diff --git a/mzLib/Readers/Readers.csproj b/mzLib/Readers/Readers.csproj index 076ed9e40..b81a8e2b0 100644 --- a/mzLib/Readers/Readers.csproj +++ b/mzLib/Readers/Readers.csproj @@ -17,6 +17,7 @@ + diff --git a/mzLib/Readers/SearchResults/SpectrumMatchTsvReader.cs b/mzLib/Readers/SearchResults/SpectrumMatchTsvReader.cs index 62a720c63..659fe413a 100644 --- a/mzLib/Readers/SearchResults/SpectrumMatchTsvReader.cs +++ b/mzLib/Readers/SearchResults/SpectrumMatchTsvReader.cs @@ -54,10 +54,12 @@ public static List ReadTsv(string filePath, out List ".mgf", SupportedFileType.BrukerD => ".d", SupportedFileType.psmtsv => ".psmtsv", + SupportedFileType.IntralinkResults => "Intralinks.tsv", //SupportedFileType.osmtsv => ".osmtsv", SupportedFileType.ToppicPrsm => "_prsm.tsv", SupportedFileType.ToppicPrsmSingle => "_prsm_single.tsv", @@ -116,6 +118,8 @@ public static SupportedFileType ParseFileType(this string filePath) return SupportedFileType.MsPathFinderTDecoys; if (filePath.EndsWith(SupportedFileType.MsPathFinderTAllResults.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase)) return SupportedFileType.MsPathFinderTAllResults; + if (filePath.EndsWith(SupportedFileType.IntralinkResults.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase)) + return SupportedFileType.IntralinkResults; // these tsv cases are just .tsv and need an extra step to determine the type // currently need to distinguish between FlashDeconvTsv and MsFraggerPsm diff --git a/mzLib/Test/FileReadingTests/SearchResults/XL_Intralinks.tsv b/mzLib/Test/FileReadingTests/SearchResults/XL_Intralinks.tsv new file mode 100644 index 000000000..2adc7e829 --- /dev/null +++ b/mzLib/Test/FileReadingTests/SearchResults/XL_Intralinks.tsv @@ -0,0 +1,7 @@ +File Name Scan Number Precursor Scan Number Precursor MZ Precursor Charge Precursor Mass Cross Type Link Residues Peptide Info --> Protein Accession Protein Link Site Base Sequence Full Sequence Peptide Monoisotopic Mass Score Matched Ion Series Matched Ion Mass-To-Charge Ratios Matched Ion Mass Diff (Da) Matched Ion Mass Diff (Ppm) Matched Ion Intensities Matched Ion Counts Beta Peptide Info --> Beta Peptide Protein Accession Beta Peptide Protein LinkSite Beta Peptide Base Sequence Beta Peptide Full Sequence Beta Peptide Theoretical Mass Beta Peptide Score Beta Peptide Matched Ions Beta Peptide Matched Ion Mass-To-Charge Ratios Beta Peptide Matched Ion Mass Diff (Da) Beta Peptide Matched Ion Mass Diff (Ppm) Beta Peptide Matched Ion Intensities Beta Peptide Matched Ion Counts Summary Info --> XL Total Score Mass Diff (Da) AlphaIndexingRank Parent Ions ParentIonsNum AlphaParentIonMaxIntensityRank BetaParentIonMaxIntensityRank Decoy/Contaminant/Target QValue PEP PEP_QValue +C:\Users\Alex\Source\Repos\MetaMorpheus\MetaMorpheus\Test\bin\Debug\net6.0-windows\XlTestData\2017-11-21_XL_DSSO_Ribosome_RT60min_28800-28898.mzML 13 12 814.2442253405868 5 4066.184744368539 Intra K;K P62399 69 LLDNAAADLAAISGQKPLITKAR LLDNAAADLAAISGQKPLITKAR(21) 2349.337993761 29.169323073176578 [y1+1, y4+1, y7+1, y7+1, y8+1, y8+1, y10+1, y10+1, y11+1, y11+1, y12+1, y13+1, y13+1, y14+1, y14+2, y15+2, y16+2, y17+2, y17+2, y18+2, y18+2, y19+2, y21+2, y21+2];[b2+1, b3+1, b4+1, b5+1, b6+1] [y1+1:175.11894, y4+1:529.31299, y7+1:852.53026, y7+1:884.49713, y8+1:980.62671, y8+1:1012.60724, y10+1:1165.69849, y10+1:1197.67297, y11+1:1252.73770, y11+1:1284.71973, y12+1:1365.81321, y13+1:1436.86389, y13+1:1468.81409, y14+1:1507.86951, y14+2:770.43798, y15+2:810.99864, y16+2:868.50718, y17+2:904.02582, y17+2:920.01357, y18+2:939.54368, y18+2:955.52997, y19+2:975.06372, y21+2:1089.59561, y21+2:1105.58327];[b2+1:227.17535, b3+1:342.20227, b4+1:456.24362, b5+1:527.28223, b6+1:598.31659] [y1+1:-0.00001, y4+1:0.00372, y7+1:0.00010, y7+1:-0.00510, y8+1:0.00159, y8+1:0.01004, y10+1:-0.00668, y10+1:-0.00426, y11+1:0.00051, y11+1:0.01046, y12+1:-0.00805, y13+1:0.00552, y13+1:-0.01636, y14+1:-0.02598, y14+2:0.00112, y15+2:0.01045, y16+2:0.00059, y17+2:0.00076, y17+2:0.00418, y18+2:-0.00064, y18+2:-0.00013, y19+2:0.00233, y21+2:-0.00375, y21+2:-0.00052];[b2+1:-0.00006, b3+1:-0.00008, b4+1:-0.00165, b5+1:-0.00016, b6+1:-0.00291] [y1+1:-0.06, y4+1:7.04, y7+1:0.12, y7+1:-5.78, y8+1:1.62, y8+1:9.93, y10+1:-5.73, y10+1:-3.56, y11+1:0.41, y11+1:8.15, y12+1:-5.89, y13+1:3.85, y13+1:-11.14, y14+1:-17.24, y14+2:0.72, y15+2:6.45, y16+2:0.34, y17+2:0.42, y17+2:2.27, y18+2:-0.34, y18+2:-0.07, y19+2:1.20, y21+2:-1.72, y21+2:-0.23];[b2+1:-0.26, b3+1:-0.23, b4+1:-3.63, b5+1:-0.31, b6+1:-4.88] [y1+1:33225, y4+1:38394, y7+1:166030, y7+1:131941, y8+1:36154, y8+1:27795, y10+1:47857, y10+1:33075, y11+1:106378, y11+1:71289, y12+1:41232, y13+1:39860, y13+1:21336, y14+1:23503, y14+2:41531, y15+2:69178, y16+2:123224, y17+2:193930, y17+2:82412, y18+2:244088, y18+2:120438, y19+2:72031, y21+2:171274, y21+2:76124];[b2+1:167093, b3+1:80372, b4+1:25267, b5+1:86956, b6+1:23956] 29 P62399 47 ITLNMGVGEAIADKK ITLNMGVGEAIADKK(14) 1558.838878688 29.126828994478604 [y1+1, y2+1, y2+1, y3+1, y3+1, y4+1, y4+1, y5+1, y5+1, y6+1, y6+1, y8+1, y8+1, y9+1, y9+1, y10+1, y10+1, y11+1, y11+1, y12+1, y12+1, y13+1, y13+1, y14+1, y14+1];[b2+1, b5+1];[M15+1, M15+2] [y1+1:147.11284, y2+1:329.21930, y2+1:361.18985, y3+1:444.24649, y3+1:476.21674, y4+1:515.28143, y4+1:547.25348, y5+1:628.36328, y5+1:660.33710, y6+1:699.40881, y6+1:731.37738, y8+1:885.47717, y8+1:917.43610, y9+1:984.53998, y9+1:1016.50183, y10+1:1041.55862, y10+1:1073.52808, y11+1:1172.59192, y11+1:1204.56875, y12+1:1286.64578, y12+1:1318.61387, y13+1:1399.73218, y13+1:1431.69682, y14+1:1500.77225, y14+1:1532.75964];[b2+1:215.13914, b5+1:573.30548];[M15+1:1613.87341, M15+2:823.41936] [y1+1:0.00003, y2+1:0.00097, y2+1:-0.00055, y3+1:0.00122, y3+1:-0.00061, y4+1:-0.00095, y4+1:-0.00098, y5+1:-0.00317, y5+1:-0.00143, y6+1:0.00525, y6+1:0.00174, y8+1:0.00955, y8+1:-0.00360, y9+1:0.00395, y9+1:-0.00628, y10+1:0.00112, y10+1:-0.00150, y11+1:-0.00606, y11+1:-0.00130, y12+1:0.00487, y12+1:0.00089, y13+1:0.00721, y13+1:-0.00022, y14+1:-0.00040, y14+1:0.01492];[b2+1:0.00012, b5+1:-0.00101];[M15+1:0.01670, M15+2:0.00266] [y1+1:0.24, y2+1:2.96, y2+1:-1.53, y3+1:2.75, y3+1:-1.28, y4+1:-1.85, y4+1:-1.79, y5+1:-5.05, y5+1:-2.16, y6+1:7.52, y6+1:2.39, y8+1:10.80, y8+1:-3.93, y9+1:4.01, y9+1:-6.18, y10+1:1.08, y10+1:-1.39, y11+1:-5.17, y11+1:-1.08, y12+1:3.79, y12+1:0.67, y13+1:5.15, y13+1:-0.16, y14+1:-0.27, y14+1:9.74];[b2+1:0.55, b5+1:-1.77];[M15+1:10.35, M15+2:1.62] [y1+1:21722, y2+1:38487, y2+1:64403, y3+1:22145, y3+1:25565, y4+1:46929, y4+1:56360, y5+1:22780, y5+1:28692, y6+1:40853, y6+1:35980, y8+1:142248, y8+1:108807, y9+1:25118, y9+1:25294, y10+1:123048, y10+1:145438, y11+1:58818, y11+1:66025, y12+1:98161, y12+1:83413, y13+1:80308, y13+1:78009, y14+1:33858, y14+1:29881];[b2+1:206883, b5+1:21241];[M15+1:26033, M15+2:38150] 29 58.296152067655186 158.0078719195394 27 0;2 2 - 39 T 0 NaN NaN +C:\Users\Alex\Source\Repos\MetaMorpheus\MetaMorpheus\Test\bin\Debug\net6.0-windows\XlTestData\2017-11-21_XL_DSSO_Ribosome_RT60min_28800-28898.mzML 28 23 1084.1672036127347 5 5415.799635729279 Intra K;K P0AG55 134 GNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADK GNVINLSLGFSHPVDHQLPAGITAEC[Common Fixed:Carbamidomethyl on C]PTQTEIVLKGADK(35) 4126.115728742 33.15043652341575 [y1+1, y2+1, y3+1, y4+1, y5+1, y5+1, y6+1, y6+1, y7+1, y7+1, y8+1, y8+1, y9+1, y9+1, y10+1, y10+1, y11+1, y11+1, y13+1, y13+1, y14+1, y14+1];[b2+1, b3+1, b4+1, b5+1, b6+1, b12+1, b14+1, b17+2, b18+2, b21+2, b25+2] [y1+1:147.11241, y2+1:262.13977, y3+1:333.17648, y4+1:390.19775, y5+1:572.30359, y5+1:604.27533, y6+1:685.38922, y6+1:717.36584, y7+1:784.45807, y7+1:816.43065, y8+1:897.54584, y8+1:929.51123, y9+1:1026.58035, y9+1:1058.55078, y10+1:1127.62377, y10+1:1159.60073, y11+1:1255.69104, y11+1:1287.65793, y13+1:1453.78977, y13+1:1485.76018, y14+1:1613.82542, y14+1:1645.79053];[b2+1:172.07158, b3+1:271.13966, b4+1:384.22473, b5+1:498.26654, b6+1:611.35284, b12+1:1239.66736, b14+1:1435.76085, b17+2:908.46129, b18+2:965.00287, b21+2:1077.55606, b25+2:1284.66319] [y1+1:-0.00039, y2+1:0.00002, y3+1:-0.00038, y4+1:-0.00058, y5+1:-0.00026, y5+1:-0.00059, y6+1:0.00131, y6+1:0.00586, y7+1:0.00174, y7+1:0.00225, y8+1:0.00545, y8+1:-0.00123, y9+1:-0.00264, y9+1:-0.00428, y10+1:-0.00689, y10+1:-0.00201, y11+1:0.00180, y11+1:-0.00339, y13+1:0.00009, y13+1:-0.00158, y14+1:0.00509, y14+1:-0.00188];[b2+1:-0.00009, b3+1:-0.00042, b4+1:0.00059, b5+1:-0.00053, b6+1:0.00171, b12+1:0.01931, b14+1:-0.00838, b17+2:0.00165, b18+2:0.00074, b21+2:-0.00422, b25+2:-0.00142] [y1+1:-2.69, y2+1:0.09, y3+1:-1.14, y4+1:-1.48, y5+1:-0.46, y5+1:-0.98, y6+1:1.91, y6+1:8.18, y7+1:2.23, y7+1:2.76, y8+1:6.08, y8+1:-1.33, y9+1:-2.57, y9+1:-4.04, y10+1:-6.11, y10+1:-1.73, y11+1:1.44, y11+1:-2.63, y13+1:0.06, y13+1:-1.06, y14+1:3.16, y14+1:-1.14];[b2+1:-0.52, b3+1:-1.54, b4+1:1.53, b5+1:-1.07, b6+1:2.80, b12+1:15.59, b14+1:-5.84, b17+2:0.91, b18+2:0.38, b21+2:-1.96, b25+2:-0.55] [y1+1:18356, y2+1:21066, y3+1:14448, y4+1:126868, y5+1:40753, y5+1:37258, y6+1:41476, y6+1:42567, y7+1:35688, y7+1:30814, y8+1:31066, y8+1:27161, y9+1:30150, y9+1:18243, y10+1:54474, y10+1:40244, y11+1:15273, y11+1:12609, y13+1:55269, y13+1:45169, y14+1:14049, y14+1:11369];[b2+1:193557, b3+1:211700, b4+1:36208, b5+1:23370, b6+1:32397, b12+1:50968, b14+1:13321, b17+2:20184, b18+2:44882, b21+2:21506, b25+2:39454] 33 P0AG55 86 KLQLVGVGYR KLQLVGVGYR(1) 1131.676427989 16.121691012123826 [y1+1, y3+1, y4+1, y5+1, y6+1, y7+1, y8+1, y9+1];[b2+1, b2+1, b3+1, b3+1, b4+1, b5+1];[M10+1, M10+1] [y1+1:175.11893, y3+1:395.20447, y4+1:494.27682, y5+1:551.29364, y6+1:650.36253, y7+1:763.44794, y8+1:891.50470, y9+1:1004.59125];[b2+1:296.19656, b2+1:328.16858, b3+1:424.25467, b3+1:456.22659, b4+1:537.34149, b5+1:636.41693];[M10+1:1186.69480, M10+1:1218.66543] [y1+1:-0.00003, y3+1:0.00072, y4+1:0.00467, y5+1:0.00002, y6+1:0.00050, y7+1:0.00184, y8+1:0.00002, y9+1:0.00251];[b2+1:-0.00030, b2+1:-0.00036, b3+1:-0.00077, b3+1:-0.00092, b4+1:0.00199, b5+1:0.00901];[M10+1:0.00053, M10+1:-0.00091] [y1+1:-0.14, y3+1:1.83, y4+1:9.46, y5+1:0.03, y6+1:0.77, y7+1:2.41, y8+1:0.02, y9+1:2.50];[b2+1:-1.02, b2+1:-1.10, b3+1:-1.82, b3+1:-2.03, b4+1:3.70, b5+1:14.18];[M10+1:0.45, M10+1:-0.75] [y1+1:20203, y3+1:45618, y4+1:13754, y5+1:147463, y6+1:85195, y7+1:79095, y8+1:133920, y9+1:20558];[b2+1:64963, b2+1:20745, b3+1:47077, b3+1:23057, b4+1:18911, b5+1:13653];[M10+1:354422, M10+1:85849] 16 49.272127535539575 158.0074789982782 1 0;2 2 - 1 T 0 NaN NaN +C:\Users\Alex\Source\Repos\MetaMorpheus\MetaMorpheus\Test\bin\Debug\net6.0-windows\XlTestData\2017-11-21_XL_DSSO_Ribosome_RT60min_28800-28898.mzML 43 34 1354.956639502793 4 5415.797452143656 Intra K;K P0AG55 134 GNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADK GNVINLSLGFSHPVDHQLPAGITAEC[Common Fixed:Carbamidomethyl on C]PTQTEIVLKGADK(35) 4126.115728742 33.15257139640505 [y1+1, y2+1, y4+1, y5+1, y5+1, y6+1, y6+1, y7+1, y7+1, y8+1, y10+1, y11+1, y12+1, y13+1, y13+1, y14+1, y14+1, y17+1, y17+1, y31+2, y33+2];[b2+1, b3+1, b4+1, b5+1, b6+1, b7+1, b8+1, b12+1, b14+1, b15+1, b17+2, b18+2] [y1+1:147.11313, y2+1:262.13937, y4+1:390.19834, y5+1:572.30579, y5+1:604.27258, y6+1:685.39026, y6+1:717.36273, y7+1:784.46301, y7+1:816.43219, y8+1:897.53223, y10+1:1159.59424, y11+1:1287.64099, y12+1:1388.70512, y13+1:1453.78772, y13+1:1485.74756, y14+1:1613.82678, y14+1:1645.80371, y17+1:1914.92432, y17+1:1946.89417, y31+2:1685.82558, y33+2:1785.88229];[b2+1:172.07152, b3+1:271.13977, b4+1:384.22446, b5+1:498.26614, b6+1:611.35291, b7+1:698.37854, b8+1:811.45807, b12+1:1239.67212, b14+1:1435.75635, b15+1:1550.77061, b17+2:908.45964, b18+2:965.00365] [y1+1:0.00032, y2+1:-0.00037, y4+1:0.00002, y5+1:0.00194, y5+1:-0.00334, y6+1:0.00235, y6+1:0.00275, y7+1:0.00669, y7+1:0.00379, y8+1:-0.00816, y10+1:-0.00850, y11+1:-0.02032, y12+1:-0.00387, y13+1:-0.00196, y13+1:-0.01420, y14+1:0.00645, y14+1:0.01131, y17+1:-0.02340, y17+1:-0.02562, y31+2:-0.02972, y33+2:-0.03240];[b2+1:-0.00015, b3+1:-0.00031, b4+1:0.00031, b5+1:-0.00093, b6+1:0.00177, b7+1:-0.00463, b8+1:-0.00916, b12+1:0.02407, b14+1:-0.01288, b15+1:-0.02556, b17+2:-0.00165, b18+2:0.00231] [y1+1:2.22, y2+1:-1.43, y4+1:0.05, y5+1:3.39, y5+1:-5.54, y6+1:3.43, y6+1:3.83, y7+1:8.54, y7+1:4.65, y8+1:-9.11, y10+1:-7.33, y11+1:-15.79, y12+1:-2.79, y13+1:-1.35, y13+1:-9.56, y14+1:4.00, y14+1:6.87, y17+1:-12.23, y17+1:-13.17, y31+2:-8.82, y33+2:-9.08];[b2+1:-0.88, b3+1:-1.15, b4+1:0.81, b5+1:-1.87, b6+1:2.90, b7+1:-6.63, b8+1:-11.30, b12+1:19.43, b14+1:-8.98, b15+1:-16.49, b17+2:-0.91, b18+2:1.20] [y1+1:2173, y2+1:2972, y4+1:15793, y5+1:6849, y5+1:4887, y6+1:6797, y6+1:5165, y7+1:3977, y7+1:3092, y8+1:2123, y10+1:2168, y11+1:1787, y12+1:1574, y13+1:8405, y13+1:5930, y14+1:4425, y14+1:3775, y17+1:2756, y17+1:1708, y31+2:3596, y33+2:3140];[b2+1:20613, b3+1:28129, b4+1:6155, b5+1:5077, b6+1:5181, b7+1:1944, b8+1:1572, b12+1:11832, b14+1:1516, b15+1:2291, b17+2:5168, b18+2:9011] 33 P0AG55 86 KLQLVGVGYR KLQLVGVGYR(1) 1131.676427989 7.136792208777973 [y1+1, y3+1, y5+1, y8+1];[b2+1];[M10+1, M10+1] [y1+1:175.11925, y3+1:395.20401, y5+1:551.29877, y8+1:891.49396];[b2+1:296.19684];[M10+1:1186.69402, M10+1:1218.66714] [y1+1:0.00030, y3+1:0.00027, y5+1:0.00515, y8+1:-0.01072];[b2+1:-0.00003];[M10+1:-0.00024, M10+1:0.00080] [y1+1:1.70, y3+1:0.67, y5+1:9.35, y8+1:-12.04];[b2+1:-0.08];[M10+1:-0.20, M10+1:0.66] [y1+1:2475, y3+1:1832, y5+1:3073, y8+1:1734];[b2+1:1682];[M10+1:121491, M10+1:39484] 7 40.28936360518303 158.00529541265587 1 0;2 2 - 3 T 0 NaN NaN +C:\Users\Alex\Source\Repos\MetaMorpheus\MetaMorpheus\Test\bin\Debug\net6.0-windows\XlTestData\2017-11-21_XL_DSSO_Ribosome_RT60min_28800-28898.mzML 27 23 903.6405490884255 6 5415.799635729279 Intra K;K P0AG55 134 GNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADK GNVINLSLGFSHPVDHQLPAGITAEC[Common Fixed:Carbamidomethyl on C]PTQTEIVLKGADK(35) 4126.115728742 24.126683253963822 [y1+1, y2+1, y3+1, y4+1, y5+1, y5+1, y6+1, y7+1, y7+1, y8+1, y8+1, y9+1, y9+1, y10+1, y10+1, y11+1, y11+1, y13+1, y13+1, y14+2];[b2+1, b3+1, b4+1, b6+1] [y1+1:147.11278, y2+1:262.14023, y3+1:333.17590, y4+1:390.19732, y5+1:572.30322, y5+1:604.27552, y6+1:685.38910, y7+1:784.46252, y7+1:816.43109, y8+1:897.54047, y8+1:929.51474, y9+1:1026.58535, y9+1:1058.55688, y10+1:1127.62061, y10+1:1159.60266, y11+1:1255.68005, y11+1:1287.65918, y13+1:1453.78932, y13+1:1485.76611, y14+2:807.41543];[b2+1:172.07167, b3+1:271.13977, b4+1:384.22406, b6+1:611.34302] [y1+1:-0.00003, y2+1:0.00048, y3+1:-0.00096, y4+1:-0.00100, y5+1:-0.00063, y5+1:-0.00040, y6+1:0.00119, y7+1:0.00620, y7+1:0.00269, y8+1:0.00008, y8+1:0.00228, y9+1:0.00237, y9+1:0.00183, y10+1:-0.01006, y10+1:-0.00008, y11+1:-0.00918, y11+1:-0.00213, y13+1:-0.00036, y13+1:0.00436, y14+2:0.00325];[b2+1:0.00000, b3+1:-0.00031, b4+1:-0.00009, b6+1:-0.00812] [y1+1:-0.18, y2+1:1.84, y3+1:-2.88, y4+1:-2.58, y5+1:-1.09, y5+1:-0.66, y6+1:1.74, y7+1:7.91, y7+1:3.30, y8+1:0.09, y8+1:2.45, y9+1:2.31, y9+1:1.73, y10+1:-8.93, y10+1:-0.06, y11+1:-7.32, y11+1:-1.66, y13+1:-0.25, y13+1:2.93, y14+2:2.01];[b2+1:0.02, b3+1:-1.15, b4+1:-0.22, b6+1:-13.30] [y1+1:15375, y2+1:19547, y3+1:11896, y4+1:94285, y5+1:30408, y5+1:33765, y6+1:34318, y7+1:32010, y7+1:35654, y8+1:25188, y8+1:26826, y9+1:20595, y9+1:20744, y10+1:45958, y10+1:37701, y11+1:17083, y11+1:14519, y13+1:34308, y13+1:36039, y14+2:21331];[b2+1:297776, b3+1:184639, b4+1:26539, b6+1:11787] 24 P0AG55 86 KLQLVGVGYR KLQLVGVGYR(1) 1131.676427989 15.112740044577905 [y1+1, y3+1, y4+1, y5+1, y6+1, y7+1, y8+1, y9+1];[b2+1, b2+1, b3+1, b3+1, b4+1];[M10+1, M10+1] [y1+1:175.11873, y3+1:395.20248, y4+1:494.27310, y5+1:551.29425, y6+1:650.36171, y7+1:763.44788, y8+1:891.50525, y9+1:1004.58844];[b2+1:296.19714, b2+1:328.16907, b3+1:424.25446, b3+1:456.22751, b4+1:537.34222];[M10+1:1186.69434, M10+1:1218.66241] [y1+1:-0.00022, y3+1:-0.00126, y4+1:0.00094, y5+1:0.00063, y6+1:-0.00033, y7+1:0.00178, y8+1:0.00057, y9+1:-0.00030];[b2+1:0.00028, b2+1:0.00013, b3+1:-0.00099, b3+1:-0.00001, b4+1:0.00272];[M10+1:0.00007, M10+1:-0.00393] [y1+1:-1.28, y3+1:-3.20, y4+1:1.91, y5+1:1.14, y6+1:-0.50, y7+1:2.33, y8+1:0.64, y9+1:-0.30];[b2+1:0.95, b2+1:0.39, b3+1:-2.33, b3+1:-0.02, b4+1:5.07];[M10+1:0.06, M10+1:-3.23] [y1+1:21593, y3+1:38231, y4+1:17572, y5+1:152087, y6+1:89434, y7+1:78355, y8+1:114958, y9+1:22446];[b2+1:55329, b2+1:22709, b3+1:57425, b3+1:28988, b4+1:14214];[M10+1:220667, M10+1:70101] 15 39.23942329854172 158.0074789982782 5 0;2 2 - 1 T 0 NaN NaN +C:\Users\Alex\Source\Repos\MetaMorpheus\MetaMorpheus\Test\bin\Debug\net6.0-windows\XlTestData\2017-11-21_XL_DSSO_Ribosome_RT60min_28800-28898.mzML 51 45 678.704623045646 6 4066.184079472602 Intra K;K P62399 47 ITLNMGVGEAIADKK ITLNMGVGEAIADKK(14) 1558.838878688 20.089596895792027 [y1+1, y2+1, y2+1, y3+1, y3+1, y4+1, y4+1, y5+1, y5+1, y6+1, y6+1, y8+1, y8+1, y10+1, y10+1, y11+1, y12+1, y12+1, y13+1];[b2+1] [y1+1:147.11273, y2+1:329.22083, y2+1:361.19110, y3+1:444.24945, y3+1:476.22574, y4+1:515.28436, y4+1:547.25384, y5+1:628.36487, y5+1:660.33893, y6+1:699.40552, y6+1:731.38312, y8+1:885.47797, y8+1:917.44286, y10+1:1041.56860, y10+1:1073.53394, y11+1:1204.58508, y12+1:1286.66272, y12+1:1318.62988, y13+1:1431.71167];[b2+1:215.13919] [y1+1:-0.00007, y2+1:0.00250, y2+1:0.00070, y3+1:0.00418, y3+1:0.00839, y4+1:0.00198, y4+1:-0.00062, y5+1:-0.00158, y5+1:0.00041, y6+1:0.00196, y6+1:0.00748, y8+1:0.01035, y8+1:0.00317, y10+1:0.01111, y10+1:0.00436, y11+1:0.01503, y12+1:0.02181, y12+1:0.01690, y13+1:0.01462];[b2+1:0.00017] [y1+1:-0.49, y2+1:7.61, y2+1:1.94, y3+1:9.43, y3+1:17.66, y4+1:3.85, y4+1:-1.13, y5+1:-2.52, y5+1:0.61, y6+1:2.80, y6+1:10.24, y8+1:11.70, y8+1:3.46, y10+1:10.67, y10+1:4.07, y11+1:12.49, y12+1:16.97, y12+1:12.83, y13+1:10.22];[b2+1:0.80] [y1+1:74724, y2+1:16137, y2+1:18663, y3+1:8680, y3+1:8874, y4+1:19015, y4+1:18702, y5+1:10478, y5+1:13384, y6+1:26267, y6+1:11389, y8+1:59509, y8+1:31219, y10+1:22269, y10+1:26060, y11+1:10336, y12+1:9065, y12+1:12012, y13+1:8226];[b2+1:33318] 20 P62399 69 LLDNAAADLAAISGQKPLITKAR LLDNAAADLAAISGQKPLITKAR(21) 2349.337993761 18.08918756365762 [y1+1, y4+1, y4+1, y6+1, y7+1, y7+1, y8+1, y11+2, y11+1, y12+2, y13+2, y14+2];[b2+1, b3+1, b5+1, b6+1, b8+1, b9+1] [y1+1:175.11913, y4+1:529.30933, y4+1:561.28784, y6+1:755.46906, y7+1:852.53164, y7+1:884.50635, y8+1:1012.59882, y11+2:626.87416, y11+1:1284.71545, y12+2:683.41356, y13+2:718.93366, y14+2:770.44121];[b2+1:227.17451, b3+1:342.20462, b5+1:527.28415, b6+1:598.31836, b8+1:784.38336, b9+1:897.47479] [y1+1:0.00017, y4+1:0.00006, y4+1:0.00650, y6+1:-0.00834, y7+1:0.00148, y7+1:0.00411, y8+1:0.00162, y11+2:0.00385, y11+1:0.00619, y12+2:-0.00141, y13+2:0.00167, y14+2:0.00759];[b2+1:-0.00089, b3+1:0.00227, b5+1:0.00176, b6+1:-0.00114, b8+1:-0.00020, b9+1:0.00717] [y1+1:0.99, y4+1:0.11, y4+1:11.60, y6+1:-11.05, y7+1:1.73, y7+1:4.66, y8+1:1.60, y11+2:3.08, y11+1:4.82, y12+2:-1.03, y13+2:1.17, y14+2:4.93];[b2+1:-3.93, b3+1:6.66, b5+1:3.34, b6+1:-1.91, b8+1:-0.25, b9+1:8.00] [y1+1:16344, y4+1:10137, y4+1:7731, y6+1:18453, y7+1:77950, y7+1:42608, y8+1:8493, y11+2:41998, y11+1:8207, y12+2:31722, y13+2:51822, y14+2:15292];[b2+1:15084, b3+1:9008, b5+1:23851, b6+1:11368, b8+1:35923, b9+1:10333] 18 38.178784459449645 158.0072070236024 16 0;0 0 - - T 0 NaN NaN +C:\Users\Alex\Source\Repos\MetaMorpheus\MetaMorpheus\Test\bin\Debug\net6.0-windows\XlTestData\2017-11-21_XL_DSSO_Ribosome_RT60min_28800-28898.mzML 38 34 1017.5533194495598 4 4066.184171930723 Intra K;K P62399 69 LLDNAAADLAAISGQKPLITKAR LLDNAAADLAAISGQKPLITKAR(21) 2349.337993761 19.066530501486493 [y1+1, y2+1, y4+1, y7+1, y7+1, y10+1, y10+1, y11+1, y11+1, y12+1, y13+1, y13+1, y14+1, y17+2, y18+2];[b2+1, b3+1, b5+1, b8+1] [y1+1:175.11909, y2+1:246.15567, y4+1:529.30151, y7+1:852.53503, y7+1:884.50214, y10+1:1165.70642, y10+1:1197.65442, y11+1:1252.74023, y11+1:1284.70789, y12+1:1397.77319, y13+1:1436.86865, y13+1:1468.80823, y14+1:1507.88306, y17+2:904.03063, y18+2:939.54384];[b2+1:227.17517, b3+1:342.20706, b5+1:527.27515, b8+1:784.39410] [y1+1:0.00014, y2+1:-0.00040, y4+1:-0.00775, y7+1:0.00487, y7+1:-0.00010, y10+1:0.00126, y10+1:-0.02282, y11+1:0.00304, y11+1:-0.00138, y12+1:-0.02014, y13+1:0.01028, y13+1:-0.02222, y14+1:-0.01243, y17+2:0.01038, y18+2:-0.00031];[b2+1:-0.00023, b3+1:0.00471, b5+1:-0.00724, b8+1:0.01054] [y1+1:0.82, y2+1:-1.61, y4+1:-14.68, y7+1:5.72, y7+1:-0.11, y10+1:1.08, y10+1:-19.07, y11+1:2.43, y11+1:-1.08, y12+1:-14.42, y13+1:7.16, y13+1:-15.14, y14+1:-8.25, y17+2:5.75, y18+2:-0.17];[b2+1:-1.03, b3+1:13.82, b5+1:-13.76, b8+1:13.46] [y1+1:19152, y2+1:17940, y4+1:5648, y7+1:27755, y7+1:16131, y10+1:9283, y10+1:5413, y11+1:21020, y11+1:11989, y12+1:5051, y13+1:6971, y13+1:5121, y14+1:5244, y17+2:13005, y18+2:13447];[b2+1:16642, b3+1:8156, b5+1:27418, b8+1:5894] 19 P62399 47 ITLNMGVGEAIADKK ITLNMGVGEAIADKK(14) 1558.838878688 17.041200589470144 [y1+1, y2+1, y2+1, y4+1, y4+1, y5+1, y6+1, y6+1, y8+1, y8+1, y10+1, y10+1, y11+1, y12+1];[b2+1];[M15+1, M15+1] [y1+1:147.11266, y2+1:329.21808, y2+1:361.18799, y4+1:515.27832, y4+1:547.25623, y5+1:660.33276, y6+1:699.40576, y6+1:731.37079, y8+1:885.47741, y8+1:917.44482, y10+1:1041.55688, y10+1:1073.51660, y11+1:1172.58313, y12+1:1286.64441];[b2+1:215.13843];[M15+1:1613.85203, M15+1:1645.83004] [y1+1:-0.00015, y2+1:-0.00025, y2+1:-0.00241, y4+1:-0.00406, y4+1:0.00177, y5+1:-0.00576, y6+1:0.00220, y6+1:-0.00485, y8+1:0.00979, y8+1:0.00513, y10+1:-0.00061, y10+1:-0.01297, y11+1:-0.01485, y12+1:0.00350];[b2+1:-0.00059];[M15+1:-0.00468, M15+1:0.00125] [y1+1:-1.02, y2+1:-0.76, y2+1:-6.70, y4+1:-7.90, y4+1:3.23, y5+1:-8.74, y6+1:3.15, y6+1:-6.64, y8+1:11.07, y8+1:5.60, y10+1:-0.59, y10+1:-12.09, y11+1:-12.68, y12+1:2.72];[b2+1:-2.76];[M15+1:-2.90, M15+1:0.76] [y1+1:7699, y2+1:7426, y2+1:5976, y4+1:5789, y4+1:6294, y5+1:5404, y6+1:7919, y6+1:5598, y8+1:19976, y8+1:9969, y10+1:9908, y10+1:6715, y11+1:5183, y12+1:5561];[b2+1:5749];[M15+1:17383, M15+1:16870] 17 36.107731090956634 158.0072994817233 7 0;2 2 - 13 T 0 NaN NaN diff --git a/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs b/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs index 2018158b1..68d0f5481 100644 --- a/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs +++ b/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs @@ -22,6 +22,8 @@ public static class TestPsmFromTsv [TestCase("oglycoSinglePsms.psmtsv", 2)] // oglyco [TestCase("nglyco_f5.psmtsv", 5)] // nglyco [TestCase("VariantCrossTest.psmtsv", 15)] // variant crossing + [TestCase("XL_Intralinks.tsv", 6)] // variant crossing + [TestCase("XLink.psmtsv", 19)] // variant crossing public static void TestPsmReaderWithMultipleEntryPoints(string path, int expected) { string psmFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"FileReadingTests\SearchResults", diff --git a/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs b/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs index ef7a238b0..1f2d91ed8 100644 --- a/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs +++ b/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs @@ -37,6 +37,8 @@ internal class TestSupportedFileExtensions [TestCase(@"FileReadingTests\ExternalFileTypes\MsPathFinderT_DecoyResults_IcDecoy.tsv", SupportedFileType.MsPathFinderTDecoys)] [TestCase(@"FileReadingTests\ExternalFileTypes\MsPathFinderT_AllResults_IcTda.tsv", SupportedFileType.MsPathFinderTAllResults)] [TestCase(@"FileReadingTests\ExternalFileTypes\crux.txt", SupportedFileType.CruxResult)] + [TestCase(@"FileReadingTests\ExternalFileTypes\XL_Intralinks.tsv", SupportedFileType.IntralinkResults)] + [TestCase(@"FileReadingTests\ExternalFileTypes\XLink.psmtsv", SupportedFileType.psmtsv)] public static void TestSupportedFileTypeExtensions(string filePath, SupportedFileType expectedType) { var supportedType = filePath.ParseFileType(); diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj index b58d87522..797157c8b 100644 --- a/mzLib/Test/Test.csproj +++ b/mzLib/Test/Test.csproj @@ -447,6 +447,9 @@ Always + + Always + Always