Mercurial > repos > tomnl > create_sqlite_db
changeset 4:ff61a6fb23bf draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
| author | tomnl |
|---|---|
| date | Wed, 04 Apr 2018 17:08:30 -0400 |
| parents | 2766f2a85997 |
| children | 9ab472c5714c |
| files | anticipated_purity_lcms.R create_sqlite_db.xml frag4feature.R test-data/assess_purity_msms_output_LCMSMS1.tsv test-data/cpeakgroup_msms.tsv test-data/frag4feature_output.tsv test-data/library_spectra.db test-data/scan_hits.tsv test-data/xcms_hits.tsv test-data/xset_peaks.tsv track_rt_raw.R |
| diffstat | 11 files changed, 4393 insertions(+), 1491 deletions(-) [+] |
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--- a/anticipated_purity_lcms.R Fri Mar 30 10:12:19 2018 -0400 +++ b/anticipated_purity_lcms.R Wed Apr 04 17:08:30 2018 -0400 @@ -164,7 +164,7 @@ iwNormFun = iwNormFun, singleFile = opt$singleFile, fileignore = ignore_files, - rtraw_columns=rtraw_columns) + rtrawColumns=rtraw_columns) dfp <- ppLCMS@predictions
--- a/create_sqlite_db.xml Fri Mar 30 10:12:19 2018 -0400 +++ b/create_sqlite_db.xml Wed Apr 04 17:08:30 2018 -0400 @@ -1,15 +1,18 @@ -<tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.3"> +<tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.4"> + <description> + Create SQLite database of an XCMS-CAMERA dataset + </description> + + <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation--> + </expand> - <description> - Create SQLite database of an XCMS-CAMERA dataset - </description> + <stdio> <exit_code range="1:" /> </stdio> @@ -72,9 +75,9 @@ </inputs> <outputs> <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db" - from_work_dir="lcms_data.sqlite" visible="true"/> + from_work_dir="lcms_data.sqlite" /> <data name="cpeakgroup_msms" format="sqlite" label="${tool.name} on ${on_string}: c-peak-group-msms" - from_work_dir="cpeakgroup_msms.tsv" visible="true"/> + from_work_dir="cpeakgroup_msms.tsv" /> </outputs> <tests> @@ -97,7 +100,7 @@ </output> </test> </tests> - <expand macro="citations" /> + <help><![CDATA[ ============================================================= Create SQLite database for LC-MS(/MS) dataset @@ -114,5 +117,5 @@ * cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra ]]></help> - +<expand macro="citations" /> </tool>
--- a/frag4feature.R Fri Mar 30 10:12:19 2018 -0400 +++ b/frag4feature.R Wed Apr 04 17:08:30 2018 -0400 @@ -65,12 +65,28 @@ loadRData <- function(rdata_path, name){ #loads an RData file, and returns the named xset object if it is there load(rdata_path) - return(get(ls()[ls() == name])) + return(get(ls()[ls() %in% name])) +} + +# This function retrieve a xset like object +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + sampclass(xset) <- xset@phenoData$sample_group + return (xset) + } } # Requires pa <- loadRData(opt$pa, 'pa') -xset <- loadRData(opt$xset, 'xset') +xset <- loadRData(opt$xset, c('xset','xdata')) +xset <- getxcmsSetObject(xset) pa@cores <- opt$cores @@ -102,8 +118,6 @@ if(is.null(opt$grp_peaklist)){ grp_peaklist = NA - - }else{ grp_peaklist = opt$grp_peaklist }
--- a/test-data/assess_purity_msms_output_LCMSMS1.tsv Fri Mar 30 10:12:19 2018 -0400 +++ b/test-data/assess_purity_msms_output_LCMSMS1.tsv Wed Apr 04 17:08:30 2018 -0400 @@ -1,830 +1,830 @@ "pid" "fileid" "seqNum" "precursorIntensity" "precursorMZ" "precursorRT" "precursorScanNum" "id" "filename" "precursorNearest" "seqNum" "aMz" "aPurity" "apkNm" "iMz" "iPurity" "ipkNm" "inPkNm" "inPurity" -1 "1" 7 2338044.25 391.283841833865 2.70701592 6 7 "dataset_1.dat" 6 7 391.283843994141 1 1 391.283843994141 1 1 1 1 -2 "1" 8 1415939.75 149.023234587846 2.70701592 6 8 "dataset_1.dat" 6 8 149.023254394531 0.85356996593666 2 149.023254394531 0.85356996593666 2 2 0.84752404379021 -3 "1" 9 1319700.25 135.101521833482 2.70701592 6 9 "dataset_1.dat" 6 9 135.101531982422 0.761668785396351 4 135.101531982422 0.761668785396351 4 4 0.75587307549212 -4 "1" 10 1179373.875 219.17415532154 2.70701592 6 10 "dataset_1.dat" 12 10 219.174194335938 0.71736356553493 3 219.174194335938 0.71736356553493 3 3 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--- a/test-data/frag4feature_output.tsv Fri Mar 30 10:12:19 2018 -0400 +++ b/test-data/frag4feature_output.tsv Wed Apr 04 17:08:30 2018 -0400 @@ -1,324 +1,324 @@ "grpid" "mz" "mzmin" "mzmax" "rt" "rtmin" "rtmax" "into" "intf" "maxo" "maxf" "i" "sn" "sample" "cid" "filename" "precurMtchID" "precurMtchRT" "precurMtchMZ" "precurMtchPPM" "inPurity" "pid" -"12" 112.050766766484 112.050651550293 112.087196350098 67.47903 55.2769038 80.361672 36223791.266206 133522503.549415 7158012.5 8555976.39592391 1 21.054952458659 1 9 "dataset_6.dat" 466 64.427298 112.050704956055 0.55162878935702 1 384 -"12" 112.05085569128 112.050621032715 112.120460510254 67.634034 55.4140188 80.555406 36139265.8017591 133395720.51942 7426335.5 8522973.08164079 1 20.3803986860233 2 400 "dataset_5.dat" 472 65.376156 112.050743103027 1.00479600749392 1 1218 -"14" 113.035371704924 113.034713745117 113.059936523438 83.64567 72.171048 96.141564 92812020.095242 366177037.564437 20943314 23904502.6814248 1 27.9839052693883 2 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15.0460240597249 1 356 "dataset_25.dat" 377 52.9810356 429.136749267578 0.0851636661584605 1 310 +"678" 429.136767529428 429.136199951172 429.138092041016 71.396808 50.0837946 83.64567 53515366.4335274 137082701.660503 5492228 6980810.3518927 1 14.783580013865 2 747 "dataset_24.dat" 377 53.1376686 429.136810302734 0.0996729000089511 1 1139 +"678" 429.13678581444 429.13623046875 429.137237548828 71.233434 50.6971758 83.441172 51996787.3010654 134809462.339879 5404011.5 7211461.39434763 1 15.0460240597249 1 356 "dataset_25.dat" 514 70.461672 429.136657714844 0.298505279838225 1 424 +"678" 429.136767529428 429.136199951172 429.138092041016 71.396808 50.0837946 83.64567 53515366.4335274 137082701.660503 5492228 6980810.3518927 1 14.783580013865 2 747 "dataset_24.dat" 520 71.396808 429.136688232422 0.184782597017714 1 1258 +"699" 436.215002909334 436.145385742188 436.219696044922 113.597328 101.49993 125.413584 5904448.03806087 20144723.3651187 764445.4375 1303884.29795751 1 10.3653444790918 1 361 "dataset_25.dat" 827 111.16869 436.216247558594 2.85329310399634 0.921419706133938 685 +"705" 437.26196926482 437.259826660156 437.268768310547 82.686066 69.717042 95.067042 3032670.80090554 11322819.978798 739371.1875 730667.904455794 1 12.1784701858079 1 362 "dataset_25.dat" 605 81.93093 437.259979248047 4.55108587845037 0.534230165424194 500 +"705" 437.262039320009 437.259765625 437.345703125 82.86993 70.627524 95.269182 3072296.30017716 11642746.3242237 832326.375 755209.503933987 1 12.2874657221692 2 751 "dataset_24.dat" 605 82.10931 437.260040283203 4.57171358505199 0.612492534699059 1329 +"739" 452.191973065994 452.189270019531 452.224395751953 112.786446 99.89805 125.413584 6698054.22775966 25121192.6204043 801245.875 1552769.73925228 1 10.6990378753924 1 368 "dataset_25.dat" 821 110.36505 452.190155029297 4.02049749895926 0.940645050319878 680 +"739" 452.191556747302 452.150634765625 452.224822998047 112.983072 100.10529 125.668188 6949753.68966263 25983143.0046032 813885.0625 1605073.99568666 1 10.4472184123822 2 758 "dataset_24.dat" 821 110.559792 452.190155029297 3.09983232557278 0.936953196044324 1509 +"757" 461.207113324101 461.110168457031 461.2431640625 76.520544 65.179668 88.866054 48904711.0742877 195241268.75592 14374106 12850193.8354307 1 21.2071228333724 1 371 "dataset_25.dat" 563 76.520544 461.209899902344 6.04192381657049 1 465 +"757" 461.20738152051 461.121826171875 461.243560791016 77.474424 65.376156 89.831544 48607882.314214 192672537.990574 14159047 12716867.2850009 1 20.5600686941203 2 761 "dataset_24.dat" 569 77.474424 461.209899902344 5.460410945608 1 1299 +"759" 462.22122959389 462.213439941406 462.291839599609 57.7060356 44.7995376 75.972048 38559454.0832874 105979165.236253 3445839.75 5926579.6352243 1 10.2307809194678 2 762 "dataset_24.dat" 435 60.766158 462.218811035156 5.23247003559527 0.944176192726551 1187 +"787" 476.190702761819 476.186126708984 476.307098388672 81.162672 69.717042 92.725812 39151803.0473944 118893746.090445 7816689 8198001.40019319 1 14.9845576620757 1 378 "dataset_25.dat" 574 78.035046 476.186828613281 8.13570805892727 0.977294138555063 474 +"787" 476.190794182677 476.186218261719 476.307495117188 81.344292 69.864534 92.927058 43745001.5410773 135433069.148731 8875996 9304027.49811656 1 15.612354791168 2 768 "dataset_24.dat" 574 78.227304 476.186981201172 8.00725581423595 0.917917041077806 1303 +"787" 476.190794182677 476.186218261719 476.307495117188 81.344292 69.864534 92.927058 43745001.5410773 135433069.148731 8875996 9304027.49811656 1 15.612354791168 2 768 "dataset_24.dat" 581 78.998916 476.187042236328 7.87908207170328 0.990314571321696 1309 +"812" 487.181176540989 487.099060058594 487.239410400391 66.710418 54.5086626 79.585674 58453273.9503532 230378509.09492 15813294 14998690.3403142 1 19.4416133244468 1 384 "dataset_25.dat" 478 65.949288 487.177612304688 7.31603861859596 1 394 +"812" 487.180877999963 487.099700927734 487.239501953125 66.865908 54.6427758 78.998916 60132074.4709007 238189012.918308 18110170 15528706.5784369 1 19.1064097764383 2 774 "dataset_24.dat" 479 66.147648 487.177856445312 6.20212078776047 1 1224 +"830" 494.196757645669 494.119018554688 494.198516845703 49.9356528 37.8964158 62.153292 31096636.998985 121560345.75829 6061495.5 8000920.55155143 1 19.2246142395834 1 387 "dataset_25.dat" 341 48.4095336 494.197631835938 1.76891138083971 1 280 +"830" 494.1970608933 494.119293212891 494.197875976562 50.0837946 38.0417766 62.309778 31975460.900009 125089224.818786 5749075.5 8239138.02501223 1 18.9671855740286 2 776 "dataset_24.dat" 345 49.3156656 494.197631835938 1.15529347093956 1 1112 +"840" 498.169308539313 498.16845703125 498.28955078125 81.162672 68.984166 93.504684 46040504.6258466 180736904.384221 9105023 11919892.2978446 1 18.9934607564632 1 389 "dataset_25.dat" 580 78.808182 498.168731689453 1.15793937994546 1 479 +"840" 498.169196251216 498.168304443359 498.216522216797 81.344292 69.864534 93.704046 47195241.5238887 185121008.239345 9710354 12214248.0689462 1 17.5782472187331 2 778 "dataset_24.dat" 586 79.776168 498.168914794922 0.564981329073345 1 1313 +"840" 498.169196251216 498.168304443359 498.216522216797 81.344292 69.864534 93.704046 47195241.5238887 185121008.239345 9710354 12214248.0689462 1 17.5782472187331 2 778 "dataset_24.dat" 657 89.058666 498.169708251953 1.02776474439097 1 1372 +"843" 499.250391260917 499.216522216797 499.254547119141 129.525558 116.993448 134.305698 60960211.430872 197064903.836068 13479257 15776334.7230698 1 17.5991745757 2 780 "dataset_24.dat" 937 126.441198 499.250396728516 0.0109516161922676 1 1605 +"843" 499.250501059464 499.216003417969 499.255126953125 129.271086 116.806434 134.058318 55312967.4069412 179331694.489759 13120593 14382850.9535263 1 18.1627514816931 1 391 "dataset_25.dat" 939 126.186204 499.250396728516 0.208975150626037 1 778
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scan_hits.tsv Wed Apr 04 17:08:30 2018 -0400 @@ -0,0 +1,40 @@ +"mid" "score" "perc_mtch" "match" "lid" "pid" "lid" "name" "other_names" "collision_energy" "ms_level" "accession" "resolution" "polarity" "fragmentation_type" "exact_mass" "precursor_mz" "precursor_type" "instrument_type" "instrument" "copyright" "column" "molecular_formula" "molecular_weight" "mass_accuracy" "mass_error" "compound_class" "library_spectra_source_id" "source_name" "pid" "seqNum" "precursorIntensity" "precursorMZ" "precursorRT" "precursorScanNum" "id" "precursorNearest" "aMz" "aPurity" "apkNm" "iMz" "iPurity" "ipkNm" "inPkNm" "inPurity" "fileid" "fileid" "filename" "filepth" "sampletype" +1 0.889580232933972 0.333333333333333 1 40963 1 40963 "Di(ethylhexyl) phthalate" "dioctan-3-yl benzene-1,2-dicarboxylate" "35" 2 "UF417801" "15000" "positive" "CID" 390.277 391.2843 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2013 UFZ, Leipzig, Germany" "Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex" "C24H38O4" 390.277009696 0.036556539553993 1.43039999898065e-05 NA 1 "massbank" 1 7 2307227.25 391.283760714446 2.7169029 6 7 6 391.283905029297 1 1 391.283905029297 1 1 1 1 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +2 0.889580232933973 0.333333333333333 1 40964 1 40964 "Di(ethylhexyl) phthalate" "dioctan-3-yl benzene-1,2-dicarboxylate" "50" 2 "UF417803" "15000" "positive" "HCD" 390.277 391.2843 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2013 UFZ, Leipzig, Germany" "Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex" "C24H38O4" 390.277009696 0.036556539553993 1.43039999898065e-05 NA 1 "massbank" 1 7 2307227.25 391.283760714446 2.7169029 6 7 6 391.283905029297 1 1 391.283905029297 1 1 1 1 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +3 0.889580232933972 0.333333333333333 1 40965 1 40965 "Di(ethylhexyl) phthalate" "dioctan-3-yl benzene-1,2-dicarboxylate" "80" 2 "UF417804" "15000" "positive" "HCD" 390.277 391.2843 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2013 UFZ, Leipzig, Germany" "Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex" "C24H38O4" 390.277009696 0.036556539553993 1.43039999898065e-05 NA 1 "massbank" 1 7 2307227.25 391.283760714446 2.7169029 6 7 6 391.283905029297 1 1 391.283905029297 1 1 1 1 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +4 0.756107592201661 0.142857142857143 2 44652 1 44652 "Di(2-ethylhexyl)phthalate (DEHP)" "DEHP #<::::># Bis(2-ethylhexyl) benzene-1,2-dicarboxylate" "35 (nominal)" 2 "SM818501" "35000" "positive" "HCD" 390.27701 391.2843 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2016 UFZ/Eawag" "Kinetex C18 EVO 2.6 um, 2.1x50 mm, precolumn 2.1x5 mm, Phenomenex" "C24H38O4" 390.277009696 0.036556539553993 36.556539553993 NA 1 "massbank" 1 7 2307227.25 391.283760714446 2.7169029 6 7 6 391.283905029297 1 1 391.283905029297 1 1 1 1 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +5 0.688419566364713 0.0769230769230769 1 14159 11 14159 "Di-n-butyl phthalate" "Dibutyl phthalate #<::::># dibutyl benzene-1,2-dicarboxylate" "15 (nominal)" 2 "EQ367001" "35000" "positive" "HCD" 278.15181 279.1591 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +6 0.837111679653525 0.0833333333333333 1 14160 11 14160 "Di-n-butyl phthalate" "Dibutyl phthalate #<::::># dibutyl benzene-1,2-dicarboxylate" "30 (nominal)" 2 "EQ367002" "35000" "positive" "HCD" 278.15181 279.1591 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +7 0.838980060607133 0.0769230769230769 1 14161 11 14161 "Di-n-butyl phthalate" "Dibutyl phthalate #<::::># dibutyl benzene-1,2-dicarboxylate" "45 (nominal)" 2 "EQ367003" "35000" "positive" "HCD" 278.15181 279.1591 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +8 0.814845638661253 0.0588235294117647 1 14162 11 14162 "Di-n-butyl phthalate" "Dibutyl phthalate #<::::># dibutyl benzene-1,2-dicarboxylate" "60 (nominal)" 2 "EQ367004" "35000" "positive" "HCD" 278.15181 279.1591 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +9 0.737062475204889 0.0526315789473684 1 14163 11 14163 "Di-n-butyl phthalate" "Dibutyl phthalate #<::::># dibutyl benzene-1,2-dicarboxylate" "75 (nominal)" 2 "EQ367005" "35000" "positive" "HCD" 278.15181 279.1591 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +10 0.618282048393228 0.0357142857142857 1 14164 11 14164 "Di-n-butyl phthalate" "Dibutyl phthalate #<::::># dibutyl benzene-1,2-dicarboxylate" "90 (nominal)" 2 "EQ367006" "35000" "positive" "HCD" 278.15181 279.1591 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +12 0.842564661157152 0.142857142857143 1 40970 11 40970 "Dibutyl phthalate" "Benzene-1,2-dicarboxylate-dibuthyl" "55 (nominal)" 2 "UF418001" "15000" "positive" "HCD" 278.1518 279.1591 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2017" "Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +13 0.779210370214074 0.142857142857143 1 40971 11 40971 "Dibutyl phthalate" "Benzene-1,2-dicarboxylate-dibuthyl" "80 (nominal)" 2 "UF418002" "15000" "positive" "HCD" 278.1518 279.1591 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2017" "Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex" "C16H22O4" 278.151809184 0.0530736774555067 1.48160000321695e-05 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +16 0.765467884012391 0.0666666666666667 1 44686 11 44686 "Dibutyl phthalate" "dibutyl benzene-1,2-dicarboxylate" "35 (nominal)" 2 "SM822401" "35000" "positive" "HCD" 278.15181 279.1591 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2016 UFZ/Eawag" "Kinetex C18 EVO 2.6 um, 2.1x50 mm, precolumn 2.1x5 mm, Phenomenex" "C16H22O4" 278.151809184 0.0530736774555067 53.0736774555067 NA 1 "massbank" 11 19 522140.46875 279.16 4.46726694 18 19 18 279.158782958984 0.778745945763546 2 279.158782958984 0.778745945763546 2 2 0.781940110910545 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +17 0.620630245378104 0.181818181818182 2 6593 15 6593 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "35 % (nominal)" 2 "EA030301" "7500" "positive" "CID" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +18 0.660971496854926 0.2 2 6594 15 6594 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "15 % (nominal)" 2 "EA030302" "7500" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +19 0.678517919219253 0.2 2 6595 15 6595 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "30 % (nominal)" 2 "EA030303" "7500" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +20 0.708866632718685 0.153846153846154 2 6596 15 6596 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "45 % (nominal)" 2 "EA030304" "7500" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +21 0.682622905973895 0.111111111111111 2 6597 15 6597 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "60 % (nominal)" 2 "EA030305" "7500" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +24 0.653488152611387 0.1 1 6600 15 6600 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "15 % (nominal)" 2 "EA030308" "15000" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +25 0.677303054407418 0.2 2 6601 15 6601 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "30 % (nominal)" 2 "EA030309" "15000" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +26 0.708665450067972 0.142857142857143 2 6602 15 6602 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "45 % (nominal)" 2 "EA030310" "15000" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +27 0.680576121315443 0.117647058823529 2 6603 15 6603 "Caffeine" "1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione #<::::># 1,3,7-trimethylpurine-2,6-dione" "60 % (nominal)" 2 "EA030311" "15000" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2012 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +31 0.696535906162931 0.125 2 40587 15 40587 "Caffeine" "1,3,7-Trimethylpurine-2,6-dione" "55 (nominal)" 2 "UF408901" "15000" "positive" "HCD" 194.0804 195.0877 "[M+H]+" "LC-ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) 2017" "Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +35 0.702795148253534 0.153846153846154 2 42359 15 42359 "Caffeine" NA "10 ev" 2 "BML00696" NA "positive" NA 194.080376 195.0877 "[M+H]+" "LC-ESI-QTOF" "Agilent 1200 RRLC; Agilent 6520 QTOF" NA "Agilent C8 Cartridge Column 2.1X30mm 3.5 micron (guard); Agilent SB-Aq 2.1x50mm 1.8 micron (analytical)" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +36 0.627225072889698 0.0909090909090909 2 42367 15 42367 "Caffeine" NA "20 ev" 2 "BML00705" NA "positive" NA 194.080376 195.0877 "[M+H]+" "LC-ESI-QTOF" "Agilent 1200 RRLC; Agilent 6520 QTOF" NA "Agilent C8 Cartridge Column 2.1X30mm 3.5 micron (guard); Agilent SB-Aq 2.1x50mm 1.8 micron (analytical)" "C8H10N4O2" 194.08037556 0.24829858586115 4.84400000289043e-05 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +37 0.704680986301775 0.1 2 45042 15 45042 "Caffeine" NA "35 (nominal)" 2 "SM866601" "35000" "positive" "HCD" 194.08038 195.0877 "[M+H]+" "LC-ESI-QFT" "Q Exactive Plus Orbitrap Thermo Scientific" "Copyright (C) 2016 UFZ/Eawag" "Kinetex C18 EVO 2.6 um, 2.1x50 mm, precolumn 2.1x5 mm, Phenomenex" "C8H10N4O2" 194.08037556 0.24829858586115 248.29858586115 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +38 0.641096170126432 0.125 2 46333 15 46333 "Caffeine" "1,3,7-trimethylpurine-2,6-dione" "35 % (nominal)" 2 "UA005001" "30000" "positive" "CID" 194.0804 195.0877 "[M+H]+" "ESI-ITFT" "LTQ Orbitrap XL Thermo Scientific" "Copyright (C) Eawag, 2014" "N/A" "C8H10N4O2" 194.08037556 0.24829858586115 248.29858586115 NA 1 "massbank" 15 23 398638.59375 195.087538239222 4.46726694 18 23 24 195.08757019043 0.427238293287608 7 195.08757019043 0.427238293287608 7 7 0.42561698809495 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +67 0.627404488861637 0.4 2 37338 247 37338 "L-Histidine" "L-His #<::::># L-alpha-Amino-beta-imidazolepropionic Acid #<::::># Glyoxaline-5-alanine #<::::># (S)-2-Amino-3-(4-imidazolyl)propionic acid" "Ramp 5-60 V" 2 "PR100027" NA "positive" NA 155.06948 156.07727 "[M+H]+" "LC-ESI-QTOF" "UPLC Q-Tof Premier, Waters" NA NA "C6H9N3O2" 155.069476528 3.31548597699544 0.000517472000012731 "Amino acids" 1 "massbank" 247 302 2627554.5 156.076676546982 43.9150368 300 302 300 156.076675415039 0.64648407336059 2 156.076675415039 0.64648407336059 2 2 0.672380618767158 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +68 0.71126945347125 0.5 2 37339 247 37339 "L-Histidine" "L-His #<::::># L-alpha-Amino-beta-imidazolepropionic Acid #<::::># Glyoxaline-5-alanine #<::::># (S)-2-Amino-3-(4-imidazolyl)propionic acid" "30 V" 2 "PR100028" NA "positive" NA 155.06948 156.07727 "[M+H]+" "LC-ESI-QTOF" "UPLC Q-Tof Premier, Waters" NA NA "C6H9N3O2" 155.069476528 3.31548597699544 0.000517472000012731 "Amino acids" 1 "massbank" 247 302 2627554.5 156.076676546982 43.9150368 300 302 300 156.076675415039 0.64648407336059 2 156.076675415039 0.64648407336059 2 2 0.672380618767158 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +69 0.868467084372246 0.4 2 37625 247 37625 "L-Histidine" "L-His #<::::># L-alpha-Amino-beta-imidazolepropionic Acid #<::::># Glyoxaline-5-alanine #<::::># (S)-2-Amino-3-(4-imidazolyl)propionic acid" "Ramp 5-60 V" 2 "PR100321" NA "positive" NA 155.06948 156.07727 "[M+H]+" "LC-ESI-QTOF" "UPLC Q-Tof Premier, Waters" NA NA "C6H9N3O2" 155.069476528 3.31548597699544 0.000517472000012731 "Amino acids" 1 "massbank" 247 302 2627554.5 156.076676546982 43.9150368 300 302 300 156.076675415039 0.64648407336059 2 156.076675415039 0.64648407336059 2 2 0.672380618767158 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +118 0.726640102125439 0.25 2 37706 490 37706 "Oxypurinol" "DHPP #<::::># Alloxanthine #<::::># Oxipurinol #<::::># Oxoallopurinol #<::::># Ossipurinolo" "Ramp 5-60 V" 2 "PR100403" NA "positive" NA 152.03343 153.04122 "[M+H]+" "LC-ESI-QTOF" "UPLC Q-Tof Premier, Waters" NA NA "C5H4N4O2" 152.033425368 3.38883864114155 0.000518632000023445 "Pyrazolopyrimidines" 1 "massbank" 490 593 37041112 153.040505704485 80.361672 588 593 594 153.040512084961 1 1 153.040512084961 1 1 1 1 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +119 0.902872587543067 0.2 1 37347 499 37347 "Uracil" "2,4-Dihydroxypyrimidine #<::::># 2,4(1H,3H)-Pyrimidinedione #<::::># 2,4-Pyrimidinediol" "Ramp 5-60 V" 2 "PR100037" NA "positive" NA 112.02728 113.03508 "[M+H]+" "LC-ESI-QTOF" "UPLC Q-Tof Premier, Waters" NA NA "C4H4N2O2" 112.027277368 4.65901382109904 0.000526631999989036 "Pyrimidines" 1 "massbank" 499 604 13451539 113.034732421855 81.93093 600 604 606 113.034736633301 1 1 113.034736633301 1 1 1 1 1 1 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj3__incl2___2.mzML" "/tmp/tmpVgDapk/files/000/dataset_6.dat" "lcmsms" +171 0.714943823713569 0.0833333333333333 1 34804 1208 34804 "FAD" "Flavin adenine dinucleotide" "35eV" 2 "KNA00249" NA "positive" NA 785.15713 348.07 NA "LC-ESI-ITFT" "LTQ Orbitrap XL, Thermo Scientfic" NA "TOSOH TSKgel ODS-100V 5um Part no. 21456" "C27H33N9O15P2" 785.157134616 NA NA "Natural Product" 1 "massbank" 1208 460 12493925 348.069833425315 63.848922 456 460 462 348.069854736328 1 1 348.069854736328 1 1 3 0.967571799659265 2 2 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj1__dynamicExclu_NoLists.mzML" "/tmp/tmpVgDapk/files/000/dataset_5.dat" "lcmsms" +275 0.993179318644969 0.142857142857143 1 12648 1577 12648 "Allopurinol" "1,2-dihydropyrazolo[3,4-d]pyrimidin-4-one" "15 (nominal)" 2 "EQ333601" "35000" "positive" "HCD" 136.03851 137.0458 "[M+H]+" "LC-ESI-QFT" "Q Exactive Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C5H4N4O" 136.038510748 0.096697600587988 1.32520000306613e-05 NA 1 "massbank" 1577 903 11443519 137.045670850101 121.840812 900 903 900 137.045669555664 1 1 137.045669555664 1 1 1 1 2 2 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj1__dynamicExclu_NoLists.mzML" "/tmp/tmpVgDapk/files/000/dataset_5.dat" "lcmsms" +276 0.992612540102602 0.166666666666667 1 12649 1577 12649 "Allopurinol" "1,2-dihydropyrazolo[3,4-d]pyrimidin-4-one" "30 (nominal)" 2 "EQ333602" "35000" "positive" "HCD" 136.03851 137.0458 "[M+H]+" "LC-ESI-QFT" "Q Exactive Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C5H4N4O" 136.038510748 0.096697600587988 1.32520000306613e-05 NA 1 "massbank" 1577 903 11443519 137.045670850101 121.840812 900 903 900 137.045669555664 1 1 137.045669555664 1 1 1 1 2 2 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj1__dynamicExclu_NoLists.mzML" "/tmp/tmpVgDapk/files/000/dataset_5.dat" "lcmsms" +277 0.98081416435913 0.125 1 12650 1577 12650 "Allopurinol" "1,2-dihydropyrazolo[3,4-d]pyrimidin-4-one" "45 (nominal)" 2 "EQ333603" "35000" "positive" "HCD" 136.03851 137.0458 "[M+H]+" "LC-ESI-QFT" "Q Exactive Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C5H4N4O" 136.038510748 0.096697600587988 1.32520000306613e-05 NA 1 "massbank" 1577 903 11443519 137.045670850101 121.840812 900 903 900 137.045669555664 1 1 137.045669555664 1 1 1 1 2 2 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj1__dynamicExclu_NoLists.mzML" "/tmp/tmpVgDapk/files/000/dataset_5.dat" "lcmsms" +278 0.922683891831826 0.0833333333333333 1 12651 1577 12651 "Allopurinol" "1,2-dihydropyrazolo[3,4-d]pyrimidin-4-one" "60 (nominal)" 2 "EQ333604" "35000" "positive" "HCD" 136.03851 137.0458 "[M+H]+" "LC-ESI-QFT" "Q Exactive Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C5H4N4O" 136.038510748 0.096697600587988 1.32520000306613e-05 NA 1 "massbank" 1577 903 11443519 137.045670850101 121.840812 900 903 900 137.045669555664 1 1 137.045669555664 1 1 1 1 2 2 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj1__dynamicExclu_NoLists.mzML" "/tmp/tmpVgDapk/files/000/dataset_5.dat" "lcmsms" +279 0.802971840675363 0.0588235294117647 1 12652 1577 12652 "Allopurinol" "1,2-dihydropyrazolo[3,4-d]pyrimidin-4-one" "75 (nominal)" 2 "EQ333605" "35000" "positive" "HCD" 136.03851 137.0458 "[M+H]+" "LC-ESI-QFT" "Q Exactive Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C5H4N4O" 136.038510748 0.096697600587988 1.32520000306613e-05 NA 1 "massbank" 1577 903 11443519 137.045670850101 121.840812 900 903 900 137.045669555664 1 1 137.045669555664 1 1 1 1 2 2 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj1__dynamicExclu_NoLists.mzML" "/tmp/tmpVgDapk/files/000/dataset_5.dat" "lcmsms" +280 0.66378502218352 0.0454545454545455 1 12653 1577 12653 "Allopurinol" "1,2-dihydropyrazolo[3,4-d]pyrimidin-4-one" "90 (nominal)" 2 "EQ333606" "35000" "positive" "HCD" 136.03851 137.0458 "[M+H]+" "LC-ESI-QFT" "Q Exactive Orbitrap Thermo Scientific" "Copyright (C) 2015 Eawag, Duebendorf, Switzerland" "XBridge C18 3.5um, 2.1x50mm, Waters" "C5H4N4O" 136.038510748 0.096697600587988 1.32520000306613e-05 NA 1 "massbank" 1577 903 11443519 137.045670850101 121.840812 900 903 900 137.045669555664 1 1 137.045669555664 1 1 1 1 2 2 "Daph_P_WAX_1_LCMSMS-FC_Phenyl_pos_inj1__dynamicExclu_NoLists.mzML" "/tmp/tmpVgDapk/files/000/dataset_5.dat" "lcmsms"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xcms_hits.tsv Wed Apr 04 17:08:30 2018 -0400 @@ -0,0 +1,5 @@ +"grpid" "best_name" "best_median_score" "best_median_perc_mtch" "best_median_match" "all_names" "all_pids" "all_lids" "all_scores" "numb_unique_scans" +14 "Uracil" "0.902872587543067" "0.2" "1" "Uracil" "499" "37347" "0.903" "1" +47 "Allopurinol" "0.951749028095478" "0.104166666666667" "1" "Allopurinol, Allopurinol, Allopurinol, Allopurinol, Allopurinol, Allopurinol" "1577, 1577, 1577, 1577, 1577, 1577" "12648, 12649, 12650, 12651, 12652, 12653" "0.993, 0.993, 0.981, 0.923, 0.803, 0.664" "1" +72 "Oxypurinol" "0.726640102125439" "0.25" "2" "Oxypurinol" "490" "37706" "0.727" "1" +75 "L-Histidine" "0.71126945347125" "0.4" "2" "L-Histidine, L-Histidine, L-Histidine" "247, 247, 247" "37625, 37339, 37338" "0.868, 0.711, 0.627" "1"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xset_peaks.tsv Wed Apr 04 17:08:30 2018 -0400 @@ -0,0 +1,2835 @@ +"mz" "mzmin" "mzmax" "rt" "rtmin" "rtmax" "into" "intf" "maxo" "maxf" "i" "sn" "sample" "rt_raw" "rtmin_raw" "rtmax_raw" +104.107135381295 104.070930480957 104.107345581055 51.4450368 39.4231566 64.427298 515766711.944419 1975194582.42605 66404008 126924717.26074 1 29.3681933242409 1 51.4450368 39.4231566 64.427298 +105.039053107253 104.99259185791 105.110679626465 45.3966672 32.492523 58.3416642 72064600.8288636 246316975.257377 7541076.5 15046921.6703262 1 22.4165764114421 1 45.3966672 32.492523 58.3416642 +106.059749874819 106.050048828125 106.111587524414 43.1829192 29.960895 56.7980382 5389481.46787405 18673995.146755 550976.0625 1128205.69666791 1 17.342858295391 1 43.1829192 29.960895 56.7980382 +107.048982431691 107.04859161377 107.04931640625 70.461672 59.113914 84.215802 1899706.36368764 6495523.40566681 463533.71875 425762.9407497 1 12.0027546345951 1 70.461672 59.113914 84.215802 +108.030734176149 107.967041015625 108.081275939941 47.662548 34.8182742 61.39704 2238982.07880418 6387793.29840524 251532.515625 383201.171624171 1 10.5064006220258 1 47.662548 34.8182742 61.39704 +110.071500069279 110.060173034668 110.071632385254 48.4095336 36.347289 62.924034 22425554.5636639 70367484.2021562 2791395 4313730.2460218 1 16.3779525670294 1 48.4095336 36.347289 62.924034 +111.014416009159 111.011039733887 111.044403076172 91.18956 78.808182 103.89993 8051899.07476691 28559421.5967984 1585939.375 1809819.33202627 1 17.1848105217722 1 91.18956 78.808182 103.89993 +112.037131924592 112.021553039551 112.039581298828 41.6846646 29.0840262 53.7376638 5077137.70662181 20248756.8671218 1169368.875 1324399.20463866 1 19.0439772178047 1 41.6846646 29.0840262 53.7376638 +112.050766766484 112.050651550293 112.087196350098 67.47903 55.2769038 80.361672 36223791.266206 133522503.549415 7158012.5 8555976.39592391 1 21.054952458659 1 67.47903 55.2769038 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--- a/track_rt_raw.R Fri Mar 30 10:12:19 2018 -0400 +++ b/track_rt_raw.R Wed Apr 04 17:08:30 2018 -0400 @@ -1,10 +1,11 @@ library(optparse) -library(xcms) + print(sessionInfo()) option_list <- list( make_option(c("--xset_path"), type="character"), - make_option(c("-o", "--out_dir"), type="character") + make_option(c("-o", "--out_dir"), type="character"), + make_option(c("--extract_peaks"), action="store_true") ) # store options @@ -21,3 +22,7 @@ print('saving RData') save.image(file.path(opt$out_dir, 'xset_rt_raw_tracked.RData')) + +if(!is.null(opt$extract_peaks)){ + write.table(xset@peaks, file.path(opt$out_dir, 'xset_peaks.tsv'), row.names=FALSE, sep='\t') +}