 0 | 17 | 1.0 | 834.428635 | 483.435307 |
| 1 | 20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_sp... | AAAAAAALESWQAAAPR | 2 | 19.9050 | 1.19500 | NaN | Q9UH36 | SRRD | 30029 | 0.995505 | 0.000184 | 30028 | Acetyl@Any N-term | 0 | 17 | 1.0 | 834.428635 | 482.595308 |
| 2 | 20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_sp... | AAAAAAALESWQAAAPR | 2 | 19.8893 | 1.19409 | NaN | Q9UH36 | SRRD | 30005 | 0.997286 | 0.000185 | 30004 | Acetyl@Any N-term | 0 | 17 | 1.0 | 834.428635 | 482.227809 |
Note that, to support both Bruker and Thermo data, we did not use Scan Number in the output dataframe but spec_idx (starts with 0). spec_idx = scan_num - 1 in thermo data.
We can also read spectronaut/openswath’s TSV library with out fragment information.
Spectronaut’s output library:
[7]:
from io import StringIO
tsv = StringIO('''ReferenceRun PrecursorCharge Workflow IntModifiedPeptide CV AllowForNormalization ModifiedPeptide StrippedPeptide iRT IonMobility iRTSourceSpecific BGSInferenceId IsProteotypic IntLabeledPeptide LabeledPeptide PrecursorMz ReferenceRunQvalue ReferenceRunMS1Response FragmentLossType FragmentNumber FragmentType FragmentCharge FragmentMz RelativeIntensity ExcludeFromAssay Database ProteinGroups UniProtIds Protein Name ProteinDescription Organisms OrganismId Genes Protein Existence Sequence Version FASTAName
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 noloss 3 y 1 301.187031733932 53.1991 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 _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
''')
psm_reader_provider.get_reader('spectronaut').import_file(tsv)
[7]:
| raw_name | sequence | charge | rt | precursor_mz | mobility | proteins | uniprot_ids | genes | mods | mod_sites | nAA | rt_norm | ccs | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phosph... | ALVATPGK | 2 | -5.032703 | 418.717511 | 0.758 | NUCL_HUMAN | P19338 | NCL | Phospho@T | 5 | 8 | 0.0 | 308.612143 |
| 1 | 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phosph... | TLTPCPLR | 2 | 27.716590 | 439.230786 | 0.818 | ZC3HD_HUMAN | Q5T200 | ZC3H13 | Phospho@T;Carbamidomethyl@C | 3;5 | 8 | 1.0 | 332.788837 |
| 2 | 202106018_TIMS03_EVO03_PaSk_SA_HeLa_EGF_Phosph... | LFVSPPEGSSR | 2 | 38.050310 | 635.297385 | 0.917 | MAP7_HUMAN | Q14244;Q14244-6;Q14244-7 | MAP7 | Acetyl@Protein N-term;Phospho@S | 0;4 | 11 | 1.0 | 371.282739 |
OpenSWATH’s library:
[8]:
from io import StringIO
tsv = StringIO('''PrecursorMz ProductMz Tr_recalibrated transition_name CE LibraryIntensity transition_group_id decoy PeptideSequence ProteinName Annotation FullUniModPeptideName PrecursorCharge GroupLabel UniprotID FragmentType FragmentCharge FragmentSeriesNumber
685.732240417 886.020494795 59.0 255_AAAAAAAAAASGAAIPPLIPPRR_3 -1 5257.9 13_AAAAAAAAAASGAAIPPLIPPRR_3 0 AAAAAAAAAASGAAIPPLIPPRR 1/O14654 y19^2/0.002 AAAAAAAAAASGAAIPPLIPPRR 3 light 1/O14654 y 2 19
514.550999438 473.303261576 59.2 268_AAAAAAAAAASGAAIPPLIPPRR_4 -1 10000.0 14_AAAAAAAAAASGAAIPPLIPPRR_4 0 AAAAAAAAAASGAAIPPLIPPRR 1/O14654 y8^2/0.002 AAAAAAAAAASGAAIPPLIPPRR 4 light 1/O14654 y 2 8
514.550999438 629.39313922 59.2 276_AAAAAAAAAASGAAIPPLIPPRR_4 -1 5923.1 14_AAAAAAAAAASGAAIPPLIPPRR_4 0 AAAAAAAAAASGAAIPPLIPPRR 1/O14654 y12^2/0.001 AAAAAAAAAASGAAIPPLIPPRR 4 light 1/O14654 y 2 12
514.550999438 672.909153425 59.2 279_AAAAAAAAAASGAAIPPLIPPRR_4 -1 5249.8 14_AAAAAAAAAASGAAIPPLIPPRR_4 0 AAAAAAAAAASGAAIPPLIPPRR 1/O14654 y13^2/0.001 AAAAAAAAAASGAAIPPLIPPRR 4 light 1/O14654 y 2 13
514.550999438 356.19284545 59.2 262_AAAAAAAAAASGAAIPPLIPPRR_4 -1 5233.6 14_AAAAAAAAAASGAAIPPLIPPRR_4 0 AAAAAAAAAASGAAIPPLIPPRR 1/O14654 b5/0.001,b10^2/0.001,m6:10/0.001 AAAAAAAAAASGAAIPPLIPPRR 4 light 1/O14654 b 1 5
514.550999438 498.26707303 59.2 269_AAAAAAAAAASGAAIPPLIPPRR_4 -1 4976.0 14_AAAAAAAAAASGAAIPPLIPPRR_4 0 AAAAAAAAAASGAAIPPLIPPRR 1/O14654 b7/0.001,m4:10/0.001 AAAAAAAAAASGAAIPPLIPPRR 4 light 1/O14654 b 1 7
514.550999438 427.22995924 59.2 265_AAAAAAAAAASGAAIPPLIPPRR_4 -1 4859.4 14_AAAAAAAAAASGAAIPPLIPPRR_4 0 AAAAAAAAAASGAAIPPLIPPRR 1/O14654 b6/0.002,m5:10/0.002 AAAAAAAAAASGAAIPPLIPPRR 4 light 1/O14654 b 1 6
728.201724416 356.19284545 101.8 292_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 -1 10000.0 15_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 0 AAAAAAAAAASGAAIPPLIPPRRVITLYQCFSVSQR 1/O14654 b5/0.003,b10^2/0.003,m6:10/0.003 AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR 5 light 1/O14654 b 1 5
728.201724416 576.310000482 101.8 297_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 -1 7611.0 15_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 0 AAAAAAAAAASGAAIPPLIPPRRVITLYQCFSVSQR 1/O14654 y5/0.002 AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR 5 light 1/O14654 y 1 5
728.201724416 427.22995924 101.8 293_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 -1 6805.1 15_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 0 AAAAAAAAAASGAAIPPLIPPRRVITLYQCFSVSQR 1/O14654 b6/-0.002,m5:10/-0.002 AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR 5 light 1/O14654 b 1 6
728.201724416 569.30418682 101.8 296_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 -1 6312.7 15_AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR_5 0 AAAAAAAAAASGAAIPPLIPPRRVITLYQCFSVSQR 1/O14654 b8/0.009,m3:10/0.009 AAAAAAAAAASGAAIPPLIPPRRVITLYQC(UniMod:4)FSVSQR 5 light 1/O14654 b 1 8
''')
osw_reader = psm_reader_provider.get_reader('openswath')
osw_reader.import_file(tsv)
osw_reader.psm_df
[8]:
| sequence | charge | rt | precursor_mz | proteins | mods | mod_sites | nAA | rt_norm | |
|---|---|---|---|---|---|---|---|---|---|
| 0 | AAAAAAAAAASGAAIPPLIPPRR | 3 | 59.0 | 685.732240 | 1/O14654 | 23 | 0.579568 | ||
| 1 | AAAAAAAAAASGAAIPPLIPPRR | 4 | 59.2 | 514.550999 | 1/O14654 | 23 | 0.581532 | ||
| 2 | AAAAAAAAAASGAAIPPLIPPRRVITLYQCFSVSQR | 5 | 101.8 | 728.201724 | 1/O14654 | Carbamidomethyl@C | 30 | 36 | 1.000000 |
Spectronaut report:
[9]:
tsv = StringIO('''R.FileName,R.Replicate,EG.PrecursorId,EG.ApexRT,FG.CalibratedMassAccuracy (PPM),FG.CalibratedMz
20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01,1,_VIETPENDFK_.2,40.826847076416,-0.6350307649846,596.298998773218
20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01,1,_GFSNEVSSK_.2,19.1254806518555,-1.54873822486555,477.730400257423
20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01,1,_HLLNQAVGEEEVPK_.3,42.0593299865723,-0.309173676987587,521.611288926824
20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01,1,_DATM[Oxidation (M)]EVQR_.2,12.8398199081421,-3.31103772642203,483.222124398527
''')
spn_reader = psm_reader_provider.get_reader('spectronaut_report')
spn_reader.import_file(tsv)
spn_reader.psm_df
[9]:
| raw_name | rt | charge | mods | mod_sites | sequence | nAA | rt_norm | precursor_mz | |
|---|---|---|---|---|---|---|---|---|---|
| 0 | 20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01 | 12.839820 | 2 | Oxidation@M | 4 | DATMEVQR | 8 | 0.305279 | 483.221474 |
| 1 | 20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01 | 19.125481 | 2 | GFSNEVSSK | 9 | 0.454726 | 477.729989 | ||
| 2 | 20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01 | 40.826847 | 2 | VIETPENDFK | 10 | 0.970697 | 596.298236 | ||
| 3 | 20211203_EXPL2_SoSt_SA_DIA_HeLa_1000mz_noCB_01 | 42.059330 | 3 | HLLNQAVGEEEVPK | 14 | 1.000000 | 521.610617 |
[ ]: