diff --git a/R/clean_Metamorpheus.R b/R/clean_Metamorpheus.R index 1ebeb10d..ffd992da 100644 --- a/R/clean_Metamorpheus.R +++ b/R/clean_Metamorpheus.R @@ -1,10 +1,28 @@ #' Clean raw Metamorpheus files #' @param msstats_object an object of class `MSstatsMetamorpheusFiles`. +#' @param MBR If TRUE, the function will include peaks detected by MBR +#' @param qvalue_cutoff The q-value cutoff for filtering peaks detected by MBR #' @return data.table #' @keywords internal -.cleanRawMetamorpheus = function(msstats_object) { +.cleanRawMetamorpheus = function(msstats_object, MBR = TRUE, qvalue_cutoff = 0.05) { metamorpheus_input = getInputFile(msstats_object, "input") metamorpheus_input = data.table::as.data.table(metamorpheus_input) + # Remove peptide decoys + if ("DecoyPeptide" %in% colnames(metamorpheus_input)) { + metamorpheus_input <- metamorpheus_input[!metamorpheus_input$DecoyPeptide, ] + } + # Remove peak decoys + if ("RandomRT" %in% colnames(metamorpheus_input)) { + metamorpheus_input <- metamorpheus_input[!metamorpheus_input$RandomRT, ] + } + if (MBR) { + metamorpheus_input = metamorpheus_input[ + metamorpheus_input$PeakDetectionType == "MSMS" | + metamorpheus_input$`PIPQ-Value` <= qvalue_cutoff , ] + } else { + metamorpheus_input = metamorpheus_input[ + metamorpheus_input$PeakDetectionType == "MSMS", ] + } req_cols = c('FileName', 'ProteinGroup', 'FullSequence', 'PrecursorCharge', 'Peakintensity') metamorpheus_input = metamorpheus_input[, req_cols, with = FALSE] diff --git a/R/converters_MetamorpheusToMSstatsFormat.R b/R/converters_MetamorpheusToMSstatsFormat.R index 9314d3d2..c6425dbb 100644 --- a/R/converters_MetamorpheusToMSstatsFormat.R +++ b/R/converters_MetamorpheusToMSstatsFormat.R @@ -1,7 +1,9 @@ #' Import Metamorpheus files #' #' @param input name of Metamorpheus output file, which is tabular format. Use the AllQuantifiedPeaks.tsv file from the Metamorpheus output. -#' @param annotation name of 'annotation.txt' data which includes Condition, BioReplicate. +#' @param annotation name of 'annotation.txt' data which includes Condition, BioReplicate. +#' @param MBR If TRUE, the function will include peaks detected by MBR +#' @param qvalue_cutoff The q-value cutoff for filtering peaks detected by MBR #' @inheritParams .sharedParametersAmongConverters #' #' @return data.frame in the MSstats required format. @@ -11,17 +13,18 @@ #' @export #' #' @examples -#' input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", +#' input = system.file("tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv", #' package = "MSstatsConvert") #' input = data.table::fread(input) -#' annot = system.file("tinytest/raw_data/Metamorpheus/Annotation.tsv", +#' annot = system.file("tinytest/raw_data/Metamorpheus/annotation.csv", #' package = "MSstatsConvert") #' annot = data.table::fread(annot) #' metamorpheus_imported = MSstatsConvert:::MetamorpheusToMSstatsFormat(input, annotation = annot) #' head(metamorpheus_imported) #' MetamorpheusToMSstatsFormat = function( - input, annotation = NULL, useUniquePeptide = TRUE, removeFewMeasurements = TRUE, + input, annotation = NULL, MBR = TRUE, qvalue_cutoff = 0.05, + useUniquePeptide = TRUE, removeFewMeasurements = TRUE, removeProtein_with1Feature = FALSE, summaryforMultipleRows = max, use_log_file = TRUE, append = FALSE, verbose = TRUE, log_file_path = NULL, ... @@ -31,7 +34,7 @@ MetamorpheusToMSstatsFormat = function( input = MSstatsConvert::MSstatsImport(list(input = input), "MSstats", "Metamorpheus", ...) - input = MSstatsConvert::MSstatsClean(input) + input = MSstatsConvert::MSstatsClean(input, MBR, qvalue_cutoff) annotation = MSstatsConvert::MSstatsMakeAnnotation(input, annotation) feature_columns = c("PeptideSequence", "PrecursorCharge") diff --git a/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds b/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds index 252a0912..3f102e6e 100644 Binary files a/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds and b/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds differ diff --git a/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv b/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv deleted file mode 100644 index 03775dca..00000000 --- a/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv +++ /dev/null @@ -1,339 +0,0 @@ -File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS2 Retention Time Precursor Charge Theoretical MZ Peak intensity Peak RT Start Peak RT Apex Peak RT End Peak MZ Peak Charge Num Charge States Observed Peak Detection Type MBR Score PSMs Mapped Base Sequences Mapped Full Sequences Mapped Peak Split Valley RT Peak Apex Mass Error (ppm) -NEG1-calib TVGEDPQGLFQK TVGEDPQGLFQK P16050 1317.65648 86.938486 2 659.8355167 15166783.5 86.927964 87.035749 87.517789 659.8357909 2 1 MSMS 1 1 1 87.543239 0.416310106 -NEG1-calib EITEIGLQGAQDR EITEIGLQGAQDR P16050 1428.720872 84.743684 2 715.3677122 9480717.125 84.561362 84.84008 85.483566 715.3674502 2 2 MSMS 1 1 1 0 -0.366845642 -NEG1-calib WVEGNGVLSLPEGTGR WVEGNGVLSLPEGTGR P16050 1669.842384 105.05633 2 835.9284683 4480404.5 104.73165 105.00633 105.55682 835.9295845 2 2 MSMS 1 1 1 0 1.336876738 -NEG1-calib AGVETTKPSK AGVETTKPSK B9A064 1016.550224 37.578584 2 509.2823887 4201663.292 37.474181 37.659279 38.335502 339.8574822 3 3 MSMS 2 1 1 0 0.386285903 -NEG1-calib LYDLPVDER LYDLPVDER P16050 1118.560789 90.623037 2 560.287671 4096823.719 90.588529 90.756475 91.122376 560.2881225 2 1 MSMS 1 1 1 0 0.80732065 -NEG1-calib NAKLDMPYEYLRPSVVENSVAI NAKLDMPYEYLRPSVVENSVAI P16050 2507.273011 118.57469 3 836.7649467 3934907.125 118.48588 118.68333 118.93602 837.0987787 3 1 MSMS 1 1 1 0 -0.562665918 -NEG1-calib HREEELEER HREEELEER P16050 1225.568728 41.664865 3 409.5301858 3319623.521 41.581982 41.748276 42.142118 409.5300885 3 1 MSMS 1 1 1 0 -0.238199821 -NEG1-calib GFPVSLQAR GFPVSLQAR P16050 973.5345148 88.657615 2 487.7745339 2290916.813 88.163096 88.567392 88.868132 487.774669 2 2 MSMS 1 1 1 0 0.277721942 -NEG1-calib VTVLGQPK VTVLGQPK B9A064 840.5069031 64.310559 2 421.260728 2192819.797 63.609653 64.293801 65.169948 421.2604986 2 2 MSMS 1 1 1 0 -0.545763046 -NEG1-calib ADGSPVK ADGSPVK B9A064 672.3442544 37.926781 2 337.1794037 2103839.625 37.878198 38.027652 38.361698 337.1791264 2 2 MSMS 1 1 1 0 -0.824674728 -NEG1-calib SAHLPAR SAHLPAR P16050 750.4136714 42.08738 3 251.1451669 1965723.667 41.428459 41.987404 42.781588 251.1451938 3 3 MSMS 3 1 1 0 0.107509637 -NEG1-calib LLPMVIQLQLPR LLPM[Common Variable:Oxidation on M]VIQLQLPR P16050 1435.858492 121.22161 2 718.9365224 1746463.273 121.01968 121.3375 121.6019 718.9372138 2 2 MSMS 1 1 1 0 0.962981574 -NEG1-calib VGAHAGEYGAEALER VGAHAGEYGAEALER P69905 1528.72702 68.267413 2 765.3707862 1668202.797 68.18988 68.209403 68.388092 510.5822669 3 2 MSMS 1 1 1 0 -1.339860118 -NEG1-calib KSAPSTGGVK "K[UniProt:N6,N6,N6-trimethyllysine on K]SAPSTGGVK" P84243 972.5603955 35.688772 2 487.2874742 1664404.719 35.627887 35.731787 36.035686 487.2872557 2 1 MSMS 1 1 1 0 -0.44931205 -NEG1-calib RQPVMVAVGQHEEEYFSGPEPK RQPVMVAVGQHEEEYFSGPEPK P16050 2513.200908 87.219415 3 838.7409126 1526203.32 86.950234 87.249422 87.698333 629.558227 4 2 MSMS 2 1 1 0 0.009853668 -NEG1-calib GISQEQMQEFR GISQEQMQEFR O43707 1351.61905 79.652223 2 676.8168012 1501485.425 79.570521 79.718111 79.915653 676.8169115 2 1 MSMS 1 1 1 0 0.163162193 -NEG1-calib LSGSNPYTTVTPQIINSKWEK LSGSNPYTTVTPQIINSKWEK O43707 2362.216876 98.927757 3 788.4129017 1462195.604 98.70122 98.930579 99.101998 788.7469798 3 1 MSMS 1 1 1 0 -0.289909225 -NEG1-calib YTLEINVR YTLEINVR P16050 1006.544745 90.839733 2 504.279649 1442408.375 90.732721 90.928522 91.418524 504.2797761 2 1 MSMS 1 1 1 0 0.252522933 -NEG1-calib NAKLDMPYEYLRPSVVENSVAI NAKLDM[Common Variable:Oxidation on M]PYEYLRPSVVENSVAI P16050 2523.267925 111.29545 3 842.0965849 1433827.651 111.13655 111.29096 111.30333 842.4302381 3 1 MSMS 1 1 1 111.30771 -0.771673703 -NEG1-calib LAGAPSEDPQFPK LAGAPSEDPQFPK O00391 1355.67213 81.147499 2 678.8433417 1276014.75 81.051221 81.252625 81.407461 678.8433926 2 1 MSMS 1 1 1 0 0.075078339 -NEG1-calib IAESNHIK IAESNHIK O43707 910.4872302 39.977162 2 456.2508916 1231231 39.889658 39.997706 40.08926 304.5028512 3 2 MSMS 1 1 1 0 -0.555758052 -NEG1-calib VNVDEVGGEALGR VNVDEVGGEALGR P68871 1313.657543 84.00776 2 657.836048 1195931.75 83.962888 84.094638 84.267478 657.8362282 2 1 MSMS 1 1 1 0 0.274324323 -NEG1-calib LLPMVIQLQLPR LLPMVIQLQLPR P16050 1419.863577 130.89546 2 710.9390651 1165820.207 130.78084 131.02519 131.37566 710.9391598 2 2 MSMS 1 1 1 0 0.13331393 -NEG1-calib LPPPTTK LPPPTTK P16050 752.4432402 47.272675 2 377.2288965 1163455.148 46.613591 47.381375 48.341816 377.2287956 2 1 MSMS 2 1 1 0 -0.268301028 -NEG1-calib RQPVMVAVGQHEEEYFSGPEPK RQPVM[Common Variable:Oxidation on M]VAVGQHEEEYFSGPEPK P16050 2529.195823 79.640565 4 633.3062322 1149844.461 79.564903 79.771513 80.030434 633.5567265 4 2 MSMS 1 1 1 0 -0.352624726 -NEG1-calib LQPDGKLLPMVIQLQLPR LQPDGKLLPMVIQLQLPR P16050 2058.202352 125.48848 3 687.0747273 1137769.104 125.35933 125.59479 125.83682 687.40959 3 1 MSMS 1 1 1 125.84415 0.830644453 -NEG1-calib FREELAALDKEIEIR FREELAALDKEIEIR P16050 1830.983963 98.18448 3 611.335264 1112742.885 98.083628 98.272039 98.849935 611.3356658 3 2 MSMS 2 1 1 0 0.658444655 -NEG1-calib SSDFQLHELQSHLLR SSDFQLHELQSHLLR P16050 1808.916946 92.945977 3 603.9795917 1052010.5 92.848523 93.01423 93.272171 603.9799395 3 2 MSMS 2 1 1 0 0.576852155 -NEG1-calib SSFYAQDALR SSFYAQDALR P16050 1156.551287 82.640299 2 579.28292 990423.8281 82.608093 82.728799 82.871283 579.2827224 2 1 MSMS 1 1 1 82.880197 -0.341747826 -NEG1-calib KSAPSTGGVK "K[UniProt:N6,N6-dimethyllysine on K]SAPSTGGVK" P84243 958.544745 36.145133 2 480.279649 972237.1406 36.058867 36.184909 36.497811 480.2796919 2 1 MSMS 1 1 1 0 0.089687583 -NEG1-calib TGSPPPPLFLPTDPPMAWLLAK TGSPPPPLFLPTDPPMAWLLAK P16050 2345.249362 152.42215 3 782.7570639 955975.2708 151.70265 152.32563 152.96968 783.0912017 3 2 MSMS 1 1 1 0 -0.23726638 -NEG1-calib TIPWLEDRVPQK TIPWLEDRVPQK O43707 1480.803813 93.763567 3 494.6085476 839821.2226 93.750349 93.787455 94.272579 494.6092208 3 2 MSMS 1 1 1 0 1.36384805 -NEG1-calib EQSEGVGAR EQSEGVGAR O00625 931.4359229 40.354412 2 466.7252379 828546.6328 40.2629 40.386936 40.62904 466.7249416 2 1 MSMS 1 1 1 0 -0.636359993 -NEG1-calib VLSPADKTNVK VLSPADKTNVK P69905 1170.660837 51.502512 2 586.3376952 817038.1875 51.364698 51.508639 51.710613 391.2276332 3 2 MSMS 2 1 1 0 0.198775029 -NEG1-calib VLSAMIR VLSAMIR O43598 788.4578449 76.483862 2 395.2361989 791004.0352 76.360018 76.504371 76.671938 395.2360666 2 1 MSMS 1 1 1 0 -0.335518987 -NEG1-calib TDVAVKDDPELQTWCR TDVAVKDDPELQTWC[Common Fixed:Carbamidomethyl on C]R P16050 1931.904726 86.184129 3 644.9755186 743105.2917 86.100336 86.225705 86.456332 645.3097541 3 2 MSMS 1 1 1 0 -0.076117378 -NEG1-calib SAVTALWGK SAVTALWGK P68871 931.5127167 91.965789 2 466.7636348 627128.7109 91.924054 92.024324 92.22246 466.7631402 2 1 MSMS 1 1 1 0 -1.062073621 -NEG1-calib ADGSPVKAGVETTKPSK ADGSPVKAGVETTKPSK B9A064 1670.883914 49.448235 3 557.9685812 626499.7402 49.367896 49.522173 49.624234 418.7282231 4 2 MSMS 2 1 1 0 -0.076299613 -NEG1-calib ICDQWDALGSLTHSRR IC[Common Fixed:Carbamidomethyl on C]DQWDALGSLTHSRR O43707 1913.916628 91.464492 4 479.4864336 607012.8438 91.372457 91.458343 91.685362 479.7369985 4 2 MSMS 1 1 1 0 -0.259167804 -NEG1-calib AVAFNKR AVAFNKR O43598 804.4606216 42.812995 3 269.160817 589704.9818 42.696067 42.882388 43.039338 269.1606701 3 2 MSMS 1 1 1 0 -0.547785054 -NEG1-calib GISQEQMQEFR GISQEQM[Common Variable:Oxidation on M]QEFR O43707 1367.613964 65.439943 2 684.8142585 580284.2969 65.352983 65.500767 65.683306 684.8145199 2 1 MSMS 1 1 1 0 0.382255182 -NEG1-calib VVAGVANALAHKYH VVAGVANALAHKYH P68871 1448.788832 71.305534 3 483.9368871 568534.9896 71.283939 71.31563 71.612406 483.9369962 3 2 MSMS 1 1 1 71.26828 0.225935031 -NEG1-calib KVTLSVLSR KVTLSVLSR O00625 1001.62333 73.396796 2 501.8189414 560355.125 73.33177 73.492128 73.608974 501.8187277 2 2 MSMS 1 1 1 0 -0.42654917 -NEG1-calib GSTAVGVR GSTAVGVR O14818 745.4082516 44.996662 2 373.7114023 542553.1094 44.929277 45.046467 45.186932 373.7115538 2 2 MSMS 1 1 1 0 0.406557323 -NEG1-calib EALEKTEK EALEKTEK O43707 946.4971262 36.716279 2 474.2558396 535809.3828 36.62973 36.743905 36.862951 474.2554721 2 2 MSMS 1 1 1 0 -0.776576146 -NEG1-calib QLEAIDQLHLEYAKR QLEAIDQLHLEYAKR O43707 1825.968647 89.206919 4 457.4994382 534989.1328 89.116239 89.232376 89.605193 609.6635254 3 2 MSMS 1 1 1 0 0.054773807 -NEG1-calib QAGAFLTYSSFCPPDDLADR QAGAFLTYSSFC[Common Fixed:Carbamidomethyl on C]PPDDLADR P16050 2230.000083 119.06971 2 1116.007318 500687.3926 118.88437 119.0857 119.24989 1116.509024 2 2 MSMS 1 1 1 0 0.230874984 -NEG1-calib HRPELIEYDKLR HRPELIEYDKLR O43707 1567.847075 71.746657 4 392.9690452 485801.2793 71.690848 71.765143 71.772412 392.9686882 4 2 MSMS 1 1 1 71.776791 -0.911018598 -NEG1-calib VQQLVPKR VQQLVPKR O43707 966.5974494 51.740972 3 323.2064263 453381.1302 51.552633 51.736529 51.92229 323.2065938 3 2 MSMS 1 1 1 0 0.52012998 -NEG1-calib AAAMVPGR [UniProt:N-acetylalanine on A]AAAM[Common Variable:Oxidation on M]VPGR O43598 829.4116233 69.649449 2 415.7130881 451073.6953 69.582556 69.743037 69.743037 415.7132012 2 2 MSMS 1 1 1 0 0.272850589 -NEG1-calib DGLILNMAGAK DGLILNMAGAK P16050 1101.58523 101.78956 2 551.7998916 438589.418 101.72626 101.86907 102.00854 551.8001322 2 1 MSMS 1 1 1 0 0.436973888 -NEG1-calib VSTGASLYAGSNNQVQLWLVGQHGEAALGKR VSTGASLYAGSNNQVQLWLVGQHGEAALGKR P16050 3210.653408 105.45536 4 803.6706284 438103.2324 105.37203 105.44916 105.67795 803.9218333 4 2 MSMS 1 1 1 0 0.620304804 -NEG1-calib HREEELEERR HREEELEERR P16050 1381.669839 40.329437 3 461.5638895 419962.75 40.194229 40.307485 40.547654 346.4245045 4 3 MSMS 2 1 1 0 -0.671000908 -NEG1-calib HRPELIEYDK HRPELIEYDK O43707 1298.6619 62.084847 3 433.8945765 417627.0156 61.988907 62.068255 62.244618 433.8949918 3 2 MSMS 1 1 1 0 0.959333909 -NEG1-calib RSAHLPAR RSAHLPAR P16050 906.5147824 38.760269 3 303.1788706 395120.6771 38.439809 38.877207 39.417078 303.1784856 3 1 MSMS 1 1 1 0 -1.274039753 -NEG1-calib VHKPPKVQEK VHKPPKVQEK O43707 1188.697892 35.582778 4 298.1817494 390654.8555 35.395229 35.639112 35.832898 298.1815395 4 3 MSMS 1 1 1 0 -0.706348197 -NEG1-calib TYFPHFDLSHGSAQVK TYFPHFDLSHGSAQVK P69905 1832.884583 89.692934 4 459.2284222 385158.5625 89.613951 89.736835 89.982921 612.3021872 3 2 MSMS 1 1 1 0 -1.502724172 -NEG1-calib ILCLFRPQSGR ILC[Common Fixed:Carbamidomethyl on C]LFRPQSGR O43598 1345.728875 86.366988 3 449.583568 360702.4323 86.225705 86.421911 86.741974 449.5834083 3 2 MSMS 1 1 1 0 -0.356203358 -NEG1-calib ICDQWDALGSLTHSR IC[Common Fixed:Carbamidomethyl on C]DQWDALGSLTHSR O43707 1757.815517 101.15901 3 586.9457823 350888.7344 101.03869 101.13904 101.26904 586.945385 3 1 MSMS 1 1 1 0 -0.678052105 -NEG1-calib RDHALLEEQSK RDHALLEEQSK O43707 1324.673527 48.260007 3 442.5651189 305802.0156 48.131036 48.289174 48.668685 442.564954 3 3 MSMS 1 1 1 0 -0.373490976 -NEG1-calib GEVGLLVCK GEVGLLVC[Common Fixed:Carbamidomethyl on C]K O14975 973.5266527 82.605282 2 487.7706028 297236.5781 82.509199 82.58871 82.737558 487.7710856 2 1 MSMS 2 1 1 0 0.991815214 -NEG1-calib KGSTAVGVR KGSTAVGVR O14818 873.5032147 37.69962 2 437.7588838 296121.6709 37.620074 37.712827 37.811466 437.7590598 2 2 MSMS 1 1 1 0 0.402961367 -NEG1-calib DHALLEEQSKQQSNEHLRR DHALLEEQSKQQSNEHLRR O43707 2317.152318 53.904883 5 464.4377401 283449.1123 53.813289 53.946321 54.245519 580.5457355 4 3 MSMS 1 1 1 0 -0.529186141 -NEG1-calib AHFSPSNIILDFPAAGSAAR AHFSPSNIILDFPAAGSAAR O00391 2041.038123 111.7891 3 681.3533176 273046.1328 111.70984 111.8643 111.96112 681.6854613 3 1 MSMS 1 1 1 0 -3.151779879 -NEG1-calib VHKINNVNK VHKINNVNK O43707 1064.609077 34.840636 3 355.8769687 206481.3646 34.75342 34.822953 34.934812 355.8767741 3 2 MSMS 1 1 1 0 -0.548271709 -NEG1-calib GRDIVVLGVEKK GRDIVVLGVEKK O14818 1311.787435 65.938292 3 438.2697548 200404.3164 65.81253 65.912809 66.081938 328.9542946 4 2 MSMS 1 1 1 0 0.486097382 -NEG1-calib REALEKTEK REALEKTEK O43707 1102.598237 34.807499 3 368.5400222 162099.7682 34.716482 34.813003 34.890814 368.539781 3 2 MSMS 1 1 1 0 -0.656317717 -NEG1-calib HREEELEER HREEELEER P16050 1225.568728 41.72619 2 613.7916405 0 - - - - - 0 MSMS 1 1 1 0 NaN -NEG2-calib TVGEDPQGLFQK TVGEDPQGLFQK P16050 1317.65648 86.444941 2 659.8355167 14614838.25 86.43001 86.571937 87.051625 659.8356155 2 2 MSMS 1 1 1 87.057231 0.149997876 -NEG2-calib EITEIGLQGAQDR EITEIGLQGAQDR P16050 1428.720872 84.16003 2 715.3677122 12161274.38 84.123316 84.31915 84.870065 715.3672763 2 2 MSMS 1 1 1 0 -0.610206024 -NEG2-calib LYDLPVDER LYDLPVDER P16050 1118.560789 90.1878 2 560.287671 10524236.88 90.102245 90.321603 90.758797 560.287921 2 1 MSMS 1 1 1 0 0.447052064 -NEG2-calib SSFYAQDALR SSFYAQDALR P16050 1156.551287 82.096749 2 579.28292 4861129 82.0199 82.201269 82.606654 579.2830962 2 2 MSMS 1 1 1 0 0.30475068 -NEG2-calib KSAPSTGGVK "K[UniProt:N6,N6,N6-trimethyllysine on K]SAPSTGGVK" P84243 972.5603955 35.307654 2 487.2874742 4803388.625 35.240419 35.359513 35.59289 487.287515 2 3 MSMS 1 1 1 35.597269 0.083880243 -NEG2-calib HREEELEER HREEELEER P16050 1225.568728 41.216995 3 409.5301858 4743224.083 41.136441 41.302025 41.929627 409.5302953 3 2 MSMS 2 1 1 0 0.267908357 -NEG2-calib AGVETTKPSK AGVETTKPSK B9A064 1016.550224 37.179258 2 509.2823887 4427577.417 37.078273 37.271557 37.621938 339.8575083 3 3 MSMS 2 1 1 0 0.463353126 -NEG2-calib VTVLGQPK VTVLGQPK B9A064 840.5069031 64.008976 2 421.260728 4271284.375 63.658833 63.814831 64.775913 421.2603115 2 2 MSMS 1 1 1 0 -0.990981173 -NEG2-calib KSAPSTGGVK "K[UniProt:N6,N6-dimethyllysine on K]SAPSTGGVK" P84243 958.544745 35.777665 2 480.279649 4174200.313 35.703672 35.876943 36.365851 480.2793724 2 2 MSMS 1 1 1 0 -0.577009648 -NEG2-calib TDVAVKDDPELQTWCR TDVAVKDDPELQTWC[Common Fixed:Carbamidomethyl on C]R P16050 1931.904726 85.753127 3 644.9755186 4166829.083 85.632757 85.744272 86.060345 645.3098843 3 2 MSMS 2 1 1 0 0.126064033 -NEG2-calib ADGSPVK ADGSPVK B9A064 672.3442544 37.550052 2 337.1794037 4083391.625 37.500403 37.642205 37.999234 337.1790785 2 2 MSMS 1 1 1 0 -0.967364543 -NEG2-calib LLPMVIQLQLPR LLPMVIQLQLPR P16050 1419.863577 130.41812 2 710.9390651 3892968.953 130.32782 130.6153 131.25591 710.939006 2 2 MSMS 2 1 1 0 -0.083268245 -NEG2-calib GFPVSLQAR GFPVSLQAR P16050 973.5345148 87.788232 2 487.7745339 3728404.563 87.59708 88.016086 88.411281 487.7746205 2 2 MSMS 1 1 1 0 0.177974455 -NEG2-calib YTLEINVR YTLEINVR P16050 1006.544745 90.363492 2 504.279649 3162585.875 90.307488 90.498483 91.340464 504.2799083 2 1 MSMS 1 1 1 0 0.515096617 -NEG2-calib ALLEVVQSGGK ALLEVVQSGGK O14818 1099.623724 84.989891 2 550.8191383 3042278.844 84.870065 85.02169 85.452553 550.8192916 2 1 MSMS 2 1 1 0 0.278864496 -NEG2-calib LIIPHLR LIIPHLR P16050 860.5596073 83.041715 2 431.2870801 2812427.177 82.944267 83.127578 83.290911 287.8601648 3 2 MSMS 1 1 1 83.415428 -1.094906254 -NEG2-calib VQQLVPK VQQLVPK O43707 810.4963384 59.81517 2 406.2554457 2673448.578 59.61846 59.824592 60.064838 406.2554503 2 2 MSMS 2 1 1 0 0.011426469 -NEG2-calib RQPVMVAVGQHEEEYFSGPEPK RQPVMVAVGQHEEEYFSGPEPK P16050 2513.200908 86.550155 4 629.3075036 2643286.828 86.454468 86.763115 87.3547 629.5582856 4 2 MSMS 1 1 1 0 0.103081927 -NEG2-calib LPPPTTK LPPPTTK P16050 752.4432402 46.826473 2 377.2288965 2521750.539 46.196935 46.797109 48.088735 377.2288487 2 2 MSMS 2 1 1 0 -0.127273348 -NEG2-calib RQPVMVAVGQHEEEYFSGPEPK RQPVM[Common Variable:Oxidation on M]VAVGQHEEEYFSGPEPK P16050 2529.195823 79.228503 4 633.3062322 2405928.633 79.111482 79.291812 79.83111 633.5566125 4 2 MSMS 1 1 1 0 -0.532842575 -NEG2-calib SAHLPAR SAHLPAR P16050 750.4136714 41.701398 3 251.1451669 2375227 40.995564 41.554038 41.951627 251.1451247 3 2 MSMS 3 1 1 0 -0.168969736 -NEG2-calib SSDFQLHELQSHLLR SSDFQLHELQSHLLR P16050 1808.916946 92.474353 3 603.9795917 2307980.927 92.344349 92.531205 92.725195 603.9798165 3 3 MSMS 2 1 1 92.743643 0.372836624 -NEG2-calib FLEDKRVDFEVSLAK FLEDKRVDFEVSLAK P16050 1794.9516 93.187261 4 449.7451764 2294506.375 93.06401 93.258843 93.605542 599.324773 3 3 MSMS 2 1 1 0 0.495727695 -NEG2-calib FQSAAIGALQEASEAYLVGLFEDTNLCAIHAK FQSAAIGALQEASEAYLVGLFEDTNLC[Common Fixed:Carbamidomethyl on C]AIHAK P84243 3436.697306 156.54106 3 1146.573045 2048861.542 156.41391 156.69401 157.15757 1147.24135 3 3 MSMS 2 1 1 0 -0.166514363 -NEG2-calib FGTVLTEHVAAAELGAR FGTVLTEHVAAAELGAR O43598 1740.915883 95.539941 3 581.3125708 1958847.687 95.484297 95.505927 96.188198 581.3148697 3 2 MSMS 1 1 1 0 3.961581961 -NEG2-calib GISQEQMQEFR GISQEQMQEFR O43707 1351.61905 79.132421 2 676.8168012 1879904.406 79.069824 79.209566 79.416372 676.8168478 2 1 MSMS 1 1 1 79.033434 0.06895371 -NEG2-calib NYTDEAIETDDLTIK NYTDEAIETDDLTIK O14818 1739.81014 98.295479 2 870.9123465 1850112.891 98.216502 98.309417 98.49295 870.9130546 2 1 MSMS 1 1 1 0 0.813949965 -NEG2-calib LTVEDPVTVEYITR LTVEDPVTVEYITR O14818 1633.856302 107.07632 2 817.9354277 1752337.875 107.01065 107.20256 107.40645 817.9349827 2 2 MSMS 1 1 1 0 -0.544626163 -NEG2-calib EAILAIHK EAILAIHK O43707 893.5334522 66.063205 2 447.7740025 1708760.391 65.971172 66.072658 66.358227 447.7739146 2 3 MSMS 1 1 1 0 -0.196784797 -NEG2-calib DGLILNMAGAK DGLILNM[Common Variable:Oxidation on M]AGAK P16050 1117.580145 82.305512 2 559.7973489 1618246.328 82.246773 82.462673 82.665244 559.7977052 2 1 MSMS 1 1 1 0 0.637746134 -NEG2-calib LLPMVIQLQLPR LLPM[Common Variable:Oxidation on M]VIQLQLPR P16050 1435.858492 120.78061 3 479.6267738 1591735.961 120.55711 120.8687 121.2882 718.9371327 2 2 MSMS 2 1 1 0 0.850039471 -NEG2-calib LWEIIYR LWEIIYR P16050 991.5491022 108.64357 2 496.7818276 1550476.234 108.58241 108.76991 109.17323 496.7819153 2 1 MSMS 1 1 1 0 0.177036832 -NEG2-calib QFASQANVVGPWIQTK QFASQANVVGPWIQTK O43707 1772.920968 104.93148 2 887.4677606 1463131.391 104.85284 105.07707 105.28274 887.468591 2 2 MSMS 1 1 1 0 0.936687143 -NEG2-calib IAESNHIK IAESNHIK O43707 910.4872302 39.656087 2 456.2508916 1423128.365 39.569544 39.689342 39.90743 304.5027968 3 2 MSMS 2 1 1 0 -0.734952506 -NEG2-calib DGLILNMAGAK DGLILNMAGAK P16050 1101.58523 101.22313 2 551.7998916 1407253.75 101.15624 101.34157 101.51611 551.8000271 2 1 MSMS 1 1 1 0 0.24607782 -NEG2-calib YVEGIVSLHYK YVEGIVSLHYK P16050 1306.692138 84.854754 2 654.3533453 1362727.875 84.74061 84.888411 85.21944 654.3539969 2 2 MSMS 2 1 1 0 0.997312488 -NEG2-calib VLAGDKNFITAEELRR VLAGDKNFITAEELRR O43707 1830.995196 81.652995 4 458.7560754 1349927.104 81.57312 81.720987 81.907239 611.3395109 3 2 MSMS 1 1 1 0 0.823340927 -NEG2-calib ANVILCSQQHLAAPLVMLK ANVILC[Common Fixed:Carbamidomethyl on C]SQQHLAAPLVMLK P16050 2105.148937 109.01664 3 702.7235888 1305551.813 108.93782 109.11823 109.30161 703.0583831 3 2 MSMS 1 1 1 0 0.734907674 -NEG2-calib FREELAALDKEIEIR FREELAALDKEIEIR P16050 1830.983963 97.715776 3 611.335264 1173575.49 97.610395 97.779614 98.346162 611.3355172 3 3 MSMS 2 1 1 0 0.414954954 -NEG2-calib LAGAPSEDPQFPK LAGAPSEDPQFPK O00391 1355.67213 80.709194 2 678.8433417 1124093.156 80.585001 80.788903 80.989667 678.8435791 2 1 MSMS 1 1 1 0 0.350256104 -NEG2-calib DLDDFNR DLDDFNR P16050 893.3879101 76.192354 2 447.7012315 1098836.234 76.064417 76.223324 76.458245 447.7010812 2 2 MSMS 1 1 1 0 -0.336455593 -NEG2-calib ANVILCSQQHLAAPLVMLK ANVILC[Common Fixed:Carbamidomethyl on C]SQQHLAAPLVM[Common Variable:Oxidation on M]LK P16050 2121.143852 102.39103 3 708.055227 1058176.099 102.30138 102.44841 102.59588 708.3898059 3 2 MSMS 1 1 1 0 0.424639456 -NEG2-calib WGNWKDGLILNMAGAK WGNWKDGLILNMAGAK P16050 1772.90321 111.7757 3 591.9750132 956308.6458 111.69771 111.83255 112.11261 591.9748175 3 2 MSMS 1 1 1 0 -0.331234396 -NEG2-calib LVSIGAEEIVDGNAK LVSIGAEEIVDGNAK O43707 1513.798788 95.850168 2 757.9066702 948141.6289 95.704498 95.822889 96.183819 757.9068593 2 1 MSMS 1 1 1 0 0.249817609 -NEG2-calib VLNTEANVVR VLNTEANVVR O00391 1113.614222 67.024523 2 557.8143873 887002.0234 66.864365 66.970815 67.171105 557.8145828 2 1 MSMS 1 1 1 0 0.351098569 -NEG2-calib GSTAVGVR GSTAVGVR O14818 745.4082516 44.619817 2 373.7114023 879084.9531 44.534796 44.654574 44.77668 373.7115119 2 2 MSMS 1 1 1 0 0.294047698 -NEG2-calib GISQEQMQEFR GISQEQM[Common Variable:Oxidation on M]QEFR O43707 1367.613964 65.011581 2 684.8142585 870609.1602 64.908694 65.022736 65.242182 684.8139014 2 1 MSMS 1 1 1 0 -0.522259246 -NEG2-calib TGSPPPPLFLPTDPPMAWLLAK TGSPPPPLFLPTDPPMAWLLAK P16050 2345.249362 152.22411 3 782.7570639 853377.901 151.44054 152.07697 152.83803 783.0909244 3 2 MSMS 1 1 1 0 -0.591844141 -NEG2-calib VLSAMIR VLSAMIR O43598 788.4578449 75.914835 2 395.2361989 853287.3555 75.816421 75.948125 76.193482 395.2362961 2 1 MSMS 1 1 1 0 0.246586032 -NEG2-calib MLDAEDIVNTARPDEK MLDAEDIVNTARPDEK O43707 1815.867278 93.373174 3 606.2963692 771373.3906 93.172383 93.377648 93.556933 606.2956795 3 2 MSMS 1 1 1 0 -1.139442172 -NEG2-calib AVAFNKR AVAFNKR O43598 804.4606216 42.444417 3 269.160817 765477.6354 42.396715 42.530238 42.651613 269.1607121 3 2 MSMS 1 1 1 0 -0.390996754 -NEG2-calib KDDPVTNLNNAFEVAEK KDDPVTNLNNAFEVAEK O43707 1902.932321 96.283693 3 635.3180501 760968.8854 96.214332 96.434361 96.825461 635.3184099 3 2 MSMS 2 1 1 0 0.567278951 -NEG2-calib WGNWKDGLILNMAGAK WGNWKDGLILNM[Common Variable:Oxidation on M]AGAK P16050 1788.898125 100.47796 3 597.3066514 757939.7292 100.41387 100.54228 100.68584 597.3071689 3 1 MSMS 1 1 1 0 0.867856048 -NEG2-calib VSTGASLYAGSNNQVQLWLVGQHGEAALGKR VSTGASLYAGSNNQVQLWLVGQHGEAALGKR P16050 3210.653408 104.87847 4 803.6706284 743410.1133 104.79589 104.95977 105.19124 803.9198593 4 2 MSMS 1 1 1 0 -1.838288977 -NEG2-calib KSAPSTGGVK K[UniProt:N6-methyllysine on K]SAPSTGGVK P84243 944.529095 35.42855 2 473.271824 737121.2813 35.347328 35.422428 35.53888 473.2717805 2 1 MSMS 1 1 1 0 -0.092099636 -NEG2-calib NIELAVMR NIELAVMR O14818 944.511337 90.253194 2 473.262945 715987.6437 90.216976 90.303109 90.408134 473.2618927 2 1 MSMS 1 1 1 0 -2.228156727 -NEG2-calib VPVLMESR VPVLMESR O00391 929.5004379 77.542366 2 465.7574954 691068.5156 77.342233 77.568421 77.677771 465.7572481 2 1 MSMS 1 1 1 0 -0.532136733 -NEG2-calib ICDQWDALGSLTHSR IC[Common Fixed:Carbamidomethyl on C]DQWDALGSLTHSR O43707 1757.815517 100.58102 3 586.9457823 690592.9427 100.53664 100.68584 100.76619 586.9455388 3 1 MSMS 1 1 1 0 -0.415575914 -NEG2-calib RDHALLEEQSK RDHALLEEQSK O43707 1324.673527 47.754949 3 442.5651189 677585.9375 47.49246 47.782037 48.005835 442.5649653 3 3 MSMS 1 1 1 48.047862 -0.348052753 -NEG2-calib EQSEGVGAR EQSEGVGAR O00625 931.4359229 39.980675 2 466.7252379 665760.3789 39.911809 40.017455 40.176615 466.7249937 2 1 MSMS 1 1 1 0 -0.524343677 -NEG2-calib ACLISLGYDVENDRQGEAEFNR AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR O43707 2555.171065 103.0545 3 852.7309647 655481.1641 102.99 103.10998 103.24409 853.065598 3 2 MSMS 1 1 1 0 0.41997312 -NEG2-calib TIPWLEDRVPQK TIPWLEDRVPQK O43707 1480.803813 93.25102 3 494.6085476 654261.3371 93.241508 93.405781 94.008857 494.6080411 3 2 MSMS 1 1 1 0 -1.026056149 -NEG2-calib QLEAIDQLHLEYAK QLEAIDQLHLEYAK O43707 1669.867536 97.818157 3 557.6297884 650361.9948 97.759162 97.853566 98.012991 557.6300505 3 2 MSMS 1 1 1 0 0.47083298 -NEG2-calib SFYTAYLQR SFYTAYLQR O00391 1147.566209 96.220468 2 574.7903809 588468.6484 96.048642 96.214332 96.398817 574.7905207 2 1 MSMS 1 1 1 0 0.243596331 -NEG2-calib VEVPEYLGPLLFVK VEVPEYLGPLLFVK P16050 1601.906881 137.2829 2 801.9607172 585298.9688 137.14828 137.41028 137.66182 801.9601882 2 2 MSMS 1 1 1 0 -0.660455905 -NEG2-calib DSWKEDALFGYQFLNGANPVVLR DSWKEDALFGYQFLNGANPVVLR P16050 2638.317987 136.89987 3 880.4466053 553826.2578 136.8382 136.98439 137.31906 880.781251 3 1 MSMS 1 1 1 0 0.386989538 -NEG2-calib HREEELEERR HREEELEERR P16050 1381.669839 39.858008 3 461.5638895 532993.1953 39.73399 39.870742 40.187169 346.4245192 4 3 MSMS 2 1 1 0 -0.628192459 -NEG2-calib AHFSPSNIILDFPAAGSAAR AHFSPSNIILDFPAAGSAAR O00391 2041.038123 111.23912 3 681.3533176 527484.6615 111.17433 111.28161 111.3494 681.6875498 3 1 MSMS 1 1 1 0 -0.083539428 -NEG2-calib HRPELIEYDK HRPELIEYDK O43707 1298.6619 61.585303 3 433.8945765 524752.8177 61.48032 61.511829 61.744885 433.8946594 3 2 MSMS 1 1 1 0 0.191438794 -NEG2-calib KAGTQIENIDEDFRDGLK KAGTQIENIDEDFRDGLK O43707 2048.017447 87.513115 3 683.679759 502625.9323 87.423748 87.544719 87.653013 684.0144514 3 2 MSMS 2 1 1 0 0.591489006 -NEG2-calib RSAHLPAR RSAHLPAR P16050 906.5147824 38.415463 3 303.1788706 490355.0625 38.222605 38.612181 39.08641 303.1787251 3 1 MSMS 1 1 1 0 -0.481374019 -NEG2-calib RFGTVLTEHVAAAELGAR RFGTVLTEHVAAAELGAR O43598 1897.016994 90.08175 3 633.3462745 488627.4453 89.991082 90.124565 90.17119 633.6810125 3 2 MSMS 1 1 1 0 0.735487017 -NEG2-calib ILCLFRPQSGR ILC[Common Fixed:Carbamidomethyl on C]LFRPQSGR O43598 1345.728875 85.762061 3 449.583568 479812.9354 85.54619 85.744272 86.027147 449.5835253 3 2 MSMS 1 1 1 0 -0.095394612 -NEG2-calib KVTLSVLSR KVTLSVLSR O00625 1001.62333 72.744843 2 501.8189414 461398.9673 72.641193 72.763056 72.927143 501.8188097 2 2 MSMS 1 1 1 0 -0.26289224 -NEG2-calib ALAEDVK ALAEDVK O00391 744.4017693 52.080274 2 373.2081611 434895.3516 51.960597 52.11331 52.251976 373.2080143 2 2 MSMS 1 1 1 51.951839 -0.394423515 -NEG2-calib QLEAIDQLHLEYAKR QLEAIDQLHLEYAKR O43707 1825.968647 88.773907 4 457.4994382 404379.4935 88.721223 88.819564 88.894985 609.662884 3 2 MSMS 1 1 1 0 -0.999103744 -NEG2-calib AAAMVPGR [UniProt:N-acetylalanine on A]AAAM[Common Variable:Oxidation on M]VPGR O43598 829.4116233 69.187842 2 415.7130881 394692.8867 69.107123 69.270346 69.335621 415.7131696 2 2 MSMS 2 1 1 0 0.196424569 -NEG2-calib ITQLTPFNGYAGAK ITQLTPFNGYAGAK O14975 1479.772179 94.080019 2 740.8933659 389446.1453 94.004477 94.116086 94.255065 740.8921138 2 1 MSMS 1 1 1 0 -1.692269999 -NEG2-calib NVNVQNFHISWK NVNVQNFHISWK O43707 1484.752446 95.575387 3 495.9247586 383027.2418 95.484297 95.60565 95.739927 495.9243893 3 2 MSMS 2 1 1 0 -0.746208514 -NEG2-calib VGSPNAAVLWLWSSHNR VGSPNAAVLWLWSSHNR O00391 1892.964564 113.60537 3 631.9954646 366334.362 113.53155 113.64817 113.87044 632.32951 3 1 MSMS 1 1 1 0 -0.366612191 -NEG2-calib IGMASIK IGMASIK O14975 718.4047467 67.859482 2 360.2096498 364963.6748 67.725889 67.842757 67.949122 360.2099377 2 1 MSMS 1 1 1 0 0.801426362 -NEG2-calib DHALLEEQSK DHALLEEQSK O43707 1168.572416 56.07209 3 390.5314153 334574.1523 56.002317 56.106869 56.276909 585.293518 2 2 MSMS 2 1 1 0 0.057024113 -NEG2-calib GEVGLLVCK GEVGLLVC[Common Fixed:Carbamidomethyl on C]K O14975 973.5266527 82.015399 2 487.7706028 327312.4844 81.989468 82.071012 82.153871 487.7715004 2 1 MSMS 1 1 1 0 1.844074878 -NEG2-calib KVGAVGR KVGAVGR O14975 685.4235078 35.473667 2 343.7190304 312365.7109 35.381161 35.47644 35.612307 343.7190772 2 2 MSMS 1 1 1 0 0.136593651 -NEG2-calib EVALDLSQHK EVALDLSQHK O00391 1138.598237 67.864449 3 380.5400222 298619.7754 67.75932 67.842757 68.003083 570.30638 2 2 MSMS 1 1 1 0 -0.026549812 -NEG2-calib IQDTIEITGTFK IQDTIEITGTFK O14975 1364.718746 97.754661 2 683.3666496 293352.6445 97.684922 97.797966 98.005691 683.3678825 2 1 MSMS 1 1 1 0 1.806815349 -NEG2-calib EEELEER EEELEER P16050 932.4087051 50.77651 2 467.211629 276629.6846 50.676202 50.7531 50.864194 467.211732 2 1 MSMS 1 1 1 0 0.220781293 -NEG2-calib VDFEVSLAK VDFEVSLAK P16050 1006.533512 94.481669 2 504.2740323 274052.3869 94.364798 94.486188 94.640532 504.2734765 2 1 MSMS 1 1 1 0 -1.104375476 -NEG2-calib EALEKTEK EALEKTEK O43707 946.4971262 36.379668 2 474.2558396 267370.3975 36.304078 36.417066 36.485437 474.2558282 2 2 MSMS 1 1 1 0 -0.024088491 -NEG2-calib VRDSWKEDALFGYQFLNGANPVVLR VRDSWKEDALFGYQFLNGANPVVLR P16050 2893.487512 125.20064 4 724.3791543 267012.3945 125.12261 125.2859 125.58683 724.6300941 4 2 MSMS 1 1 1 0 0.301218244 -NEG2-calib GLADLAIKDSLNVLTCWK GLADLAIKDSLNVLTC[Common Fixed:Carbamidomethyl on C]WK P16050 2016.071398 138.29014 3 673.0310757 265025.8545 138.151 138.28567 138.57807 673.3651858 3 2 MSMS 1 1 1 138.58371 -0.281930156 -NEG2-calib GRDIVVLGVEKK GRDIVVLGVEKK O14818 1311.787435 65.482836 3 438.2697548 256920.4063 65.390714 65.506803 65.664235 438.269869 3 2 MSMS 1 1 1 0 0.261251267 -NEG2-calib KICALDDNVCMAFAGLTADAR KIC[Common Fixed:Carbamidomethyl on C]ALDDNVC[Common Fixed:Carbamidomethyl on C]MAFAGLTADAR O14818 2311.075909 114.82922 3 771.3659127 228562.0846 114.72905 114.86712 114.98598 771.7003715 3 1 MSMS 1 1 1 0 0.244422864 -POS1-calib TVGEDPQGLFQK TVGEDPQGLFQK P16050 1317.65648 86.025794 2 659.8355167 5885669.063 86.012559 86.120498 86.654711 659.835772 2 1 MSMS 1 1 1 86.665388 0.387588281 -POS1-calib EITEIGLQGAQDR EITEIGLQGAQDR P16050 1428.720872 83.758387 2 715.3677122 4373463.625 83.636507 83.88624 84.377303 715.3675831 2 2 MSMS 1 1 1 0 -0.180723754 -POS1-calib RVDFEVSLAK RVDFEVSLAK P16050 1162.634623 82.146575 2 582.3245878 3968430.25 82.062928 82.095609 82.565866 582.32485 2 2 MSMS 1 1 1 0 0.45096649 -POS1-calib HRDYETATLSDIK HRDYETATLSDIK O43707 1547.757985 67.208901 3 516.9266049 3517964.667 67.1409 67.315285 67.595367 516.926192 3 2 MSMS 1 1 1 0 -0.800342138 -POS1-calib SSFYAQDALR SSFYAQDALR P16050 1156.551287 81.607869 2 579.28292 3127521.531 81.529011 81.744186 82.004278 579.2830332 2 1 MSMS 1 1 1 0 0.195857036 -POS1-calib VQQLVPK VQQLVPK O43707 810.4963384 59.224007 2 406.2554457 2914061.156 58.999732 59.194209 59.568711 406.2553004 2 2 MSMS 1 1 1 0 -0.35833459 -POS1-calib GISQEQMQEFR GISQEQMQEFR O43707 1351.61905 78.64292 2 676.8168012 2911245.406 78.573271 78.752252 79.061406 676.8166782 2 1 MSMS 1 1 1 0 -0.18198192 -POS1-calib LYDLPVDER LYDLPVDER P16050 1118.560789 89.77131 2 560.287671 2771941.906 89.607747 89.866729 90.311692 560.2879399 2 2 MSMS 1 1 1 0 0.48073639 -POS1-calib LLPMVIQLQLPR LLPMVIQLQLPR P16050 1419.863577 129.89461 2 710.9390651 2506717.375 129.80013 130.08054 130.11054 710.9396102 2 2 MSMS 2 1 1 130.11492 0.767730982 -POS1-calib EAILAIHK EAILAIHK O43707 893.5334522 65.515894 2 447.7740025 2498137.344 65.431088 65.558921 65.833865 447.7740334 2 2 MSMS 1 1 1 0 0.069132802 -POS1-calib VTVLGQPK VTVLGQPK B9A064 840.5069031 62.996035 2 421.260728 2418639.141 62.84014 63.347442 63.351821 421.2604901 2 1 MSMS 1 1 1 63.376167 -0.56615258 -POS1-calib FQSAAIGALQEASEAYLVGLFEDTNLCAIHAK FQSAAIGALQEASEAYLVGLFEDTNLC[Common Fixed:Carbamidomethyl on C]AIHAK P84243 3436.697306 157.24765 3 1146.573045 2280183.833 156.61083 157.17306 159.20312 1147.241322 3 3 MSMS 2 1 1 0 -0.190752832 -POS1-calib TIQEMQQK TIQEMQQK O43707 1004.496081 49.38981 2 503.2553169 2086422.125 49.284319 49.514848 49.593223 503.2551571 2 1 MSMS 1 1 1 49.597602 -0.318197369 -POS1-calib STLPDADRER STLPDADRER O43707 1158.562914 49.994596 3 387.1949146 2027869.375 49.884765 50.068978 50.068978 387.1941614 3 2 MSMS 2 1 1 50.073357 -1.950304586 -POS1-calib KSAPSTGGVK "K[UniProt:N6,N6-dimethyllysine on K]SAPSTGGVK" P84243 958.544745 35.027405 2 480.279649 1977862.297 34.946783 35.061568 35.29047 480.2797973 2 2 MSMS 1 1 1 35.29485 0.309472108 -POS1-calib AGVETTKPSK AGVETTKPSK B9A064 1016.550224 36.504794 2 509.2823887 1787519.333 36.386738 36.579188 37.270312 339.8573716 3 3 MSMS 2 1 1 0 0.059899603 -POS1-calib TDVAVKDDPELQTWCR TDVAVKDDPELQTWC[Common Fixed:Carbamidomethyl on C]R P16050 1931.904726 85.40432 3 644.9755186 1778569.99 85.302227 85.449862 85.880583 645.3101641 3 2 MSMS 2 1 1 0 0.560275017 -POS1-calib VTVLGQPK VTVLGQPK B9A064 840.5069031 63.51555 2 421.260728 1689835.039 63.444923 63.46244 63.668624 421.2606629 2 2 MSMS 1 1 1 63.677551 -0.154829394 -POS1-calib ALLEVVQSGGK ALLEVVQSGGK O14818 1099.623724 84.381777 2 550.8191383 1505127.047 84.294707 84.475266 84.878237 550.8191864 2 2 MSMS 2 1 1 0 0.087363639 -POS1-calib WVEGNGVLSLPEGTGR WVEGNGVLSLPEGTGR P16050 1669.842384 104.15167 2 835.9284683 1476425.727 103.82238 104.08046 104.30794 835.9281702 2 2 MSMS 1 1 1 104.31523 -0.35709326 -POS1-calib GISQEQMQEFR GISQEQM[Common Variable:Oxidation on M]QEFR O43707 1367.613964 64.533434 2 684.8142585 1461144.344 64.534562 64.534562 64.538941 684.8133003 2 1 MSMS 1 1 1 64.524377 -1.401343244 -POS1-calib KSAPSTGGVK "K[UniProt:N6,N6,N6-trimethyllysine on K]SAPSTGGVK" P84243 972.5603955 34.645242 2 487.2874742 1390164.961 34.39269 34.52593 34.859487 487.287204 2 2 MSMS 1 1 1 34.865072 -0.555796267 -POS1-calib LPPPTTK LPPPTTK P16050 752.4432402 46.231117 2 377.2288965 1357808.617 45.508555 46.219426 47.414425 377.2283967 2 1 MSMS 2 1 1 0 -1.328718281 -POS1-calib ASFNHFDKDHGGALGPEEFK ASFNHFDKDHGGALGPEEFK O43707 2202.013031 76.74285 4 551.5105342 1354265.73 76.693998 76.763179 76.984807 551.7608917 4 3 MSMS 1 1 1 0 -0.658912475 -POS1-calib LTVEDPVTVEYITR LTVEDPVTVEYITR O14818 1633.856302 106.65214 2 817.9354277 1335497.828 106.5676 106.75491 106.98056 817.9353512 2 2 MSMS 1 1 1 106.98494 -0.093663129 -POS1-calib GFPVSLQAR GFPVSLQAR P16050 973.5345148 87.202005 2 487.7745339 1318351.578 87.098564 87.469333 88.017936 487.774508 2 1 MSMS 2 1 1 0 -0.053055951 -POS1-calib LSGSNPYTTVTPQIINSK LSGSNPYTTVTPQIINSK O43707 1919.000007 94.972896 2 960.5072797 1276979.719 94.847596 95.050459 95.35408 961.0082829 2 2 MSMS 1 1 1 0 -0.470545517 -POS1-calib VLAVNQENEHLMEDYEK VLAVNQENEHLMEDYEK O43707 2059.952071 85.510278 3 687.6579666 1263637.122 85.415869 85.566944 85.745036 687.9920923 3 2 MSMS 1 1 1 0 -0.245464388 -POS1-calib DLDDFNR DLDDFNR P16050 893.3879101 75.722288 2 447.7012315 1256030.499 75.645878 75.672322 75.873581 447.7008003 2 2 MSMS 1 1 1 75.63861 -0.965411349 -POS1-calib ETTDTDTADQVIASFK ETTDTDTADQVIASFK O43707 1740.805389 105.43299 2 871.409971 1161239.352 105.32807 105.50392 105.78257 871.4099249 2 2 MSMS 1 1 1 0 -0.052899952 -POS1-calib LWEIIYR LWEIIYR P16050 991.5491022 108.11111 2 496.7818276 1098433.664 108.05918 108.21821 108.62175 496.7818369 2 2 MSMS 1 1 1 0 0.018847366 -POS1-calib ETELKVEVPEYLGPLLFVK ETELKVEVPEYLGPLLFVK P16050 2202.218773 133.09753 3 735.0802008 1031549.401 132.98445 133.15741 133.53006 735.4147473 3 1 MSMS 1 1 1 0 0.282126892 -POS1-calib NYTDEAIETDDLTIK NYTDEAIETDDLTIK O14818 1739.81014 97.767821 2 870.9123465 1024128.789 97.709126 97.848709 98.070059 870.9122349 2 1 MSMS 1 1 1 0 -0.128319193 -POS1-calib ILNPEEIEK ILNPEEIEK O14818 1083.58119 79.718948 2 542.7978716 1021782.094 79.546188 79.71009 80.127645 542.7974376 2 1 MSMS 1 1 1 0 -0.801015827 -POS1-calib RQPVMVAVGQHEEEYFSGPEPK RQPVM[Common Variable:Oxidation on M]VAVGQHEEEYFSGPEPK P16050 2529.195823 79.021112 4 633.3062322 1008881.105 78.966092 79.224142 79.505767 633.5567578 4 2 MSMS 1 1 1 0 -0.303044538 -POS1-calib RQPVMVAVGQHEEEYFSGPEPK RQPVMVAVGQHEEEYFSGPEPK P16050 2513.200908 86.75348 4 629.3075036 995802.6979 86.57407 86.901491 87.478091 839.0748303 3 2 MSMS 2 1 1 0 -0.443885121 -POS1-calib DGLILNMAGAK DGLILNM[Common Variable:Oxidation on M]AGAK P16050 1117.580145 81.7343 2 559.7973489 977702.8594 81.64749 81.808511 82.071845 559.7974893 2 1 MSMS 1 1 1 0 0.251252315 -POS1-calib QFASQANVVGPWIQTK QFASQANVVGPWIQTK O43707 1772.920968 104.4918 2 887.4677606 940247.5391 104.41738 104.6373 104.86986 887.4675941 2 2 MSMS 1 1 1 0 -0.187870501 -POS1-calib IAESNHIK IAESNHIK O43707 910.4872302 38.914996 2 456.2508916 933414.3542 38.808086 38.937684 39.392587 304.5028756 3 3 MSMS 2 1 1 0 -0.47533984 -POS1-calib MAPYQGPDAVPGALDYK MAPYQGPDAVPGALDYK O43707 1791.850172 98.437851 2 896.9323623 922101.0781 98.242153 98.360724 98.553528 896.9341534 2 1 MSMS 1 1 1 0 1.999125873 -POS1-calib HRPELIEYDK HRPELIEYDK O43707 1298.6619 61.642469 3 433.8945765 844238.375 61.623193 61.651318 61.865709 433.8943077 3 2 MSMS 1 1 1 61.615926 -0.620964929 -POS1-calib YTLEINVR YTLEINVR P16050 1006.544745 89.935503 2 504.279649 825070.9141 89.855537 90.053194 90.52789 504.2798625 2 1 MSMS 1 1 1 0 0.424189154 -POS1-calib AITVFSPDGHLFQVEYAQEAVK AITVFSPDGHLFQVEYAQEAVK O14818 2448.232526 115.51425 3 817.084785 776253.4922 115.44392 115.60749 115.8529 817.4183825 3 1 MSMS 1 1 1 0 -0.878555362 -POS1-calib SAHLPAR SAHLPAR P16050 750.4136714 40.705687 3 251.1451669 772721.9792 40.412106 41.033867 41.894697 251.1453397 3 2 MSMS 2 1 1 0 0.690596914 -POS1-calib DGLILNMAGAK DGLILNMAGAK P16050 1101.58523 100.57198 2 551.7998916 768551.9688 100.50929 100.66901 100.9369 551.7993838 2 1 MSMS 1 1 1 0 -0.921879019 -POS1-calib LYQTDPSGTYHAWK LYQTDPSGTYHAWK O14818 1665.778721 76.311314 3 556.2668501 757736.2292 76.218541 76.299083 76.303462 556.2669902 3 2 MSMS 1 1 1 76.315746 0.252472838 -POS1-calib MLDAEDIVNTARPDEK MLDAEDIVNTARPDEK O43707 1815.867278 92.891294 3 606.2963692 757116.3542 92.80695 92.97409 93.190759 606.2961168 3 2 MSMS 1 1 1 0 -0.416984068 -POS1-calib AGTQIENIDEDFRDGLK AGTQIENIDEDFRDGLK O43707 1919.922484 96.770412 3 640.981438 744990.2969 96.695066 96.856896 96.970481 640.981635 3 2 MSMS 1 1 1 0 0.30786324 -POS1-calib RDHALLEEQSK RDHALLEEQSK O43707 1324.673527 47.596071 3 442.5651189 718987.7083 47.541253 47.636888 47.877524 442.5648704 3 3 MSMS 1 1 1 0 -0.562909981 -POS1-calib LLPMVIQLQLPR LLPM[Common Variable:Oxidation on M]VIQLQLPR P16050 1435.858492 120.17058 2 718.9365224 676892.8945 120.0275 120.34443 120.74954 718.936099 2 2 MSMS 1 1 1 0 -0.589776206 -POS1-calib SSDFQLHELQSHLLR SSDFQLHELQSHLLR P16050 1808.916946 92.195051 4 453.2365129 651175.5052 92.089506 92.261839 92.502619 603.9794921 3 3 MSMS 1 1 1 0 -0.165165153 -POS1-calib YVEGIVSLHYK YVEGIVSLHYK P16050 1306.692138 84.484105 3 436.5713223 646869.7734 84.405038 84.60198 84.986731 654.3536175 2 2 MSMS 2 1 1 0 0.416703149 -POS1-calib VLAGDKNFITAEELR VLAGDKNFITAEELR O43707 1674.894085 90.068106 3 559.3053048 641572.9427 90.003708 90.16451 90.358184 559.3065436 3 2 MSMS 1 1 1 0 2.218910353 -POS1-calib ANVILCSQQHLAAPLVMLK ANVILC[Common Fixed:Carbamidomethyl on C]SQQHLAAPLVMLK P16050 2105.148937 108.65376 3 702.7235888 631992.9688 108.56736 108.6977 108.90752 703.0579741 3 2 MSMS 1 1 1 0 0.152258569 -POS1-calib GRDIVVLGVEK GRDIVVLGVEK O14818 1183.692472 76.190966 3 395.5714338 619626.1172 76.053139 76.218541 76.330091 592.8542448 2 2 MSMS 2 1 1 0 1.237416139 -POS1-calib ICDQWDALGSLTHSR IC[Common Fixed:Carbamidomethyl on C]DQWDALGSLTHSR O43707 1757.815517 100.16792 3 586.9457823 576500.3802 100.03479 100.21915 100.35157 586.9452236 3 2 MSMS 1 1 1 0 -0.953468932 -POS1-calib GSTAVGVR GSTAVGVR O14818 745.4082516 43.953847 2 373.7114023 548451.5391 43.856878 43.98743 44.173018 373.711385 2 2 MSMS 1 1 1 0 -0.046326577 -POS1-calib GKETELKVEVPEYLGPLLFVK GKETELKVEVPEYLGPLLFVK P16050 2387.3352 122.2443 3 796.7856764 546103.0612 121.99044 122.22667 122.46052 797.1205154 3 2 MSMS 1 1 1 122.4649 0.636960882 -POS1-calib LAGAPSEDPQFPK LAGAPSEDPQFPK O00391 1355.67213 80.253661 2 678.8433417 535902.5234 80.169147 80.32208 80.462822 678.843112 2 1 MSMS 1 1 1 0 -0.338853097 -POS1-calib FREELAALDKEIEIR FREELAALDKEIEIR P16050 1830.983963 97.538806 4 458.7532671 521128.099 97.465257 97.59243 98.204014 611.3347554 3 3 MSMS 2 1 1 0 -0.833307756 -POS1-calib QLEAIDQLHLEYAK QLEAIDQLHLEYAK O43707 1669.867536 97.358806 3 557.6297884 519550.5339 97.276934 97.447471 97.751226 557.6297678 3 2 MSMS 1 1 1 0 -0.036943304 -POS1-calib VLSAMIR VLSAMIR O43598 788.4578449 75.240084 2 395.2361989 515932.0801 75.142517 75.21832 75.468112 395.235794 2 1 MSMS 1 1 1 0 -1.027029825 -POS1-calib ANVILCSQQHLAAPLVMLK ANVILC[Common Fixed:Carbamidomethyl on C]SQQHLAAPLVM[Common Variable:Oxidation on M]LK P16050 2121.143852 101.96495 3 708.055227 512358.0244 101.88513 102.02485 102.25292 708.3899893 3 1 MSMS 1 1 1 0 0.683936871 -POS1-calib FLEDKRVDFEVSLAK FLEDKRVDFEVSLAK P16050 1794.9516 92.915756 4 449.7451764 506292.5104 92.811329 92.921261 93.089659 599.3243765 3 2 MSMS 1 1 1 0 -0.166881728 -POS1-calib ACLISLGYDVENDRQGEAEFNR AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR O43707 2555.171065 102.68834 3 852.7309647 496891.9115 102.58019 102.74419 102.96948 853.0651282 3 1 MSMS 1 1 1 0 -0.131412086 -POS1-calib HRPELIEYDKLR HRPELIEYDKLR O43707 1567.847075 71.939904 4 392.9690452 495754.5195 71.841142 72.067463 72.239583 392.9688361 4 2 MSMS 1 1 1 0 -0.533620163 -POS1-calib DHALLEEQSK DHALLEEQSK O43707 1168.572416 55.609376 2 585.2934847 490006.75 55.577883 55.622952 55.764254 585.2921633 2 2 MSMS 2 1 1 55.573504 -2.261584632 -POS1-calib QAGAFLTYSSFCPPDDLADR QAGAFLTYSSFC[Common Fixed:Carbamidomethyl on C]PPDDLADR P16050 2230.000083 118.08844 2 1116.007318 488949.9219 117.85945 118.21856 118.50092 1116.508727 2 2 MSMS 2 1 1 0 -0.035041533 -POS1-calib DHALLEEQSK DHALLEEQSK O43707 1168.572416 55.546611 3 390.5314153 486026.2773 55.472378 55.560247 55.569125 585.2926973 2 2 MSMS 1 1 1 55.573504 -1.347556671 -POS1-calib KDDPVTNLNNAFEVAEK KDDPVTNLNNAFEVAEK O43707 1902.932321 95.867917 3 635.3180501 446411.5417 95.789109 96.016347 96.373416 635.3184953 3 2 MSMS 1 1 1 0 0.701853722 -POS1-calib VTVLGQPK VTVLGQPK B9A064 840.5069031 63.70844 2 421.260728 445250.3809 63.68193 63.70398 64.071818 421.2604111 2 1 MSMS 1 1 1 63.677551 -0.754040933 -POS1-calib EVALDLSQHK EVALDLSQHK O00391 1138.598237 67.288168 3 380.5400222 442354.6523 67.233775 67.315285 67.461002 570.3056183 2 2 MSMS 1 1 1 0 -1.364400485 -POS1-calib NIELAVMR NIELAVMR O14818 944.511337 89.774632 2 473.262945 435051.1907 89.654289 89.756833 89.861125 473.2618624 2 2 MSMS 1 1 1 0 -2.292349538 -POS1-calib KSAPSTGGVK K[UniProt:N6-methyllysine on K]SAPSTGGVK P84243 944.529095 34.586984 2 473.271824 419968.3242 34.511586 34.632024 34.754201 473.2715409 2 2 MSMS 1 1 1 0 -0.599447767 -POS1-calib LVSIGAEEIVDGNAK LVSIGAEEIVDGNAK O43707 1513.798788 95.27875 2 757.9066702 393155.5117 95.166998 95.330719 95.765343 757.9063526 2 1 MSMS 1 1 1 0 -0.419594868 -POS1-calib TIPWLEDRVPQK TIPWLEDRVPQK O43707 1480.803813 92.799054 3 494.6085476 388760.5885 92.824652 92.921261 93.639726 494.6087562 3 2 MSMS 1 1 1 0 0.422724745 -POS1-calib FGTVLTEHVAAAELGAR FGTVLTEHVAAAELGAR O43598 1740.915883 95.108214 3 581.3125708 373993.819 95.037321 95.166998 95.450668 581.3123913 3 2 MSMS 1 1 1 0 -0.309238085 -POS1-calib TGSPPPPLFLPTDPPMAWLLAK TGSPPPPLFLPTDPPM[Common Variable:Oxidation on M]AWLLAK P16050 2361.244277 138.48593 3 788.0887021 366907.9173 138.23722 138.55942 138.65284 788.4237996 3 2 MSMS 1 1 1 138.65722 0.9831439 -POS1-calib AVAFNKR AVAFNKR O43598 804.4606216 41.79737 3 269.160817 350651.8763 41.702841 41.850806 42.099331 269.1608013 3 2 MSMS 1 1 1 0 -0.058328261 -POS1-calib TGLVSDMGIFDQIMSTGGGGHVQLLK TGLVSDM[Common Variable:Oxidation on M]GIFDQIMSTGGGGHVQLLK P16050 2676.325123 124.9136 3 893.1156508 346119.6094 124.84278 124.96318 125.71332 893.4497203 3 1 MSMS 1 1 1 0 -0.241931164 -POS1-calib CLPSIHPIFK C[Common Fixed:Carbamidomethyl on C]LPSIHPIFK P16050 1210.65325 89.797403 3 404.5583599 342039.3105 89.743508 89.879129 90.102346 404.5582135 3 1 MSMS 1 1 1 0 -0.362610997 -POS1-calib TGSPPPPLFLPTDPPMAWLLAK TGSPPPPLFLPTDPPMAWLLAK P16050 2345.249362 151.37077 3 782.7570639 338121.582 150.96191 151.64615 152.25268 783.0913582 3 2 MSMS 2 1 1 0 -0.037146799 -POS1-calib GLADLAIK GLADLAIK P16050 799.480354 88.582569 2 400.7474534 331991.3418 88.544673 88.675769 88.841572 400.7472127 2 1 MSMS 1 1 1 0 -0.602311064 -POS1-calib AITVFSPDGHLFQVEYAQEAVKK AITVFSPDGHLFQVEYAQEAVKK O14818 2576.327489 106.51879 4 645.0891486 290639.9004 106.46779 106.61404 106.73491 645.3403015 4 2 MSMS 1 1 1 0 0.649972946 -POS1-calib GRDIVVLGVEKK GRDIVVLGVEKK O14818 1311.787435 65.185781 4 328.9541352 288327.0417 65.067698 65.200719 65.310852 438.2697034 3 3 MSMS 1 1 1 0 -0.117460661 -POS1-calib DYETATLSDIK DYETATLSDIK O43707 1254.597962 90.243237 2 628.3062577 283853.2813 90.061952 90.22664 90.385311 628.3061486 2 1 MSMS 1 1 1 0 -0.173891004 -POS1-calib RPFGISALIVGFDFDGTPR RPFGISALIVGFDFDGTPR O14818 2064.07926 133.0025 3 689.0336964 276476.5339 132.89773 133.06684 133.57072 689.3678427 3 1 MSMS 1 1 1 133.57948 -0.225828146 -POS1-calib KGSTAVGVR KGSTAVGVR O14818 873.5032147 36.555469 2 437.7588838 262715.6484 36.485553 36.592326 36.806032 437.7588878 2 2 MSMS 1 1 1 0 0.009282328 -POS1-calib AAAMVPGR [UniProt:N-acetylalanine on A]AAAM[Common Variable:Oxidation on M]VPGR O43598 829.4116233 68.633865 2 415.7130881 261401.5444 68.502595 68.620647 68.770012 830.4193567 1 2 MSMS 1 1 1 0 0.550975319 -POS1-calib ALHDHLGLR ALHDHLGLR O14975 1030.567212 56.865475 3 344.5296804 241958.5975 56.635803 56.805336 56.904717 344.5293861 3 2 MSMS 1 1 1 0 -0.856885774 -POS1-calib TSNTDGIDSFLDKVDEVSTEPIPESWR TSNTDGIDSFLDKVDEVSTEPIPESWR O14975 3036.420005 132.34674 3 1013.147278 241581.6901 132.20396 132.36538 132.71654 1013.482702 3 1 MSMS 1 1 1 0 1.102171219 -POS1-calib KICALDDNVCMAFAGLTADAR KIC[Common Fixed:Carbamidomethyl on C]ALDDNVC[Common Fixed:Carbamidomethyl on C]MAFAGLTADAR O14818 2311.075909 114.51318 3 771.3659127 236676.86 114.42346 114.55131 114.70037 771.7006268 3 1 MSMS 1 1 1 0 0.575647594 -POS1-calib VEVPEYLGPLLFVK VEVPEYLGPLLFVK P16050 1601.906881 136.80832 2 801.9607172 236584.0723 136.55936 136.82824 137.0416 801.9607079 2 2 MSMS 1 1 1 0 -0.011623532 -POS1-calib VLAGDKNFITAEELRR VLAGDKNFITAEELRR O43707 1830.995196 81.47021 4 458.7560754 223394.4814 81.334242 81.422104 81.593928 458.7556332 4 2 MSMS 1 1 1 0 -0.966209486 -POS1-calib VRDSWKEDALFGYQFLNGANPVVLR VRDSWKEDALFGYQFLNGANPVVLR P16050 2893.487512 125.61343 4 724.3791543 221849.8125 125.51498 125.64333 126.00464 724.6291836 4 2 MSMS 1 1 1 0 -0.956989132 -POS1-calib NVNVQNFHISWK NVNVQNFHISWK O43707 1484.752446 95.130946 3 495.9247586 220688.5833 95.050459 95.141498 95.32634 495.9244801 3 2 MSMS 1 1 1 0 -0.562835104 -POS1-calib WGNWKDGLILNMAGAK WGNWKDGLILNMAGAK P16050 1772.90321 111.54813 3 591.9750132 200089.0612 111.44142 111.60015 111.73928 591.9744474 3 2 MSMS 1 1 1 0 -0.957534896 -POS1-calib SAPSTGGVK SAPSTGGVK P84243 802.418482 38.869725 2 402.2165175 168808.8389 38.73904 38.879611 39.170501 402.2163599 2 2 MSMS 1 1 1 0 -0.392648714 -POS1-calib RSAHLPAR RSAHLPAR P16050 906.5147824 38.230706 3 303.1788706 162471.3001 37.856906 38.3442 38.686163 303.1787665 3 2 MSMS 2 1 1 0 -0.344392065 -POS1-calib MLDAEDIVNTARPDEK M[Common Variable:Oxidation on M]LDAEDIVNTARPDEK O43707 1831.862193 86.985847 3 611.6280074 153394.8255 86.713818 86.991353 87.123524 611.6278031 3 2 MSMS 1 1 1 0 -0.334552318 -POS1-calib SAPSTGGVKKPHR "SAPSTGGVK[UniProt:N6,N6-dimethyllysine on K]KPHR" P84243 1348.757532 36.714225 4 338.1966594 139356.1719 36.382359 36.693236 36.989651 338.1966091 4 2 MSMS 1 1 1 0 -0.149061157 -POS1-calib VHKPPKVQEK VHKPPKVQEK O43707 1188.697892 34.869515 4 298.1817494 130801.1836 34.748614 34.875022 35.002574 298.1816539 4 3 MSMS 1 1 1 0 -0.321284523 -POS1-calib QLEAIDQLHLEYAKR QLEAIDQLHLEYAKR O43707 1825.968647 88.584231 4 457.4994382 88358.47009 88.44418 88.590965 88.667011 457.4991784 4 2 MSMS 1 1 1 0 -0.56911028 -POS2-calib FQSAAIGALQEASEAYLVGLFEDTNLCAIHAK FQSAAIGALQEASEAYLVGLFEDTNLC[Common Fixed:Carbamidomethyl on C]AIHAK P84243 3436.697306 157.86891 3 1146.573045 3220040.198 157.15044 157.68374 160.68781 1147.241803 3 3 MSMS 4 1 1 0 0.229172049 -POS2-calib EITEIGLQGAQDR EITEIGLQGAQDR P16050 1428.720872 83.537706 2 715.3677122 2885960.188 83.463702 83.653917 83.926482 715.3681527 2 2 MSMS 1 1 1 0 0.616558667 -POS2-calib KSAPSTGGVK "K[UniProt:N6,N6-dimethyllysine on K]SAPSTGGVK" P84243 958.544745 34.713707 2 480.279649 2275552.438 34.639497 34.761024 35.034418 480.2797896 2 2 MSMS 1 1 1 35.038799 0.293364027 -POS2-calib KSAPSTGGVK "K[UniProt:N6,N6,N6-trimethyllysine on K]SAPSTGGVK" P84243 972.5603955 34.2439 2 487.2874742 1979717.953 34.080967 34.251076 34.610824 487.2875993 2 2 MSMS 1 1 1 34.615203 0.257300382 -POS2-calib LYDLPVDER LYDLPVDER P16050 1118.560789 89.577711 2 560.287671 1736259.078 89.518926 89.586612 89.836387 560.2878691 2 2 MSMS 1 1 1 0 0.354189956 -POS2-calib GISQEQMQEFR GISQEQMQEFR O43707 1351.61905 78.608324 2 676.8168012 1419765.969 78.547014 78.683066 78.881421 676.8169364 2 1 MSMS 1 1 1 0 0.199955931 -POS2-calib RVDFEVSLAK RVDFEVSLAK P16050 1162.634623 82.044631 2 582.3245878 1288529.656 82.00099 82.141505 83.057533 582.3247244 2 2 MSMS 1 1 1 83.069179 0.23485585 -POS2-calib AGVETTKPSK AGVETTKPSK B9A064 1016.550224 36.197512 2 509.2823887 1262176.51 36.07421 36.246465 36.712855 339.857295 3 3 MSMS 2 1 1 0 -0.166045714 -POS2-calib LPPPTTK LPPPTTK P16050 752.4432402 46.1096 2 377.2288965 1248966.629 45.348588 46.096436 46.146116 377.228515 2 1 MSMS 2 1 1 46.158357 -1.014144709 -POS2-calib EAILAIHK EAILAIHK O43707 893.5334522 65.535704 2 447.7740025 1175883.492 65.412298 65.644711 65.712084 447.7734422 2 2 MSMS 1 1 1 65.716463 -1.254196002 -POS2-calib VQQLVPK VQQLVPK O43707 810.4963384 59.251623 2 406.2554457 1161661.492 58.927906 59.066061 59.403805 406.2550431 2 2 MSMS 1 1 1 0 -0.993291564 -POS2-calib SSFYAQDALR SSFYAQDALR P16050 1156.551287 81.507137 2 579.28292 1085170.078 81.454335 81.605109 81.925926 579.2829613 2 2 MSMS 1 1 1 0 0.071371777 -POS2-calib GFPVSLQAR GFPVSLQAR P16050 973.5345148 87.100188 2 487.7745339 1045387.594 86.968926 87.282514 87.818244 487.7744446 2 3 MSMS 1 1 1 87.823831 -0.183280193 -POS2-calib SAHLPAR SAHLPAR P16050 750.4136714 40.819735 2 376.2141122 1022005.292 40.497821 40.953467 41.267953 251.1451542 3 2 MSMS 1 1 1 0 -0.050926271 -POS2-calib VTVLGQPK VTVLGQPK B9A064 840.5069031 63.00447 2 421.260728 977060.6821 62.735952 63.161475 63.789863 421.2604624 2 2 MSMS 1 1 1 63.79983 -0.631881952 -POS2-calib TDVAVKDDPELQTWCR TDVAVKDDPELQTWC[Common Fixed:Carbamidomethyl on C]R P16050 1931.904726 85.322691 3 644.9755186 959086.4688 85.192722 85.366304 85.859952 645.3099022 3 2 MSMS 1 1 1 0 0.153797858 -POS2-calib LSGSNPYTTVTPQIINSK LSGSNPYTTVTPQIINSK O43707 1919.000007 95.0492 3 640.6739453 848113.7344 94.768656 94.981721 95.264961 961.0083305 2 2 MSMS 2 1 1 0 -0.42100392 -POS2-calib NYTDEAIETDDLTIK NYTDEAIETDDLTIK O14818 1739.81014 97.612416 2 870.9123465 800513.7266 97.525955 97.670978 97.854484 870.9124832 2 1 MSMS 1 1 1 0 0.157193656 -POS2-calib WVEGNGVLSLPEGTGR WVEGNGVLSLPEGTGR P16050 1669.842384 103.98592 2 835.9284683 745391.668 103.44332 104.04378 104.22689 835.927844 2 2 MSMS 1 1 1 0 -0.747743896 -POS2-calib DGLILNMAGAK DGLILNMAGAK P16050 1101.58523 100.42277 2 551.7998916 735641.0938 100.29766 100.50763 100.76852 551.7987579 2 2 MSMS 1 1 1 0 -2.058292321 -POS2-calib LWEIIYR LWEIIYR P16050 991.5491022 108.117 2 496.7818276 708334.125 108.03316 108.20367 108.62258 496.7820412 2 2 MSMS 1 1 1 0 0.430899544 -POS2-calib IAESNHIK IAESNHIK O43707 910.4872302 38.763998 2 456.2508916 701514.7552 38.661361 38.773882 39.143995 304.502995 3 2 MSMS 2 1 1 0 -0.082035258 -POS2-calib ALLEVVQSGGK ALLEVVQSGGK O14818 1099.623724 84.228348 2 550.8191383 693133.9297 84.153017 84.302386 84.519384 550.8190934 2 1 MSMS 1 1 1 0 -0.081625087 -POS2-calib LTVEDPVTVEYITR LTVEDPVTVEYITR O14818 1633.856302 106.52503 2 817.9354277 680480.3945 106.41257 106.61458 107.14523 817.9349963 2 2 MSMS 1 1 1 0 -0.528079275 -POS2-calib ETTDTDTADQVIASFK ETTDTDTADQVIASFK O43707 1740.805389 105.25016 2 871.409971 661093.9531 105.1519 105.33583 105.52045 871.4103653 2 2 MSMS 1 1 1 0 0.452994326 -POS2-calib HRDYETATLSDIK HRDYETATLSDIK O43707 1547.757985 68.622144 3 516.9266049 658431.4141 68.552628 68.697591 69.080358 516.9267892 3 2 MSMS 1 1 1 0 0.357195156 -POS2-calib DLDDFNR DLDDFNR P16050 893.3879101 75.346336 2 447.7012315 616586.8389 75.217503 75.426909 75.722291 447.7006688 2 2 MSMS 1 1 1 0 -1.259762064 -POS2-calib GISQEQMQEFR GISQEQM[Common Variable:Oxidation on M]QEFR O43707 1367.613964 64.386471 2 684.8142585 595651.4023 64.320172 64.374276 64.395305 684.8136338 2 1 MSMS 1 1 1 64.399685 -0.913539989 -POS2-calib QFASQANVVGPWIQTK QFASQANVVGPWIQTK O43707 1772.920968 104.44875 2 887.4677606 584857.5586 104.35174 104.51915 104.78985 887.4678546 2 2 MSMS 1 1 1 0 0.105986561 -POS2-calib YTLEINVR YTLEINVR P16050 1006.544745 89.797055 2 504.279649 577152.625 89.663883 89.891247 90.40971 504.2793007 2 2 MSMS 1 1 1 0 -0.692020942 -POS2-calib TIQEMQQK TIQEMQQK O43707 1004.496081 49.232391 2 503.2553169 570724.6094 49.129608 49.355223 49.82439 503.2552762 2 2 MSMS 1 1 1 0 -0.081082096 -POS2-calib STLPDADRER STLPDADRER O43707 1158.562914 49.967739 3 387.1949146 558483.6146 49.840363 50.040655 50.561668 387.1948643 3 2 MSMS 1 1 1 0 -0.130284767 -POS2-calib SSDFQLHELQSHLLR SSDFQLHELQSHLLR P16050 1808.916946 92.880768 3 603.9795917 517052.1917 92.770525 92.96644 93.550532 603.9794414 3 3 MSMS 2 1 1 0 -0.249219872 -POS2-calib AGTQIENIDEDFRDGLK AGTQIENIDEDFRDGLK O43707 1919.922484 96.799416 3 640.981438 495659.5286 96.700337 96.882979 97.083494 640.9816719 3 2 MSMS 1 1 1 0 0.365540118 -POS2-calib KSAPSTGGVK K[UniProt:N6-methyllysine on K]SAPSTGGVK P84243 944.529095 34.209639 2 473.271824 493579.4414 34.130328 34.255455 34.412238 473.2718183 2 2 MSMS 1 1 1 0 -0.011886039 -POS2-calib LLPMVIQLQLPR LLPM[Common Variable:Oxidation on M]VIQLQLPR P16050 1435.858492 120.15965 2 718.9365224 488481.5586 120.00786 120.27428 120.80247 718.9362623 2 2 MSMS 1 1 1 0 -0.362309205 -POS2-calib QAGAFLTYSSFCPPDDLADR QAGAFLTYSSFC[Common Fixed:Carbamidomethyl on C]PPDDLADR P16050 2230.000083 118.04654 2 1116.007318 449603.6182 117.73716 118.13023 118.44333 1116.508174 2 2 MSMS 2 1 1 0 -0.531013493 -POS2-calib VLAGDKNFITAEELR VLAGDKNFITAEELR O43707 1674.894085 90.183995 3 559.3053048 400784.8268 90.12265 90.274063 90.432069 559.3055919 3 2 MSMS 1 1 1 0 0.514352148 -POS2-calib DGLILNMAGAK DGLILNM[Common Variable:Oxidation on M]AGAK P16050 1117.580145 81.534879 2 559.7973489 397819.1406 81.425677 81.605109 81.841263 559.7976481 2 2 MSMS 1 1 1 0 0.535436714 -POS2-calib VLAVNQENEHLMEDYEK VLAVNQENEHLMEDYEK O43707 2059.952071 85.463222 3 687.6579666 387517.0482 85.366304 85.518329 85.718289 687.9918331 3 2 MSMS 1 1 1 0 -0.622723359 -POS2-calib RDHALLEEQSK RDHALLEEQSK O43707 1324.673527 48.684519 3 442.5651189 368242.8073 48.59347 48.798108 48.969274 442.5649354 3 3 MSMS 1 1 1 0 -0.415742743 -POS2-calib IFWCGQSK IFWC[Common Fixed:Carbamidomethyl on C]GQSK P16050 1024.480037 81.131299 2 513.2472949 358442.8086 80.912669 81.068412 81.29049 513.2475297 2 2 MSMS 1 1 1 0 0.458337416 -POS2-calib ILNPEEIEK ILNPEEIEK O14818 1083.58119 79.641188 2 542.7978716 332402.168 79.473688 79.747569 79.98679 542.7977733 2 1 MSMS 1 1 1 0 -0.181293406 -POS2-calib GSTAVGVR GSTAVGVR O14818 745.4082516 43.735367 2 373.7114023 327759.8672 43.664965 43.803078 44.030962 373.7112618 2 2 MSMS 1 1 1 0 -0.376962165 -POS2-calib ANVILCSQQHLAAPLVMLK ANVILC[Common Fixed:Carbamidomethyl on C]SQQHLAAPLVMLK P16050 2105.148937 108.89447 3 702.7235888 323979.4922 108.778 108.9509 109.21258 703.0577912 3 2 MSMS 1 1 1 0 -0.108270828 -POS2-calib QLEAIDQLHLEYAK QLEAIDQLHLEYAK O43707 1669.867536 97.35965 3 557.6297884 318969.9531 97.284804 97.38794 97.661952 557.629863 3 2 MSMS 1 1 1 0 0.134066074 -POS2-calib RQPVMVAVGQHEEEYFSGPEPK RQPVM[Common Variable:Oxidation on M]VAVGQHEEEYFSGPEPK P16050 2529.195823 79.946484 4 633.3062322 300770.9346 79.807449 80.066455 80.537503 633.5572166 4 2 MSMS 1 1 1 0 0.422185064 -POS2-calib DYETATLSDIK DYETATLSDIK O43707 1254.597962 89.931949 2 628.3062577 294881.3281 89.836387 89.976162 90.163052 628.3059751 2 1 MSMS 1 1 1 0 -0.450455083 -POS2-calib YVEGIVSLHYK YVEGIVSLHYK P16050 1306.692138 84.595811 3 436.5713223 286740.3464 84.481105 84.669832 84.932449 436.5713219 3 2 MSMS 2 1 1 0 -0.001115705 -POS2-calib VEVPEYLGPLLFVK VEVPEYLGPLLFVK P16050 1601.906881 136.80036 2 801.9607172 282401.6328 136.57664 136.83686 137.27088 801.9606097 2 2 MSMS 2 1 1 0 -0.134163454 -POS2-calib RQPVMVAVGQHEEEYFSGPEPK RQPVMVAVGQHEEEYFSGPEPK P16050 2513.200908 88.561929 4 629.3075036 282218.3477 88.395482 88.93397 89.767025 629.5571456 4 2 MSMS 2 1 1 0 -1.710719794 -POS2-calib LLPMVIQLQLPR LLPMVIQLQLPR P16050 1419.863577 129.98462 2 710.9390651 279707.6107 129.80326 130.10416 130.46745 710.9409361 2 2 MSMS 1 1 1 0 2.635392186 -POS2-calib MLDAEDIVNTARPDEK MLDAEDIVNTARPDEK O43707 1815.867278 92.963652 3 606.2963692 276167.0291 92.757186 92.902967 93.091336 606.2964494 3 2 MSMS 1 1 1 0 0.132505798 -POS2-calib CLPSIHPIFK C[Common Fixed:Carbamidomethyl on C]LPSIHPIFK P16050 1210.65325 89.970655 3 404.5583599 264101.6406 89.849731 90.028648 90.279666 404.5583145 3 1 MSMS 1 1 1 0 -0.112530167 -POS2-calib KDDPVTNLNNAFEVAEK KDDPVTNLNNAFEVAEK O43707 1902.932321 95.935805 3 635.3180501 262796.5911 95.776618 96.014251 96.249197 635.3181181 3 2 MSMS 1 1 1 0 0.10721899 -POS2-calib ICDQWDALGSLTHSR IC[Common Fixed:Carbamidomethyl on C]DQWDALGSLTHSR O43707 1757.815517 100.20703 3 586.9457823 261647.9714 100.06931 100.23635 100.44264 586.9454783 3 2 MSMS 1 1 1 0 -0.518790265 -POS2-calib TIPWLEDRVPQK TIPWLEDRVPQK O43707 1480.803813 93.120612 3 494.6085476 230668.7005 92.902967 93.008961 93.774634 494.6084874 3 2 MSMS 1 1 1 0 -0.121828927 -POS2-calib HRPELIEYDK HRPELIEYDK O43707 1298.6619 64.137602 3 433.8945765 214988.1302 63.88393 64.119413 64.306897 433.8941711 3 2 MSMS 1 1 1 0 -0.936547512 -POS2-calib ACLISLGYDVENDRQGEAEFNR AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDRQGEAEFNR O43707 2555.171065 102.84104 3 852.7309647 213690.9883 102.7393 102.89007 103.13497 853.0648643 3 1 MSMS 1 1 1 0 -0.441202867 -POS2-calib NIELAVMR NIELAVMR O14818 944.511337 89.611745 2 473.262945 210335.961 89.536645 89.612872 89.733485 473.2609284 2 2 MSMS 1 1 1 0 -4.270073009 -POS2-calib ACLISLGYDVENDR AC[Common Fixed:Carbamidomethyl on C]LISLGYDVENDR O43707 1623.756271 106.14035 2 812.8854121 208035.0986 106.0058 106.14585 106.37462 812.884377 2 2 MSMS 1 1 1 0 -1.274981947 -POS2-calib FGTVLTEHVAAAELGAR FGTVLTEHVAAAELGAR O43598 1740.915883 95.645548 3 581.3125708 205244.1927 95.557932 95.684142 96.059453 581.3124227 3 1 MSMS 1 1 1 0 -0.25526978 -POS2-calib KGSTAVGVR KGSTAVGVR O14818 873.5032147 36.289985 2 437.7588838 204014.9219 36.207398 36.294406 36.407692 437.758914 2 2 MSMS 1 1 1 0 0.069199404 -POS2-calib TGSPPPPLFLPTDPPMAWLLAK TGSPPPPLFLPTDPPMAWLLAK P16050 2345.249362 151.44777 3 782.7570639 203192.6947 151.02567 151.6725 152.42742 783.0915869 3 2 MSMS 1 1 1 0 0.255256956 -POS2-calib DSLNVLTCWK DSLNVLTC[Common Fixed:Carbamidomethyl on C]WK P16050 1234.601609 109.70262 2 618.3080807 191340.2042 109.55973 109.7288 109.89309 618.3079983 2 1 MSMS 1 1 1 0 -0.133618901 -POS2-calib VNVDEVGGEALGR VNVDEVGGEALGR P68871 1313.657543 83.011063 2 657.836048 185578.7168 82.808885 83.021574 83.166429 657.8365155 2 1 MSMS 1 1 1 0 0.711801348 -POS2-calib AVAFNKR AVAFNKR O43598 804.4606216 41.721551 3 269.160817 179805.7487 41.60922 41.772597 41.929937 269.1606499 3 2 MSMS 1 1 1 0 -0.622990839 -POS2-calib GRDIVVLGVEK GRDIVVLGVEK O14818 1183.692472 76.414926 3 395.5714338 179047.5938 76.270258 76.372825 76.628437 395.5715389 3 2 MSMS 1 1 1 0 0.266303454 -POS2-calib FREELAALDKEIEIR FREELAALDKEIEIR P16050 1830.983963 98.98532 3 611.335264 179014.1836 98.845816 99.119323 100.31536 611.3351743 3 2 MSMS 1 1 1 100.34164 -0.146983206 -POS2-calib NVNVQNFHISWK NVNVQNFHISWK O43707 1484.752446 95.294691 3 495.9247586 172827.0358 95.194267 95.359884 95.526053 495.9246606 3 2 MSMS 1 1 1 0 -0.198046365 -POS2-calib VGAHAGEYGAEALER VGAHAGEYGAEALER P69905 1528.72702 67.901423 3 510.5829497 159630.3262 67.742827 67.806858 68.010858 510.5832076 3 2 MSMS 1 1 1 0 0.506143503 -POS2-calib HREEELEER HREEELEER P16050 1225.568728 41.892465 3 409.5301858 151422.5534 41.768218 41.92272 42.095368 409.5297458 3 2 MSMS 1 1 1 0 -1.077139838 -POS2-calib DSWKEDALFGYQFLNGANPVVLR DSWKEDALFGYQFLNGANPVVLR P16050 2638.317987 137.15469 3 880.4466053 150643.5143 136.90391 137.27651 137.99913 880.779715 3 1 MSMS 1 1 1 0 -1.358914233 -POS2-calib RSAHLPAR RSAHLPAR P16050 906.5147824 39.096019 3 303.1788706 127595.9499 38.710965 39.082817 39.601403 303.1787552 3 1 MSMS 1 1 1 0 -0.382029023 \ No newline at end of file diff --git a/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv b/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv deleted file mode 100644 index 3745fb78..00000000 --- a/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv +++ /dev/null @@ -1,5 +0,0 @@ -Run Condition BioReplicate Fraction -NEG1-calib neg 1 1 -NEG2-calib neg 2 1 -POS1-calib pos 3 1 -POS2-calib pos 4 1 \ No newline at end of file diff --git a/inst/tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv b/inst/tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv new file mode 100644 index 00000000..ba7b17a4 --- /dev/null +++ b/inst/tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv @@ -0,0 +1,67 @@ +File Name Base Sequence Full Sequence Protein Group Organism Peptide Monoisotopic Mass MS2 Retention Time Precursor Charge Theoretical MZ Peak intensity Peak RT Start Peak RT Apex Peak RT End Peak MZ Peak Charge Num Charge States Observed Peak Detection Type PIP Q-Value PIP PEP PSMs Mapped Base Sequences Mapped Full Sequences Mapped Peak Split Valley RT Peak Apex Mass Error (ppm) Decoy Peptide Random RT +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SLYASSPGGVYATR SLYASSPGGVYATR P08670 Homo sapiens 1427.70449 54.48366 2 714.8595215 963096478.6 53.44101054 53.79100329 59.94278459 714.861313 2 3 MSMS NA NA 11 1 1 0 2.509694142 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 114.29158 2 585.3606415 508754151.7 110.5571171 112.6597296 118.7942497 585.3619506 2 2 MSMS NA NA 8 1 1 118.8103625 2.240320144 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SVEELLEAELLK SVEELLEAELLK Q86UP2 Homo sapiens 1371.74971 138.7863 2 686.8821315 2837962.567 138.5180262 138.9402988 140.6715797 686.8820851 2 2 MSMS NA NA 5 1 1 0 -0.067649262 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib GELTTLIHQLQEK GELTTLIHQLQEK Q86UP2 Homo sapiens 1508.81986 93.64236 3 503.9472298 2797108.004 93.50297013 93.77539156 94.20802241 503.9473278 3 2 MSMS NA NA 2 1 1 0 0.194859079 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ISLPLPNFSSLNLRETNLDSLPLVDTHSK ISLPLPNFSSLNLRETNLDSLPLVDTHSK P08670 Homo sapiens 3219.71394 NA 4 805.9357615 761151.4889 143.0180469 143.1423956 143.1423956 806.1833805 4 1 MBR 0.050836 0.999870896 1 1 1 0 -3.858087825 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 136.40437 2 585.3606415 407901.7045 134.8252692 136.3814433 137.3249886 585.3605668 2 1 MSMS NA NA 1 1 1 137.3436009 -0.127833812 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib EQMEAEIAHLKQENGILR EQMEAEIAHLKQENGILR Q86UP2 Homo sapiens 2108.06844 NA 4 528.0243865 334918.8696 75.98835551 75.98835551 75.98835551 528.2720613 4 1 MBR 0.037111 0.999806583 1 1 1 0 -5.743564521 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 139.12388 2 585.3606415 323546.8233 138.9402988 139.0515868 139.1355015 585.3608604 2 1 MSMS NA NA 1 1 1 0 0.374655129 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 151.98896 2 585.3606415 317248.2343 151.8897319 152.0138309 152.0387976 585.3631421 2 1 MSMS NA NA 1 1 1 0 4.279317585 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 149.79359 2 585.3606415 275361.3794 148.7186928 149.7840743 149.9710231 585.3602692 2 1 MSMS NA NA 1 1 1 0 -0.637087537 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 145.36054 2 585.3606415 259489.4109 144.9636253 145.3338075 145.516396 585.3588002 2 1 MSMS NA NA 1 1 1 145.5437713 -3.150869325 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 147.51136 2 585.3606415 252828.439 145.588377 147.6028387 147.9082378 585.3602203 2 1 MSMS NA NA 2 1 1 147.9241211 -0.720677105 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 150.87867 2 585.3606415 230537.4326 150.5163895 150.844126 151.3939265 585.3609722 2 1 MSMS NA NA 1 1 1 0 0.565988341 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 156.65722 2 585.3606415 225554.2891 156.4457493 156.5664825 157.8414105 585.359742 2 1 MSMS NA NA 1 1 1 0 -1.539333912 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 155.68641 2 585.3606415 207076.383 155.4309589 155.4729258 156.3613927 585.3621651 2 1 MSMS NA NA 1 1 1 0 2.60735401 FALSE FALSE +B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 154.51423 2 585.3606415 187258.1375 154.422426 154.4827872 154.5594599 585.360942 2 1 MSMS NA NA 1 1 1 0 0.514246461 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SLYASSPGGVYATR SLYASSPGGVYATR P08670 Homo sapiens 1427.70449 54.74513 2 714.8595215 825698092.2 53.70142096 53.99644437 59.79725358 714.8612623 2 3 MSMS NA NA 12 1 1 0 2.438661786 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 114.16626 2 585.3606415 519046271.4 110.3545574 112.5048676 118.6987262 585.3620348 2 2 MSMS NA NA 8 1 1 118.7111088 2.384375039 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SVEELLEAELLK SVEELLEAELLK Q86UP2 Homo sapiens 1371.74971 139.12025 2 686.8821315 2839122.714 138.2386225 138.8121785 140.3463197 686.8823585 2 2 MSMS NA NA 4 1 1 140.3611633 0.331060194 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib GELTTLIHQLQEK GELTTLIHQLQEK Q86UP2 Homo sapiens 1508.81986 93.5116 3 503.9472298 2175577.724 93.2840181 93.62596493 93.98919738 503.9471726 3 2 MSMS NA NA 2 1 1 0 -0.113724028 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SLYASSPGGVYATR SLYASSPGGVYATR P08670 Homo sapiens 1427.70449 59.9647 2 714.8595215 1053012.538 59.85042888 60.00353951 60.16037983 714.8619132 2 1 MSMS NA NA 2 1 1 0 3.350403823 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ISLPLPNFSSLNLRETNLDSLPLVDTHSK ISLPLPNFSSLNLRETNLDSLPLVDTHSK P08670 Homo sapiens 3219.71394 NA 4 805.9357615 607525.061 143.0551757 143.0551757 143.0551757 806.1850767 4 1 MBR 0.032309 0.999650896 1 1 1 0 -1.751438054 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 134.935 2 585.3606415 502597.4456 134.0740112 134.5253771 136.5132493 585.3597918 2 1 MSMS NA NA 3 1 1 0 -1.454084806 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 138.86992 2 585.3606415 376563.7328 138.6958095 138.8533664 139.2306825 585.3605631 2 1 MSMS NA NA 1 1 1 0 -0.134096124 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 150.62223 2 585.3606415 293830.5758 149.8980173 150.6211812 150.792471 585.360093 2 1 MSMS NA NA 1 1 1 0 -0.938553659 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 146.95452 2 585.3606415 293269.8019 144.7986108 146.2888376 148.5027478 585.3611858 2 1 MSMS NA NA 1 1 1 0 0.93147302 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 151.74322 2 585.3606415 236581.6677 151.6612372 151.734241 152.0113401 585.360645 2 1 MSMS NA NA 1 1 1 0 0.006072628 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 156.65599 2 585.3606415 229826.9666 156.4769941 156.7791432 156.9525693 585.3609506 2 1 MSMS NA NA 2 1 1 0 0.529045071 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 157.68205 2 585.3606415 215493.3658 156.9848109 157.3594058 157.8392035 585.3609543 2 1 MSMS NA NA 1 1 1 0 0.535350217 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 149.19467 2 585.3606415 209617.1153 149.0054787 149.0814791 149.364113 585.3595878 2 1 MSMS NA NA 1 1 1 0 -1.803048625 FALSE FALSE +B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SLYASSPGGVYATR SLYASSPGGVYATR P08670 Homo sapiens 1427.70449 68.50398 2 714.8595215 0 - - - - - 0 MSMS NA NA 1 1 1 0 NA FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SLYASSPGGVYATR SLYASSPGGVYATR P08670 Homo sapiens 1427.70449 54.88557 2 714.8595215 899294244.1 53.69475007 54.03055505 59.95482469 714.8615947 2 3 MSMS NA NA 13 1 1 0 2.904293657 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 117.14926 2 585.3606415 460123951 111.3621289 112.4989181 118.6882681 585.3618624 2 2 MSMS NA NA 10 1 1 111.3435098 2.089441056 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SVEELLEAELLK SVEELLEAELLK Q86UP2 Homo sapiens 1371.74971 138.65747 2 686.8821315 2774860.549 138.582007 138.9707794 140.6796273 686.8819351 2 2 MSMS NA NA 3 1 1 0 -0.28624617 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib GELTTLIHQLQEK GELTTLIHQLQEK Q86UP2 Homo sapiens 1508.81986 93.57902 3 503.9472298 2340710.244 93.34411947 93.67820589 94.10633461 503.9472099 3 2 MSMS NA NA 3 1 1 0 -0.039547027 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ISLPLPNFSSLNLRETNLDSLPLVDTHSK ISLPLPNFSSLNLRETNLDSLPLVDTHSK P08670 Homo sapiens 3219.71394 143.09282 4 805.9357615 1055651.803 143.037386 143.0672364 143.1294112 806.1870581 4 1 MSMS NA NA 1 1 1 0 0.709368559 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib EQMEAEIAHLKQENGILR EQMEAEIAHLKQENGILR Q86UP2 Homo sapiens 2108.06844 NA 4 528.0243865 788545.0448 76.0047499 76.0047499 76.04309822 528.2712905 4 1 MBR 0.055216 0.999887705 1 1 1 0 -7.205429283 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 138.93681 2 585.3606415 405410.1729 138.7331656 138.8828975 138.9992527 585.360579 2 1 MSMS NA NA 2 1 1 0 -0.10689214 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 157.7093 2 585.3606415 341283.6471 155.7203361 156.7799434 157.9725369 585.360747 2 1 MSMS NA NA 2 1 1 157.9897477 0.180647235 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 149.90724 2 585.3606415 302520.049 148.5191428 149.6859931 151.2888031 585.360381 2 1 MSMS NA NA 3 1 1 0 -0.445670269 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 159.97144 2 585.3606415 301449.2206 159.1653406 159.5608251 159.962503 585.3599682 2 1 MSMS NA NA 1 1 1 0 -1.152197282 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 147.07477 2 585.3606415 291980.3844 146.3625998 148.0046892 148.4582258 585.3602479 2 1 MSMS NA NA 1 1 1 0 -0.673550567 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 152.28589 2 585.3606415 273364.8658 151.8684146 151.9839248 152.4165389 585.3613631 2 1 MSMS NA NA 1 1 1 0 1.234975946 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 155.10242 2 585.3606415 236425.3462 154.9093247 155.0179296 155.1924175 585.3610757 2 1 MSMS NA NA 1 1 1 0 0.743138414 FALSE FALSE +B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 154.58242 2 585.3606415 215664.0229 154.3447682 154.8006372 154.8345246 585.359854 2 1 MSMS NA NA 1 1 1 0 -1.34764026 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SLYASSPGGVYATR SLYASSPGGVYATR P08670 Homo sapiens 1427.70449 54.58842 2 714.8595215 880527784.2 53.50519634 53.87293916 59.99472229 714.8617698 2 3 MSMS NA NA 13 1 1 0 3.149572886 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 113.8264 2 585.3606415 537588805.5 108.9866581 112.1774281 118.3774485 585.3619021 2 2 MSMS NA NA 8 1 1 118.3910362 2.157326037 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SVEELLEAELLK SVEELLEAELLK Q86UP2 Homo sapiens 1371.74971 138.31268 2 686.8821315 3088754.563 138.1930938 138.6771732 140.5827629 686.8820335 2 2 MSMS NA NA 4 1 1 0 -0.142794921 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib GELTTLIHQLQEK GELTTLIHQLQEK Q86UP2 Homo sapiens 1508.81986 93.52056 2 755.4172065 2655884.594 93.34646412 93.58545484 93.94857452 503.9469841 3 2 MSMS NA NA 3 1 1 0 -0.488511297 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ISLPLPNFSSLNLRETNLDSLPLVDTHSK ISLPLPNFSSLNLRETNLDSLPLVDTHSK P08670 Homo sapiens 3219.71394 NA 4 805.9357615 1056756.882 142.9827012 142.9827012 143.0684014 806.1868622 4 1 MBR 0.011311 0.278785944 1 1 1 0 0.466019654 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib SLYASSPGGVYATR SLYASSPGGVYATR P08670 Homo sapiens 1427.70449 62.6006 2 714.8595215 851568.7776 62.58877519 62.66301685 62.66301685 714.8605188 2 1 MSMS NA NA 1 1 1 0 1.397181108 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 132.78728 2 585.3606415 675614.0622 131.4576066 134.9544756 136.3429703 585.358305 2 1 MSMS NA NA 2 1 1 0 -3.99831565 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 141.74892 2 585.3606415 611568.0605 139.392738 141.0701904 142.5124137 585.3599497 2 1 MSMS NA NA 1 1 1 0 -1.183739281 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 137.55039 2 585.3606415 502208.9375 137.3421554 137.8776594 139.3047604 585.360413 2 1 MSMS NA NA 3 1 1 0 -0.390938364 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib EQMEAEIAHLKQENGILR EQMEAEIAHLKQENGILR Q86UP2 Homo sapiens 2108.06844 NA 4 528.0243865 357089.0721 75.05262063 75.05262063 75.18895738 528.2762973 4 1 MBR 0.054383 0.999865055 1 1 1 0 2.290283225 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 136.46987 2 585.3606415 300106.9532 136.4245608 136.4716313 136.8555577 585.3604799 2 1 MSMS NA NA 1 1 1 0 -0.276513414 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 147.55679 2 585.3606415 291871.1914 144.984181 147.7726682 149.3960073 585.35994 2 1 MSMS NA NA 4 1 1 0 -1.200492955 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 151.07293 2 585.3606415 276785.8672 151.0554765 151.4328673 151.5820283 585.3600313 2 1 MSMS NA NA 1 1 1 0 -1.044109354 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 156.61053 2 585.3606415 252101.3817 156.1798115 156.4071968 156.8798165 585.3593013 2 1 MSMS NA NA 2 1 1 0 -2.293447397 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 157.664 2 585.3606415 238417.5103 156.9052361 157.6966954 158.9734716 585.3611019 2 1 MSMS NA NA 2 1 1 158.9993075 0.787873789 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 159.78941 2 585.3606415 221968.5218 159.0077272 159.0497692 159.9830066 585.3611783 2 1 MSMS NA NA 1 1 1 158.9993075 0.918716831 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 150.01277 2 585.3606415 220394.9219 149.468706 149.6463437 150.011712 585.3598525 2 1 MSMS NA NA 1 1 1 0 -1.350141536 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 154.42103 2 585.3606415 211748.7558 154.3586233 155.1352887 155.3697386 585.3603395 2 1 MSMS NA NA 1 1 1 0 -0.516744508 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 153.31258 2 585.3606415 208259.7249 152.9971703 153.0924637 153.6406682 585.3612168 2 1 MSMS NA NA 1 1 1 0 0.984498585 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 152.27591 2 585.3606415 204852.0892 151.654029 152.1857063 152.4659238 585.359718 2 1 MSMS NA NA 1 1 1 0 -1.580301924 FALSE FALSE +B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib ILLAELEQLK ILLAELEQLK P08670 Homo sapiens 1168.70673 150.92518 2 585.3606415 155713.5615 150.7044338 150.8675987 151.0228324 585.3597966 2 1 MSMS NA NA 1 1 1 0 -1.445757102 FALSE FALSE \ No newline at end of file diff --git a/inst/tinytest/raw_data/Metamorpheus/annotation.csv b/inst/tinytest/raw_data/Metamorpheus/annotation.csv new file mode 100644 index 00000000..0f9930bd --- /dev/null +++ b/inst/tinytest/raw_data/Metamorpheus/annotation.csv @@ -0,0 +1,5 @@ +"Run","BioReplicate","Condition" +"B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",5,"E" +"B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",6,"E" +"B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",10,"A" +"B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",11,"A" diff --git a/inst/tinytest/test_cleanRaw.R b/inst/tinytest/test_cleanRaw.R index e5e63e98..94a21fc9 100644 --- a/inst/tinytest/test_cleanRaw.R +++ b/inst/tinytest/test_cleanRaw.R @@ -211,6 +211,6 @@ expect_true(nrow(sn_cleaned) > 0) expect_equal(sn_cleaned, sn_cleaned2) # Metamorpheus -metamorpheus_table = data.table::fread("./raw_data/Metamorpheus/AllQuantifiedPeaks.tsv") +metamorpheus_table = data.table::fread("./raw_data/Metamorpheus/QuantifiedPeaks.tsv") input = MSstatsConvert::MSstatsImport(list(input = metamorpheus_table), "MSstats", "Metamorpheus") expect_identical(is(input), c("MSstatsMetamorpheusFiles", "MSstatsInputFiles")) \ No newline at end of file diff --git a/inst/tinytest/test_converters_MetamorpheusToMSstatsFormat.R b/inst/tinytest/test_converters_MetamorpheusToMSstatsFormat.R index 5251ed03..7b1fdad9 100644 --- a/inst/tinytest/test_converters_MetamorpheusToMSstatsFormat.R +++ b/inst/tinytest/test_converters_MetamorpheusToMSstatsFormat.R @@ -1,12 +1,12 @@ # Test MetamorpheusToMSstatsFormat --------------------------- -input_file_path = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", package="MSstatsConvert") -annotation_file_path = system.file("tinytest/raw_data/Metamorpheus/Annotation.tsv", package = "MSstatsConvert") +input_file_path = system.file("tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv", package="MSstatsConvert") +annotation_file_path = system.file("tinytest/raw_data/Metamorpheus/annotation.csv", package = "MSstatsConvert") input = data.table::fread(input_file_path) annotation = data.table::fread(annotation_file_path) output = MSstatsConvert:::MetamorpheusToMSstatsFormat(input, annotation = annotation) expect_equal(ncol(output), 11) -expect_equal(nrow(output), 236) +expect_equal(nrow(output), 20) expect_true("Run" %in% colnames(output)) expect_true("ProteinName" %in% colnames(output)) expect_true("PeptideSequence" %in% colnames(output)) diff --git a/man/MSstatsClean.Rd b/man/MSstatsClean.Rd index 74591b17..93ce567e 100644 --- a/man/MSstatsClean.Rd +++ b/man/MSstatsClean.Rd @@ -64,7 +64,7 @@ MSstatsClean(msstats_object, ...) quantificationColumn = "FragmentQuantCorrected" ) -\S4method{MSstatsClean}{MSstatsMetamorpheusFiles}(msstats_object) +\S4method{MSstatsClean}{MSstatsMetamorpheusFiles}(msstats_object, MBR = TRUE, qvalue_cutoff = 0.05) \S4method{MSstatsClean}{MSstatsProteinProspectorFiles}(msstats_object) } @@ -117,6 +117,8 @@ removed based on the IsUnique column from Philosopher output} \item{MBR}{True if analysis was done with match between runs} \item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.} + +\item{qvalue_cutoff}{The q-value cutoff for filtering peaks detected by MBR} } \value{ data.table diff --git a/man/MetamorpheusToMSstatsFormat.Rd b/man/MetamorpheusToMSstatsFormat.Rd index d1b03e1f..905db768 100644 --- a/man/MetamorpheusToMSstatsFormat.Rd +++ b/man/MetamorpheusToMSstatsFormat.Rd @@ -7,6 +7,8 @@ MetamorpheusToMSstatsFormat( input, annotation = NULL, + MBR = TRUE, + qvalue_cutoff = 0.05, useUniquePeptide = TRUE, removeFewMeasurements = TRUE, removeProtein_with1Feature = FALSE, @@ -23,6 +25,10 @@ MetamorpheusToMSstatsFormat( \item{annotation}{name of 'annotation.txt' data which includes Condition, BioReplicate.} +\item{MBR}{If TRUE, the function will include peaks detected by MBR} + +\item{qvalue_cutoff}{The q-value cutoff for filtering peaks detected by MBR} + \item{useUniquePeptide}{TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.} @@ -55,10 +61,10 @@ data.frame in the MSstats required format. Import Metamorpheus files } \examples{ -input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", +input = system.file("tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv", package = "MSstatsConvert") input = data.table::fread(input) -annot = system.file("tinytest/raw_data/Metamorpheus/Annotation.tsv", +annot = system.file("tinytest/raw_data/Metamorpheus/annotation.csv", package = "MSstatsConvert") annot = data.table::fread(annot) metamorpheus_imported = MSstatsConvert:::MetamorpheusToMSstatsFormat(input, annotation = annot) diff --git a/man/dot-cleanRawMetamorpheus.Rd b/man/dot-cleanRawMetamorpheus.Rd index b977802d..e3eea032 100644 --- a/man/dot-cleanRawMetamorpheus.Rd +++ b/man/dot-cleanRawMetamorpheus.Rd @@ -4,10 +4,14 @@ \alias{.cleanRawMetamorpheus} \title{Clean raw Metamorpheus files} \usage{ -.cleanRawMetamorpheus(msstats_object) +.cleanRawMetamorpheus(msstats_object, MBR = TRUE, qvalue_cutoff = 0.05) } \arguments{ \item{msstats_object}{an object of class \code{MSstatsMetamorpheusFiles}.} + +\item{MBR}{If TRUE, the function will include peaks detected by MBR} + +\item{qvalue_cutoff}{The q-value cutoff for filtering peaks detected by MBR} } \value{ data.table