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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef commit d4b6dd6bf42d2e8faa335bcd77b681938e56a9e4" |
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added:
diapysef.xml test-data/evidence_cut.tabular test-data/irtassays.tabular test-data/msms_cut.tabular test-data/rtcalibration1.pdf test-data/rtcalibration2.pdf |
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| diff -r 000000000000 -r 8eed818f5d48 diapysef.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diapysef.xml Fri Mar 06 07:16:26 2020 -0500 |
| [ |
| @@ -0,0 +1,111 @@ +<tool id="diapysef" name="diapysef library generation" version="0.3.5.0"> + <description>generates spectral library for DIA analysis</description> + <requirements> + <requirement type="package" version="0.3.5">diapysef</requirement> + <requirement type="package" version="1.0.1">pandas</requirement> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + + python '${diapysef_script}' + + ]]> + </command> + <configfiles> + <configfile name="diapysef_script"><![CDATA[ + +import diapysef as dp +import pandas as pd + +msms = pd.read_csv("$input_msms", sep="\t") +evidence = pd.read_csv("$input_evidence", sep="\t") +irt = pd.read_csv("$input_irtassays", sep="\t") +ptsv = dp.pasef_to_tsv(evidence, msms, irt_file=irt, ion_mobility=None, rt_alignment="$alignment") +ptsv.to_csv("$output_tabular", sep="\t", index=False) + + + ]]></configfile> + </configfiles> + <inputs> + <param name="input_msms" type="data" format="tabular" label="MaxQuant output file msms.txt" help="" /> + <param name="input_evidence" type="data" format="tabular" label="MaxQuant output file evidence.txt" help="" /> + <param name="input_irtassays" type="data" format="tabular" label="Retention time alignment peptides" help="tabular file containing peptides for the alignment, e.g. iRTs or ciRTs" /> + <param name="alignment" type="select" display="radio" label="RT alignment method" help="" > + <option value="linear" selected="True">linear</option> + <option value="nonlinear">lowess</option> + </param> + </inputs> + <outputs> + <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: spectral library" from_work_dir="mqout.tabular" /> + <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: RT calibration curves" from_work_dir="rtcalibration.pdf" /> + </outputs> + <tests> + <test> + <param name="input_msms" value="msms_cut.tabular" ftype="tabular" /> + <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" /> + <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" /> + <param name="alignment" value="linear" /> + <output name="output_pdf" file="rtcalibration1.pdf" compare="sim_size"/> + </test> + <test> + <param name="input_msms" value="msms_cut.tabular" ftype="tabular" /> + <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" /> + <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" /> + <param name="alignment" value="nonlinear" /> + <output name="output_pdf" file="rtcalibration2.pdf" compare="sim_size"/> + </test> + <test> + <param name="input_msms" value="msms_cut.tabular" ftype="tabular" /> + <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" /> + <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" /> + <param name="alignment" value="nonlinear" /> + <output name="output_tabular" > + <assert_contents> + <has_text text="transition_group_id" /> + <has_text text="LibraryIntensity" /> + <has_text text="(Acetylation)DGLDAASYYAPVR" /> + <has_text text="sp|Biognosys_pep-h|iRT-Kit_WR_fusion" /> + <has_text text="sp|Biognosys_pep-k|iRT-Kit_WR_fusion" /> + <has_n_columns n="11" /> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ + + +Diapysef enables generating a DIA library. For more information: http://openswath.org/en/latest/docs/librarygeneration.html + +For most data-independent acquisition (DIA) analysis, a well-represented spectral library is required for precursors, peptide, and protein identifications. Currently, we support library generation with the diapysef package directly from a MaxQuant analysis of several DDA runs. + +**Inputs** + + - msms.txt and evidence.txt (output files from MaxQuant) + - peptides used for retention time alignment e.g. iRTs or ciRTs + + - Tabular file with at least three columns for precursor charge, normalized retention time and modified peptide sequence + - The headers of the columns must be named "PrecursorCharge" "NormalizedRetentionTime" "ModifiedPeptideSequence" + + + :: + + PrecursorCharge NormalizedRetentionTime ModifiedPeptideSequence + 2 53.2 ADVTPADFSEWSK + 3 52.9 ADVTPADFSEWSK + 2 43.6 DGLDAASYYAPVR + ... + ... + + +**Potential next Steps** + +After generating the spectral library with diapysef, the tabular file can be imported into OpenSwathAssayGenerator and OpenSwathDecoyGenerator to refine the library. + + +]]> + </help> + <citations> + <citation type="doi">10.1038/nbt.2841</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 8eed818f5d48 test-data/evidence_cut.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evidence_cut.tabular Fri Mar 06 07:16:26 2020 -0500 |
| [ |
| b'@@ -0,0 +1,253 @@\n+Sequence\tLength\tModifications\tModified sequence\tOxidation (M) Probabilities\tOxidation (M) Score Diffs\tAcetyl (Protein N-term)\tOxidation (M)\tMissed cleavages\tProteins\tLeading proteins\tLeading razor protein\tType\tRaw file\tExperiment\tMS/MS m/z\tCharge\tm/z\tMass\tResolution\tUncalibrated - Calibrated m/z [ppm]\tUncalibrated - Calibrated m/z [Da]\tMass error [ppm]\tMass error [Da]\tUncalibrated mass error [ppm]\tUncalibrated mass error [Da]\tMax intensity m/z 0\tRetention time\tRetention length\tCalibrated retention time\tCalibrated retention time start\tCalibrated retention time finish\tRetention time calibration\tMatch time difference\tMatch m/z difference\tMatch q-value\tMatch score\tNumber of data points\tNumber of scans\tNumber of isotopic peaks\tPIF\tFraction of total spectrum\tBase peak fraction\tPEP\tMS/MS count\tMS/MS scan number\tScore\tDelta score\tCombinatorics\tIntensity\tReporter PIF\tReporter fraction\tReverse\tPotential contaminant\tid\tProtein group IDs\tPeptide ID\tMod. peptide ID\tMS/MS IDs\tBest MS/MS\tOxidation (M) site IDs\n+ADVTPADFSEWSK\t13\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN11\t11\t726.835815429688\t2\t726.835714\t1451.65687\t40804.6628538042\t0.47975\t0.0003487\t-0.42588\t-0.00030955\t0.053864\t3.9151E-05\t726.835759737833\t36.159\t1.7086\t36.159\t35.604\t37.313\t0\t\t\t\t\t330\t80\t6\t0\t0\t0\t4.8078E-17\t3\t16235\t136.48\t125.32\t1\t495900000\t\t\t\t\t2316\t81\t275\t290\t1661;1662;1663\t1662\t\n+ADVTPADFSEWSK\t13\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN12\t12\t726.835754394531\t2\t726.835714\t1451.65687\t40733.5039557695\t0.28206\t0.00020501\t-0.326\t-0.00023695\t-0.043932\t-3.1931E-05\t726.835855182069\t36.158\t1.8394\t36.111\t35.499\t37.338\t-0.047638\t\t\t\t\t315\t84\t6\t0\t0\t0\t2.3068E-25\t3\t15525\t150.94\t138.31\t1\t489410000\t\t\t\t\t2317\t81\t275\t290\t1664;1665;1666\t1665\t\n+ADVTPADFSEWSK\t13\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN12\t12\t484.893768310547\t3\t484.892901\t1451.65687\t51095.7993548774\t0.71313\t0.00034579\t-0.18584\t-9.0112E-05\t0.52729\t0.00025568\t484.892685329051\t36.134\t0.50261\t36.086\t35.82\t36.322\t-0.047638\t\t\t\t\t47\t21\t4\t0\t0\t0\t0.010643\t1\t15366\t37.594\t27.285\t1\t1296100\t\t\t\t\t2318\t81\t275\t290\t1667\t1667\t\n+ADVTPADFSEWSK\t13\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN13\t13\t726.8359375\t2\t726.835714\t1451.65687\t40891.9643909921\t0.33925\t0.00024658\t-0.27471\t-0.00019967\t0.064533\t4.6905E-05\t726.835958778748\t36.271\t1.7322\t36.121\t35.55\t37.282\t-0.15025\t\t\t\t\t349\t86\t6\t0\t0\t0\t8.4539E-18\t2\t15661\t141.1\t120.31\t1\t465130000\t\t\t\t\t2319\t81\t275\t290\t1668;1669\t1669\t\n+ADVTPADFSEWSK\t13\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN14\t14\t726.835876464844\t2\t726.835714\t1451.65687\t40698.3675005038\t0.24084\t0.00017505\t-0.072029\t-5.2354E-05\t0.16881\t0.0001227\t726.836090026682\t36.259\t1.7324\t36.213\t35.616\t37.348\t-0.046562\t\t\t\t\t315\t80\t6\t0\t0\t0\t2.3068E-25\t3\t16070\t150.94\t135.08\t1\t398680000\t\t\t\t\t2320\t81\t275\t290\t1670;1671;1672\t1671\t\n+ADVTPADFSEWSK\t13\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN15\t15\t484.893768310547\t3\t484.892901\t1451.65687\t51620.3679636657\t0.71267\t0.00034557\t0.05977\t2.8982E-05\t0.77244\t0.00037455\t484.893022251297\t36.108\t0.60837\t36.157\t35.84\t36.448\t0.049464\t\t\t\t\t43\t29\t2\t0\t0\t0\t0.049208\t1\t15764\t24.964\t17.599\t1\t1345800\t\t\t\t\t2321\t81\t275\t290\t1673\t1673\t\n+ADVTPADFSEWSK\t13\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN15\t15\t726.836059570313\t2\t726.835714\t1451.6'..b'N14\t14\t547.297912597656\t2\t547.298039\t1092.58152\t47744.3322318308\t-0.20907\t-0.00011443\t0.037228\t2.0375E-05\t-0.17185\t-9.4051E-05\t547.298373377638\t20.379\t1.7943\t20.233\t19.788\t21.582\t-0.14679\t\t\t\t\t334\t96\t6\t0\t0\t0\t5.7693E-35\t2\t8599\t154.49\t74.892\t1\t304800000\t\t\t\t\t108953\t77\t13025\t13820\t72923;72924\t72924\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN15\t15\t547.298400878906\t2\t547.298039\t1092.58152\t47343.9683044276\t-0.092244\t-5.0485E-05\t0.079071\t4.3275E-05\t-0.013173\t-7.2096E-06\t547.298396398044\t20.235\t1.8749\t20.285\t19.726\t21.601\t0.049464\t\t\t\t\t355\t101\t7\t0\t0\t0\t6.2409E-26\t2\t8574\t143.45\t74.276\t1\t302510000\t\t\t\t\t108954\t77\t13025\t13820\t72925;72926\t72926\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN16\t16\t547.298217773438\t2\t547.298039\t1092.58152\t47032.9045405311\t0.35698\t0.00019537\t-0.33071\t-0.000181\t0.026263\t1.4374E-05\t547.298201028586\t20.093\t1.7931\t20.247\t19.728\t21.521\t0.15318\t\t\t\t\t324\t94\t6\t0\t0\t0\t6.859E-35\t2\t8433\t153.08\t73.486\t1\t340180000\t\t\t\t\t108955\t77\t13025\t13820\t72927;72928\t72928\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN17\t17\t547.297729492188\t2\t547.298039\t1092.58152\t47566.034224311\t0.51044\t0.00027937\t-0.54784\t-0.00029983\t-0.037396\t-2.0467E-05\t547.298038429333\t19.986\t1.7354\t20.239\t19.688\t21.424\t0.25303\t\t\t\t\t310\t81\t6\t0\t0\t0\t4.593E-35\t2\t8398\t156.01\t84.664\t1\t332710000\t\t\t\t\t108956\t77\t13025\t13820\t72929;72930\t72929\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN18\t18\t547.298217773438\t2\t547.298039\t1092.58152\t47645.5183592653\t0.13781\t7.5423E-05\t-0.11558\t-6.3259E-05\t0.022225\t1.2164E-05\t547.298272108074\t19.944\t1.83\t20.195\t19.761\t21.591\t0.25147\t\t\t\t\t355\t98\t7\t0\t0\t0\t6.859E-35\t3\t8456\t153.08\t71.786\t1\t314300000\t\t\t\t\t108957\t77\t13025\t13820\t72931;72932;72933\t72932\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN19\t19\t547.298278808594\t2\t547.298039\t1092.58152\t47298.8822004246\t0.013886\t7.6E-06\t-0.26735\t-0.00014632\t-0.25347\t-0.00013872\t547.298212013411\t19.924\t1.8185\t20.173\t19.759\t21.578\t0.24947\t\t\t\t\t392\t105\t6\t0\t0\t0\t7.8175E-46\t2\t7829\t167.23\t85.932\t1\t389870000\t\t\t\t\t108958\t77\t13025\t13820\t72934;72935\t72935\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN20\t20\t547.298156738281\t2\t547.298039\t1092.58152\t47215.0372254616\t0.27785\t0.00015207\t0.074171\t4.0593E-05\t0.35202\t0.00019266\t547.298613817171\t20.471\t1.1743\t20.521\t20.23\t21.404\t0.049706\t\t\t\t\t201\t52\t7\t0\t0\t0\t1.5856E-13\t2\t9064\t131.41\t73.215\t1\t668250000\t\t\t\t\t108959\t77\t13025\t13820\t72936;72937\t72937\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN20\t20\t365.201293945313\t3\t365.201118\t1092.58152\t57992.1226761732\t-0.36685\t-0.00013397\t0.51881\t0.00018947\t0.15196\t5.5498E-05\t365.201321331941\t20.45\t0.7732\t20.5\t20.252\t21.026\t0.049706\t\t\t\t\t109\t34\t5\t0\t0\t0\t0.00062104\t1\t8833\t76.228\t54.78\t1\t46722000\t\t\t\t\t108960\t77\t13025\t13820\t72938\t72938\t\n+YILAGVENSK\t10\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\tMULTI-MSMS\tTN21\t21\t547.298156738281\t2\t547.298039\t1092.58152\t47209.8484532584\t-0.056133\t-3.0721E-05\t0.076863\t4.2067E-05\t0.020731\t1.1346E-05\t547.298341195888\t19.803\t1.77\t20.159\t19.713\t21.483\t0.35614\t\t\t\t\t303\t85\t6\t0\t0\t0\t6.1583E-58\t3\t8668\t172.21\t90.917\t1\t290740000\t\t\t\t\t108961\t77\t13025\t13820\t72939;72940;72941\t72940\t\n' 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| diff -r 000000000000 -r 8eed818f5d48 test-data/irtassays.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/irtassays.tabular Fri Mar 06 07:16:26 2020 -0500 |
| b |
| b'@@ -0,0 +1,101 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|
| b |
| diff -r 000000000000 -r 8eed818f5d48 test-data/msms_cut.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/msms_cut.tabular Fri Mar 06 07:16:26 2020 -0500 |
| [ |
| b'@@ -0,0 +1,369 @@\n+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+TN11\t15913\t13782\tADVTPADFSEWSK\t13\t0\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\t2\tHCD\tFTMS\tMULTI-MSMS\t4\t0\t726.83571\t1451.6569\t-0.42588\t-0.00030955\t1.0833794\t35.74\t0.00028366\t82.954\t71.734\tNaN\tNaN\t1\t0\t0\t0\t15909\t1431285.875\t0.006457493056897\t-23\t0.526058197021484\ty1;y2;y3;y4;y5;y6;y7;y8;y9;y10;y4-H2O;y9-H2O;y1-NH3;y3-NH3;a2;b2;b3;b4;b3-H2O;b4-H2O\t20000;8000;9000;4000;10000;10000;20000;20000;100000;10000;2000;3000;9000;3000;6000;10000;30000;20000;6000;7000\t0.000407930365611264;0.000835388117167213;-0.000128147640623411;0.0024564036374386;0.00146615665425998;0.00169292552902789;0.00381529430012506;0.0020492618108392;0.00284183287931228;0.00853681531816619;-0.00255408344378338;0.012377371487446;0.000363345467178533;-4.88585936864183E-06;0.0004146359796664;0.000349399681255136;0.00128964555727862;0.000841967538292465;-5.94270594547197E-05;0.000499906415598161\t2.77291632817342;3.56783913824116;-0.30495059102772;4.47217071439823;2.30420064995457;2.16109281669221;4.24681150631667;2.11388499038266;2.66468174633104;7.31190243829585;-4.80760749713636;11.8052753361375;2.79311970240754;-0.0121177788574789;2.60652750362388;1.8677385129204;4.50706825041693;2.17457828788023;-0.221635876131979;1.3541127447335\t147.112396240234;234.143997192383;420.224273681641;549.264282226563;636.297300883446;783.365488030771;898.390308694;969.429188514289;1066.48115979522;1167.52314328688;531.258728027344;1048.46105957031;130.085891723633;403.197601318359;159.07600402832;187.070983886719;286.138457557043;387.186583709162;268.129241943359;369.176361083984\t20\t0.360140418656268\t0.12987012987013\tNone\tUnknown\t\t82.9536308585087;11.2195524895476;10.52345256087\tADVTPADFSEWSK;TEQETAVMERDK;VESCTIETKDDR\t_ADVTPADFSEWSK_;_TEQETAVM(Oxidation (M))ERDK_;_VESCTIETKDDR_\t\t\t1661\t81\t275\t290\t2316\t\n+TN11\t16235\t14070\tADVTPADFSEWSK\t13\t0\tUnmodified\t_ADVTPADFSEWSK_\t\t\t0\t0\tsp|Biognosys_pep-h|iRT-Kit_WR_fusion\t2\tHCD\tFTMS\tMULTI-MSMS\t1\t0\t726.83571\t1451.6569\t-0.42588\t-0.00030955\t0.1189642\t36.424\t4.8078E-17\t136.48\t125.32\tNaN\tNaN\t1\t0\t0\t0\t16234\t69014136\t0.311369176369289\t11\t-0.250759124755859\ty1;y2;y3;y4;y5;y6;y7;y8;y9;y10;y11;y2-H2O;y4-H2O;y5-H2O;y9-H2O;y10-H2O;y1-NH3;y3-NH3;y5-NH3;a2;b2;b3;b4;b3-H2O;b4-H2O\t100000;200000;400000;200000;300000;400000;600000;700000;5000000;700000;40000;40000;40000;20000;100000;50000;70000;100000;70000;100000;400000;800000;800000;40000;300000\t0.000362153998423764;0.000408142023417213;-8.94026966875572E-05;-0.000746641248042579;0.00131797395727062;0.00169180027603488;0.00337630296030511;0.00141253952688203;0.00201269041212981;-0.00161478547875049;0.0107385496498864;-0.00126067025314569;-0.00176062641253338;0.00231368192498849;0.000752088235003612;-0.00460485357029938;-9.4418204696467E-05;-0.00333618247520917;0.00146598547496524;-0.0003635622625211;0.000212070579692636;0.000448119945588132;0.000596566125295794;-0.00121909502820472;0.000457365822114753\t2.46174962130596;1.74312082978707;-0.212749977880321;-1.35933997198758;2.07131736769484;2.15965637937099;3.75816755571447;1.45708280280867;1.88722400660009;-1.38307445776'..b'358029072194;817.439833102485;216.133224487305;459.218383789063;615.298257471025;686.341674804688;799.421630859375;130.086212158203;331.161682128906;687.32861328125;800.410461425781;249.158889770508;277.153632669777\t18\t0.260409633738696\t0.109756097560976\tNone\tUnknown\t\t93.1624429296055;48.7556257175906;44.4470295250138\tYILAGVENSK;YILDGKQEK;YIASLVNADK\t_YILAGVENSK_;_YILDGKQEK_;_YIASLVNADK_\t\t\t72939\t77\t13025\t13820\t108961\t\n+TN21\t8668\t7447\tYILAGVENSK\t10\t0\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\t2\tHCD\tFTMS\tMULTI-MSMS\t1\t0\t547.29804\t1092.5815\t0.076863\t4.2067E-05\t0.29515674\t20.124\t6.1583E-58\t172.21\t90.917\tNaN\tNaN\t1\t0\t0\t0\t8667\t13643855\t0.086249454329228\t19\t-0.433937072753906\ty1;y2;y3;y4;y5;y6;y7;y8;y9;y2-H2O;y3-H2O;y4-H2O;y6-H2O;y7-H2O;y8-H2O;y1-NH3;y3-NH3;y6-NH3;y7-NH3;y8-NH3;a2;b2;b3\t40000;40000;100000;90000;30000;200000;300000;400000;20000;9000;10000;60000;10000;20000;8000;20000;40000;20000;20000;30000;700000;300000;40000\t0.000728364935923764;0.000911682062479713;0.000798641717835835;0.00150867816211075;0.00256355946839903;0.00250539532407856;0.0025104607875619;0.00275935423360352;0.00924289054466954;-0.00016203744064569;-0.0005390336000346;0.00391228862707749;0.00430719068128838;0.00821785348125559;0.0133023416938158;5.8169685928533E-05;0.00383177580937399;0.000346701262515126;-0.00576541091243143;0.000507727106878519;0.000818816325022453;0.000943594286866301;0.000663376351667466\t4.95108869842839;3.89368239406551;2.29371517720476;3.16133062716056;4.4483365549105;3.95598484571275;3.56419898899789;3.37561018968138;9.93307827465478;-0.749706748235068;-1.63255587495912;8.51949775753901;7.0000864108862;11.9734689788788;16.6400422847749;0.447162629971505;11.5708604144794;0.562558838214761;-8.38804632363811;0.634330338777745;3.28632133230641;3.40458814159926;1.6999273094128\t147.112075805664;234.143920898438;348.186961385982;477.228844445738;576.296203480632;633.317725368376;704.354834090712;817.438649177666;930.516229621755;216.134429931641;330.177734375;459.215876148973;615.305358886719;686.338562011719;799.417541503906;130.086196899414;331.157379150391;616.293334960938;687.336560860912;800.414351703293;249.158935546875;277.153725391013;390.238069589348\t23\t0.519692685553036\t0.207207207207207\tNone\tUnknown\t\t172.213335039281;81.2966791880028;65.037798472005\tYILAGVENSK;YILDGKQEK;YIASLVNADK\t_YILAGVENSK_;_YILDGKQEK_;_YIASLVNADK_\t\t\t72940\t77\t13025\t13820\t108961\t\n+TN21\t9000\t7747\tYILAGVENSK\t10\t0\tUnmodified\t_YILAGVENSK_\t\t\t0\t0\tsp|Biognosys_pep-d|iRT-Kit_WR_fusion\t2\tHCD\tFTMS\tMULTI-MSMS\t1\t0\t547.29804\t1092.5815\t0.076863\t4.2067E-05\t-0.43705407\t20.818\t0.0096992\t61.691\t28.851\tNaN\tNaN\t1\t0\t0\t0\t8999\t561533.125\t0.00354972444511\t51\t-1.11052322387695\ty1;y2;y3;y4;y5;y6;y7;y8;y2-H2O;y4-H2O;y6-H2O;y1-NH3;y3-NH3;y6-NH3;y7-NH3;a2;b2\t20000;3000;8000;3000;3000;10000;20000;20000;1000;2000;2000;10000;2000;2000;2000;40000;10000\t0.000423189154673764;0.000835388117167213;0.00134254797501399;-0.00179409289688692;-0.00177006927503953;0.00531261713399545;0.00320904891566443;0.00146712565003781;-0.00107756478439569;0.00729454111558425;-0.00399359056871162;0.000180239998428533;-1.3439034376006E-05;-0.00349851358123487;-0.00868208906251766;0.000589934489084953;0.00165384858127027\t2.87663860682902;3.56783913824116;3.85583097908224;-3.75937142405435;-3.07143436637748;8.38858675482197;4.55601629054771;1.79478096887938;-4.98560187880135;15.8848925334958;-6.49033302928236;1.38554413810487;-0.0405815457463832;-5.67666653973173;-12.6314424621773;2.36770134639677;5.96727616495324\t147.112380981445;234.143997192383;348.186417479725;477.232147216797;576.300537109375;633.314918146566;704.354135502584;817.43994140625;216.135345458984;459.212493896484;615.313659667969;130.086074829102;331.161224365234;616.297180175781;687.339477539063;249.159164428711;277.153015136719\t17\t0.175033360540618\t0.104938271604938\tNone\tUnknown\t\t61.691277971878;32.8405601941561;24.9227679487439\tYILAGVENSK;YILDGKQEK;YIASLVNADK\t_YILAGVENSK_;_YILDGKQEK_;_YIASLVNADK_\t\t\t72941\t77\t13025\t13820\t108961\t\n' 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