From 5a8d34bbfaabec7eb57bad23220968c40d44ba84 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 28 Jul 2025 11:42:08 -0400 Subject: [PATCH 1/3] docs(Philosopher): Add examples for using Philosopher/Fragpipe converter --- DESCRIPTION | 2 +- R/converters.R | 10 ++ R/utils_MSstatsTMT.R | 4 +- inst/.DS_Store | Bin 6148 -> 0 bytes .../Philosopher/MSstatsTMT_annotation.csv | 91 +++++++++++++++++ inst/raw_data/Philosopher/msstats.csv | 95 ++++++++++++++++++ man/MSstatsTMT.Rd | 3 + man/PhilosophertoMSstatsTMTFormat.Rd | 11 ++ 8 files changed, 213 insertions(+), 3 deletions(-) delete mode 100644 inst/.DS_Store create mode 100644 inst/raw_data/Philosopher/MSstatsTMT_annotation.csv create mode 100644 inst/raw_data/Philosopher/msstats.csv diff --git a/DESCRIPTION b/DESCRIPTION index 110ed17..e445e6f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,4 +23,4 @@ Encoding: UTF-8 LazyData: true URL: http://msstats.org/msstatstmt/ BugReports: https://groups.google.com/forum/#!forum/msstats -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 diff --git a/R/converters.R b/R/converters.R index 133a6f2..a72d9db 100644 --- a/R/converters.R +++ b/R/converters.R @@ -332,6 +332,16 @@ SpectroMinetoMSstatsTMTFormat <- function( #' #' @return `data.frame` of class `MSstatsTMT` #' +#' @examples +#' input_file_path = system.file("raw_data/Philosopher/msstats.csv", +#' package = "MSstatsTMT") +#' annotation_file_path = system.file("raw_data/Philosopher/MSstatsTMT_annotation.csv", +#' package = "MSstatsTMT") +#' input = data.table::fread(input_file_path) +#' annotation = data.table::fread(annotation_file_path) +#' msstats_format = PhilosophertoMSstatsTMTFormat(input, annotation) +#' head(msstats_format) +#' #' @export PhilosophertoMSstatsTMTFormat = function( input, annotation, protein_id_col = "Protein", diff --git a/R/utils_MSstatsTMT.R b/R/utils_MSstatsTMT.R index 1739f42..a72e420 100644 --- a/R/utils_MSstatsTMT.R +++ b/R/utils_MSstatsTMT.R @@ -13,9 +13,9 @@ #' \item \code{\link{groupComparisonTMT}} : tests for significant changes in protein abundance across conditions. #' } #' -#' @docType package #' @name MSstatsTMT -NULL +#' @keywords internal +"_PACKAGE" #' Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments. diff --git a/inst/.DS_Store b/inst/.DS_Store deleted file mode 100644 index afbf4d5f5ba8945fb72edf7696885b45075c3cdc..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKO-lnY5Pi`e3cd8`aesk}_y^Xyq6J&QRM5t?T@pIc%qbaVV;tydp83V?E zF<=aAjRD@-(uN~N>x}_pz!=ytAm>9w5ljNMivH+e=br$?0nNTqm$!t(L;;h4ts-aG zoQ4uL)P*O8({S3O;Fkn!6*U~rXXZK~^Vj3W`Rueu-W@JcwB8sn2D%LF>u@ah{~7-> zy^s8Eh>eT^W8j}L;0Ea;op4j(ZvC-6xoacJJw=-MwW6?5?|cMsAm_+|pVawCbowO$ WTSZw#>^_`m9|E2b>x_XdFz^W?k2kmg diff --git a/inst/raw_data/Philosopher/MSstatsTMT_annotation.csv b/inst/raw_data/Philosopher/MSstatsTMT_annotation.csv new file mode 100644 index 0000000..521f500 --- /dev/null +++ b/inst/raw_data/Philosopher/MSstatsTMT_annotation.csv @@ -0,0 +1,91 @@ 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a/inst/raw_data/Philosopher/msstats.csv b/inst/raw_data/Philosopher/msstats.csv new file mode 100644 index 0000000..21795e2 --- /dev/null +++ b/inst/raw_data/Philosopher/msstats.csv @@ -0,0 +1,95 @@ +"Spectrum.Name","Spectrum.File","Peptide.Sequence","Modified.Peptide.Sequence","Probability","Charge","Protein.Start","Protein.End","Gene","Mapped.Genes","Protein","Protein.ID","Mapped.Proteins","Protein.Description","Is.Unique","Purity","Intensity","Channel.126","Channel.127N","Channel.127C","Channel.128N","Channel.128C","Channel.129N","Channel.129C","Channel.130N","Channel.130C","Channel.131N" +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.04225.04225.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","SSDGGSEEPPDRR","n[230]SSDGGSEEPPDRR",1,3,21,33,"TANC2","","sp|Q9HCD6|TANC2_HUMAN","Q9HCD6","","Protein TANC2",TRUE,0.5,29058558,53473.1016,66971.8594,27558.7285,66180.9219,94775.4531,72129.5234,93412.9375,52533.7422,58089.5234,44198.957 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.05945.05945.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","MDDSDQDSCR","n[230]MDDSDQDSCR",1,2,198,207,"PAX8","","sp|Q06710|PAX8_HUMAN","Q06710","","Paired box protein",TRUE,1,64983984,133589.7656,277471.9688,339930.8125,458741,27250.6348,599682,374046.5,396600.1562,288080.5625,243704.3906 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.07087.07087.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","AEAEAEAGSPRPDPR","n[230]AEAEAEAGSPRPDPR",1,3,4637,4651,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,65230552,324756.4688,18408.9414,127025.6328,16732.8223,30560.0566,22088.2109,234934.5938,99157,117041.4609,88308.0156 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.07988.07988.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","QDGDYSPDNSAQPGDR","n[230]QDGDYSPDNSAQPGDR",1,2,309,324,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,1,134390016,62969.4297,68964.1328,292931.4375,112034.7734,33149.5703,53302.7773,90751.3359,231425.7344,268154.9375,173834.125 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.08116.08116.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","QDGDYSPDNSAQPGDR","n[230]QDGDYSPDNSAQPGDR",1,2,309,324,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,1,149889712,131517.6562,80017.8438,272977.5938,151596.1875,68935.0391,71528.5312,91335.1562,207628.3906,256628.2969,215388.0781 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.10882.10882.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","EGQGEGETQEAAAATAAAR","n[230]EGQGEGETQEAAAATAAAR",1,3,3681,3699,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,0.67,48511452,194037.7812,24009.9629,82478.3828,57474.3984,71291.9922,63427.7773,164748.5625,116056.3984,84174.4219,71237.1328 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.11114.11114.4","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","QTSDGNWLMVHR","n[230]QTS[316]DGNWLM[147]VHR",0.9993,4,168,179,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,0.74,34173808,178713.8594,179251.4688,138970.8125,189085.2188,146196.4531,231841.9062,233118.375,177988.6562,171249.7969,137565.25 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.14116.14116.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","LTMLNTVSK","n[230]LTM[147]LNTVSK",0.9157,3,68,76,"SH3GL1","","sp|Q99961|SH3G1_HUMAN","Q99961","","Endophilin-A2",TRUE,1,98872056,419643.4062,395606.6875,286063.0625,292227.6562,596860.1875,241903.7812,688371.25,352771.9375,357452,347223.0938 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.14145.14145.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","ESTESSNTTIEDEDVK","n[230]ESTESSNTTIEDEDVK",1,3,329,344,"CAMK2D","","sp|Q13557|KCC2D_HUMAN","Q13557","","Calcium/calmodulin-dependent protein kinase type II subunit delta",TRUE,1,289236352,124410.7422,121518.8047,152290.9375,149399.6562,216064.2969,825769.25,196175.1875,199284.9531,209662.1562,141410.4375 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.14393.14393.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","ESTESSNTTIEDEDVK","n[230]ESTESSNTTIEDEDVK",1,3,329,344,"CAMK2D","","sp|Q13557|KCC2D_HUMAN","Q13557","","Calcium/calmodulin-dependent protein kinase type II subunit delta",TRUE,0.76,229207472,70812,71602.7891,86021.3984,87021.6875,104304.7969,389823,98218.8047,111910.8359,112847.5938,82529.75 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.14625.14625.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","YQQETSVSQLPGRPK","n[230]YQQETSVSQLPGRPK",1,3,1564,1578,"TANC2","","sp|Q9HCD6|TANC2_HUMAN","Q9HCD6","","Protein TANC2",TRUE,1,28733976,162676.0156,163120.3125,136647.4844,186262.5781,288684.6562,190590.3125,258702.3438,162000.1719,160732.6875,166368.1094 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.14901.14901.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","GAILTTMLATR","n[230]GAILTTM[147]LATR",0.9999,3,302,312,"CAMK2D","CAMK2A;CAMK2B","sp|Q13557|KCC2D_HUMAN","Q13557","sp|Q13554|KCC2B_HUMAN;sp|Q9UQM7|KCC2A_HUMAN","Calcium/calmodulin-dependent protein kinase type II subunit delta",FALSE,1,40487512,87156.6953,123929.8359,136017.3125,113796.1328,325175.4062,204953.2969,183429.3438,175068,133387.4844,120227.0469 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.15525.15525.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","ALETMNK","n[230]ALETMNK",0.994,2,157,163,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,32466892,208282.125,533066.25,294146.9062,563202.25,460770.9375,823593.25,570828.875,537096.9375,312645.3438,404656.75 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.17357.17357.4","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","KGGDGIKPPPIIGR","n[230]KGGDGIKPPPIIGR",1,4,5,18,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,1,909555584,166787.9062,270603.9062,255155.9844,254222.8438,258203.4531,233064.1406,280672.3125,311485.6875,324233.6875,275042.7188 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.18897.18897.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","SSLYCSDIGK","n[230]SSLYCSDIGK",1,2,379,388,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,1,322046880,364898.125,424766.8125,1384306,574772.625,287451.5625,273002.1875,449773.7812,788061.625,1179433,859890.6875 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.19684.19684.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","GCGVVEFK","n[230]GCGVVEFK",0.9999,2,142,149,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,0.82,207355840,442496.6562,487739.3125,484301.2188,803611.875,281926.2812,1078799,718019.6875,721879.5,705089.3125,622555.375 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.21444.21444.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","YLEANMTQSALPK","n[230]YLEANM[147]TQSALPK",1,2,282,294,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,1,26254800,116355.8203,137655.3438,139374.0781,126379.3984,133682.4375,153402.6562,155367.5469,164374.6562,175618.3594,148088.8125 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.25901.25901.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NIGNTFFK","n[230]NIGNTFFK",1,2,228,235,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,1,376800160,2421456.75,1371379.25,3077288.75,1682978.25,3848730.75,4906989,2402642.75,3504737.75,3080020.25,2810615 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.28250.28250.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","LYGPTNFSPIINHVAR","n[230]LYGPTNFSPIINHVAR",1,3,391,406,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,0.54,455828640,114046.5234,148080.125,141590.0938,121584.5938,145680.7656,177571.0938,193098.9844,172152.4531,169095.2031,142382.5781 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.28315.28315.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","LYGPTNFSPIINHVAR","n[230]LYGPTNFSPIINHVAR",1,2,391,406,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,1,36354812,131424.2031,176060.875,141853.5625,130879.4219,136574.2188,210731.9219,243962.1875,172536.0781,167103.6094,133787.7344 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.28349.28349.6","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","LVGRPPLPVPAVGIGTVHLHQHEDILAK","n[230]LVGRPPLPVPAVGIGTVHLHQHEDILAK",1,6,889,916,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,1,63040900,100460.5078,99387.3672,214580.3594,101788.9766,58616.668,88769.5547,110691.8438,183040.7344,199704.375,135561.6719 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.28377.28377.5","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","LVGRPPLPVPAVGIGTVHLHQHEDILAK","n[230]LVGRPPLPVPAVGIGTVHLHQHEDILAK",1,5,889,916,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,0.37,48322436,145621.6562,147147.1875,273589.5625,172246.8281,142203.9688,411355.625,192515.2969,249207.5781,266824.125,210832.5156 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.28533.28533.5","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","LVGRPPLPVPAVGIGTVHLHQHEDILAK","n[230]LVGRPPLPVPAVGIGTVHLHQHEDILAK",1,5,889,916,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,1,60786052,104359.125,98972.8203,257540.7969,136414.8281,64393.293,178737.9375,120276.2578,212543.3125,225913.1875,168611.0781 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.34349.34349.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","VFISNIPYDMK","n[230]VFISNIPYDMK",1,2,102,112,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,135656624,141339.875,168169.3281,192865.7344,290690.75,68942.9531,515769.2188,470512.0938,255537.8438,240030.5156,203183.7969 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.34351.34351.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","VFISNIPYDMK","n[230]VFISNIPYDMK",1,2,102,112,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,141525264,187644.5781,211548.6406,237330.9844,377179.9375,67541.7344,600410.5625,550691.5,280020.7812,260654.5312,233607.5938 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.34531.34531.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","VFFDVDIGGER","n[230]VFFDVDIGGER",1,2,18,28,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,1,61006892,495034.5312,386296.7188,616756.5625,321886.5312,568345.25,712595.5625,595983.4375,633466.3125,564178.3125,559268.8125 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.34545.34545.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","VFFDVDIGGER","n[230]VFFDVDIGGER",1,2,18,28,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,0.85,133909016,516421.2188,413345.4688,677029.875,362656.0312,699778.0625,853199,621233.75,752521.0625,637508,632195.3125 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.36974.36974.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NLPFDLTWQK","n[230]NLPFDLTWQK",1,2,529,538,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,95639424,193262.8594,201530.3125,233439.0625,348824.0312,59749.125,570347.375,532727.5,275453.4062,241193,213682.25 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.37048.37048.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NLPFDLTWQK","n[230]NLPFDLTWQK",1,3,529,538,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,58497004,451318.5938,182573.125,233350.5469,393898.3438,71178.7734,611627.875,505575.3438,250232.9062,258799.3594,424330.2812 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.38089.38089.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,3,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0.46,476562400,252029.7969,364502.8438,335493.5312,326679.8438,345861.8438,298383.1875,345714.875,394625.875,394398.7188,338799.6875 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.38628.38628.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,3,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,1,25428448,61291.4375,74236.0938,74793.1719,70132.7344,86858.2422,84709.7734,78207.6562,90386.7812,81704.6797,77328.6953 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.38674.38674.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,3,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0,28157016,58978.7656,93921.3906,81770.9609,72799.4375,100891.75,87043.7891,92984.625,103720.1719,89025.9297,89494.5312 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.39183.39183.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,3,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0.51,11338453,68699.5469,112747.4609,94652.0469,85027.4844,122260.9219,97572.8906,124826.6797,134252.0469,103595.9766,99187.1328 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.39554.39554.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",0.9951,2,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0.72,88392712,139607.5156,144368.6562,139572.2031,206676.2969,180988.375,195630.7031,206411.4688,190020.9375,158484.1875,153422.9375 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.39907.39907.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","AVPVWDVLASGYVSR","n[230]AVPVWDVLASGYVSR",1,2,2533,2547,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,299018944,260604.5312,91985.125,115962.3594,100326.4375,131405.6719,185918.7344,207543.0781,144858.0938,124957.3594,123795.7578 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.39927.39927.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","AVPVWDVLASGYVSR","n[230]AVPVWDVLASGYVSR",1,3,2533,2547,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,0.64,330016224,91648.2734,32969.4844,49777.0156,28548.3887,41787.3242,42108.5586,83213.7188,51249.25,52722.7188,51162.3242 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.40654.40654.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","IGGGIGFGGLEAMNSMGGFGGVGR","n[230]IGGGIGFGGLEAMNSMGGFGGVGR",1,2,377,400,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,11922556,32318.0098,40199.4727,48802.3125,79679.25,19577.9219,135823.5312,139380.5625,63022.6055,60150.9727,52114.4062 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.40656.40656.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","AVPVWDVLASGYVSGAAR","n[230]AVPVWDVLASGYVSGAAR",1,3,4670,4687,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,23206878,27124.5215,31872.9922,30046.9648,29435.6699,36784.6758,43625.1875,32007.9844,38299.5664,31733.7734,33042.3867 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.40681.40681.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","AVPVWDVLASGYVSGAAR","n[230]AVPVWDVLASGYVSGAAR",1,3,4670,4687,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,0.5,21937412,25091.125,36462.4062,38040.6289,37406.9805,46805.7891,42903.9414,33362.8633,54484.8008,36414.4258,40665.082 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.40691.40691.2","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","IGGGIGFGGLEAMNSMGGFGGVGR","n[230]IGGGIGFGGLEAMNSMGGFGGVGR",1,2,377,400,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,23614896,19902.084,25722.5449,30856.2891,53319.3359,17193.6094,88146.3125,82855.4922,42723.2109,44937.7969,34712.3594 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.41760.41760.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","IGGGIGFGGLEAMNSMGGFGGVGR","n[230]IGGGIGFGGLEAMNSMGGFGGVGR",1,3,377,400,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,42251600,29582.5547,17857.0117,32220.4473,46160.5039,69615.25,24384.7812,24639.2344,61988.4805,28249.7246,39099.5781 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.41769.41769.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","IGGGIGFGGLEAMNSMGGFGGVGR","n[230]IGGGIGFGGLEAMNSMGGFGGVGR",0.9925,3,377,400,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,54659052,35201.3281,20490.1738,36982.5273,60244.6719,86075.9141,35940.3945,31682.4629,81067.7969,36042.9336,55780.2695 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.42141.42141.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","VTEQLIEAINNGDFEAYTK","n[230]VTEQLIEAINNGDFEAYTK",1,3,353,371,"CAMK2D","","sp|Q13557|KCC2D_HUMAN","Q13557","","Calcium/calmodulin-dependent protein kinase type II subunit delta",TRUE,1,38082916,29490.8418,42304.6992,64342.2188,53508.7109,59340.5703,120144.7266,46964.8555,75260.3672,64764.7734,55852.5195 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.43194.43194.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","VVPVSLSEVYLLQCNMK","n[230]VVPVSLSEVYLLQCNMK",1,3,678,694,"TANC2","","sp|Q9HCD6|TANC2_HUMAN","Q9HCD6","","Protein TANC2",TRUE,0.55,18145966,64383.0625,72356.75,62743.9414,83371.1094,160412.4219,65540.2969,115095.0391,73954.4844,64807.9141,74519.0156 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.43245.43245.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","VVPVSLSEVYLLQCNMK","n[230]VVPVSLSEVYLLQCNMK",1,3,678,694,"TANC2","","sp|Q9HCD6|TANC2_HUMAN","Q9HCD6","","Protein TANC2",TRUE,1,26033156,46445.7109,46907.8828,48813.9492,56522.8516,92719.6953,65682.0469,81809.6328,58241.6367,50470.1406,60289.3867 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.43806.43806.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","MSNWQGAIDSCLEALELDPSNTK","n[230]MSNWQGAIDSCLEALELDPSNTK",1,3,286,308,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,0.69,52481592,148117.8594,92800.6094,221245.25,120612.1875,274593.2812,355536.0938,204307.1875,280591.625,264797.7188,157907.4219 +"16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.43952.43952.3","16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01.mzML","PTLWALLNSEYVTEEK","n[230]PTLWALLNSEYVTEEK",1,3,2120,2135,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,0,79958.6016,78765.4922,58813.5,70517.5703,50280.9492,55388.6875,106719.5078,66978.3203,77686.1406,89003.4688 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.04217.04217.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","MDDSDQDSCR","M[147]DDS[316]DQDSCR",0.9649,2,198,207,"PAX8","","sp|Q06710|PAX8_HUMAN","Q06710","","Paired box protein",TRUE,1,0,39884.5547,24974.3711,10091.1748,45095.1836,65185.8672,11669.0918,46138.5039,12993.4316,7988.5972,28517.9414 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.04442.04442.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","SSDGGSEEPPDRR","n[230]SSDGGSEEPPDRR",1,3,21,33,"TANC2","","sp|Q9HCD6|TANC2_HUMAN","Q9HCD6","","Protein TANC2",TRUE,0.46,29357696,80028.9844,87967.7031,101598.375,100496.8203,161275.25,75225.3281,102696.9766,151036.8125,112668.5312,87605.2266 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.06260.06260.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","MDDSDQDSCR","n[230]MDDSDQDSCR",1,2,198,207,"PAX8","","sp|Q06710|PAX8_HUMAN","Q06710","","Paired box protein",TRUE,1,0,645713.125,424796.3125,158219.7656,768707.3125,1102303.375,143281.8125,740439.8125,208636,127572.9922,468972.4688 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.07347.07347.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","AEAEAEAGSPRPDPR","n[230]AEAEAEAGSPRPDPR",1,3,4637,4651,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,0,16365115,56689.6445,23033.5801,53335.7188,58941.5312,33175.4492,161275.4531,35977.3672,39647.7148,16958.6289,59307.1016 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.08148.08148.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","QDGDYSPDNSAQPGDR","n[230]QDGDYSPDNSAQPGDR",1,2,309,324,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,0,607792704,311020.75,83619.4922,15097.6104,244208.8125,32794.9023,23036.8516,147349.2031,34465.832,34978.2461,103739.0312 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.08283.08283.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","QDGDYSPDNSAQPGDR","n[230]QDGDYSPDNSAQPGDR",1,3,309,324,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,1,44890952,73168.4844,48403.0742,44231.7891,74292.75,92910.3984,37685.4336,54651.9258,40100.1172,31234.9414,47870.6953 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.08693.08693.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","QAIVNASR","n[230]QAIVNASR",0.9765,2,439,446,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,1,38503400,264351.5312,73569.4766,104912.6797,925377.4375,926166.5625,115570.0391,255436.5469,359862.0625,118511.7656,222946.0781 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.11554.11554.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","EGQGEGETQEAAAATAAAR","n[230]EGQGEGETQEAAAATAAAR",1,2,3681,3699,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,78320048,286248.1875,5069.1895,148892.875,174360.5625,23365.2344,1148353,0,90918.5547,11632.6582,230870.7344 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.14929.14929.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","ESTESSNTTIEDEDVK","n[230]ESTESSNTTIEDEDVK",1,2,329,344,"CAMK2D","","sp|Q13557|KCC2D_HUMAN","Q13557","","Calcium/calmodulin-dependent protein kinase type II subunit delta",TRUE,0.53,323311072,170361.1406,110277.1016,138648.9688,223351.3125,956790.5625,148163.6094,261563.7812,157353.5938,63688.7539,157772.6719 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.14932.14932.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","ESTESSNTTIEDEDVK","n[230]ESTESSNTTIEDEDVK",1,2,329,344,"CAMK2D","","sp|Q13557|KCC2D_HUMAN","Q13557","","Calcium/calmodulin-dependent protein kinase type II subunit delta",TRUE,0.84,367648320,294106.0938,197443.0938,211006.4219,347610.2188,1605381.625,210632.7656,287321.125,235184.5312,65819.9688,214612.3438 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.14999.14999.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","LTMLNTVSK","n[230]LTM[147]LNTVSK",0.9685,3,68,76,"SH3GL1","","sp|Q99961|SH3G1_HUMAN","Q99961","","Endophilin-A2",TRUE,1,102373936,251949.125,222550.4375,368102.75,308361.75,211980.5,354011.0312,235623,314508.6562,529611.75,287265.7812 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.15353.15353.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","YQQETSVSQLPGRPK","n[230]YQQETSVSQLPGRPK",1,3,1564,1578,"TANC2","","sp|Q9HCD6|TANC2_HUMAN","Q9HCD6","","Protein TANC2",TRUE,0.51,34279500,170198.5781,181599.8125,231989.8438,181305.1562,202064.2188,182056.5,217149.4531,250748.7031,417306.125,197622.9688 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.15360.15360.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","QETVDCLKK","n[230]QETVDCLKK",0.9997,3,285,293,"CAMK2D","CAMK2A","sp|Q13557|KCC2D_HUMAN","Q13557","sp|Q9UQM7|KCC2A_HUMAN","Calcium/calmodulin-dependent protein kinase type II subunit delta",FALSE,1,28139004,582990.0625,460514.4062,417378.2188,784666.8125,2302350,582810.6875,761050.875,905113.0625,408943.625,720424.8125 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.15775.15775.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","GAILTTMLATR","n[230]GAILTTM[147]LATR",0.9993,3,302,312,"CAMK2D","CAMK2A;CAMK2B","sp|Q13557|KCC2D_HUMAN","Q13557","sp|Q13554|KCC2B_HUMAN;sp|Q9UQM7|KCC2A_HUMAN","Calcium/calmodulin-dependent protein kinase type II subunit delta",FALSE,1,41957356,233198.9375,647530.5,291124.5938,207511.2656,183859.0625,236534.7031,259046.6719,266516,505518.5,317696.9375 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.18335.18335.4","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","KGGDGIKPPPIIGR","n[230]KGGDGIKPPPIIGR",1,4,5,18,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0.53,852943488,626924.1875,493673.1875,549643.9375,669143.25,557778.375,600955.625,620787.0625,692777.875,751812.25,614106.75 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.19909.19909.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","SSLYCSDIGK","n[230]SSLYCSDIGK",1,2,379,388,"DHTKD1","","sp|Q96HY7|DHTK1_HUMAN","Q96HY7","","2-oxoadipate dehydrogenase complex component",TRUE,0.78,574903552,1490700.375,777483.9375,274506.375,1270474.25,195244.4375,193378.8281,707655.9375,217172.8438,576605.5,493141.75 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.20818.20818.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","GCGVVEFK","n[230]GCGVVEFK",0.9993,2,142,149,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,84356144,655077.0625,691005.75,413556.125,820350.0625,1725507.25,477492.875,711612.375,480527,527165.3125,627089.5625 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.21141.21141.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","EVTLGQVAK","n[230]EVTLGQVAK",1,2,858,866,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,134854928,563873,634774.4375,276654.25,426296.1875,295429.5,1566543.25,598150.625,584907,2069509.125,634058.0625 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.22375.22375.4","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","TDAFSQHHLEPLECPFER","n[230]TDAFS[316]QHHLEPLECPFER",1,4,225,242,"PAX8","","sp|Q06710|PAX8_HUMAN","Q06710","","Paired box protein",TRUE,0.7,58449232,458507.2188,513900.5625,226675.6719,617443.75,602702.8125,242153.3906,593551.625,234262.2812,333595.3438,393703.7188 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.22693.22693.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","YLEANMTQSALPK","n[230]YLEANM[147]TQSALPK",1,2,282,294,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0,57207080,230010.5625,171998.4219,289487.75,284056.0625,279422.75,324813.2812,215798.75,300698.5625,268676.5,265244.1562 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.23568.23568.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","GFIMAEVMK","n[230]GFIMAEVM[147]K",0.9998,3,341,349,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0.53,192811952,381783.25,320458.0312,293958.4062,455412.3125,314296.4062,320917,354925.3125,412719.375,285399.3438,322876.8125 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.27297.27297.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","NIGNTFFK","n[230]NIGNTFFK",0.9999,2,228,235,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,1,308300352,1407065.5,1176072.875,1140584.875,2051653.875,2011354,953537.5625,1140141.125,1015642.375,1213439.75,1162606.25 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.27978.27978.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","MSIYQAMWK","n[230]MSIYQAM[147]WK",0.9987,2,2243,2251,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,49858092,195778.5156,156972.75,150975.2031,144945.9688,202314.625,569375.5,210106.9844,200318.7031,620879.625,221239.9688 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.30118.30118.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","LYGPTNFSPIINHVAR","n[230]LYGPTNFSPIINHVAR",1,3,391,406,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,1,818442432,444449.6562,333486.5312,336277.8125,474924.5312,583425.25,455661.5,461092.3438,509625.7188,212036.7344,393608.9062 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.33926.33926.4","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","DETSGLHLLPLPESAPALPTEEQVQR","n[230]DETS[316]GLHLLPLPESAPALPTEEQVQR",1,4,1105,1130,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,27931840,93912.0859,73017.7969,105501.5078,81444.6328,106202.4375,136859.3594,101720.3828,85035.3359,173821.5,95881.3125 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.36993.36993.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","VFISNIPYDMK","n[230]VFISNIPYDMK",1,2,102,112,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,0,213793568,274607.6562,287806.4375,142782.8906,336661.3125,613073.3125,221936.8125,309082.8125,214189.9688,216644.1094,213545.7344 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.37251.37251.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","VFFDVDIGGER","n[230]VFFDVDIGGER",1,2,18,28,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,1,135256704,423658.875,368475,375158.625,595656.125,504886.0625,410409.9062,421033.1562,481889.0938,458576.1562,390816.9375 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.37258.37258.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","VFFDVDIGGER","n[230]VFFDVDIGGER",1,2,18,28,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,0.7,119022536,247996.5781,198754.5781,182371.2031,342746.625,242807.2969,201411.5938,242962.125,177235.2969,172215.6094,215763.6875 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.37385.37385.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","VFFDVDIGGER","n[230]VFFDVDIGGER",1,2,18,28,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,0.83,34606448,269148.1875,264996.5625,207258.7031,387409.9062,385264.2812,278787.25,352958.0938,326427.5625,245497.6875,322449 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.39432.39432.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","NLPFDLTWQK","n[230]NLPFDLTWQK",1,2,529,538,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,219495120,905735.75,884228.8125,541994.5,1104416.625,2232653.5,769780.6875,1162127.625,560233.5,656731.5625,747008.125 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.40586.40586.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,2,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,1,577487424,455174.9375,374895.125,369373.9062,532853.6875,377832.5,417925.25,447886.0938,569163.5,365027.2188,428961.0625 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.41044.41044.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,2,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0,32589512,131456.6406,115541.7266,104787.4688,158574.4375,145473.2344,120317.9141,119284.8203,155569.7656,108984.6016,135410.625 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.41389.41389.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,2,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,1,23473386,146337.2031,112537.0469,121689.4531,165904.375,150646.5938,158694.375,136980.1562,189462.1875,136669.3281,147227.0938 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.41415.41415.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,2,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,1,28783936,143430.1406,115676.2188,113914.6953,163258.2344,145756.3906,129612.1094,129360,157746.9688,128474.9922,135603.2188 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.41964.41964.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","NYIVEDGDIIFFK","n[230]NYIVEDGDIIFFK",1,2,374,386,"OLA1","","sp|Q9NTK5|OLA1_HUMAN","Q9NTK5","","Obg-like ATPase 1",TRUE,0,11347740,106565.4531,107700.4766,107787.6406,118916.9922,107449.9062,101757.6875,105692.7812,122248.8281,179382.0938,105824.6094 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.42210.42210.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","TIELSDDDFLGECECTLGQIVSSK","n[230]TIELS[316]DDDFLGECECTLGQIVSSK",1,3,86,109,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,0.58,0,48777.8867,42912.3398,37636.5039,54476.2656,75080.4141,27422.7656,56114.1719,65788.3359,29758.7129,48177.3555 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.42698.42698.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","AVPVWDVLASGYVSR","n[230]AVPVWDVLASGYVSR",1,2,2533,2547,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,0.83,174371808,322448.8438,146438.1406,225681.625,305485.7812,213480.8438,980352.3125,224591.4375,249991.2344,548354.9375,340692.2188 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43223.43223.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","TIELSDDDFLGECECTLGQIVSSK","n[230]TIELSDDDFLGECECTLGQIVS[316]SK",1,3,86,109,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,0,0,47441.75,42593.125,34984.9922,51164.2109,71581.8828,27126.6055,49920.3672,61010.0586,26807.5566,50033.0078 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43482.43482.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","SDPLCVLFLNTSGQQWYEVER","n[230]SDPLCVLFLNTS[316]GQQWYEVER",1,3,27,47,"CPNE3","","sp|O75131|CPNE3_HUMAN","O75131","","Copine-3",TRUE,0.84,18769052,176958.6719,137091.8594,106044.6016,222733.8281,251033.0938,72343.1094,174954.9219,169680.6719,74412.8047,128556.2578 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43554.43554.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","IGGGIGFGGLEAMNSMGGFGGVGR","n[230]IGGGIGFGGLEAMNSMGGFGGVGR",1,3,377,400,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,43202416,41619.168,49190.7617,37504.8555,44412.4688,65305.5781,47820.7305,54133.8164,37978.6992,84100.1094,48975.4883 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43562.43562.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","IGGGIGFGGLEAMNSMGGFGGVGR","n[230]IGGGIGFGGLEAMNSMGGFGGVGR",1,2,377,400,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,1,40426140,87986.5312,117469.6172,53320.3477,111176.1875,246044.4219,67546.0859,131629.4844,70657.6875,77868.3594,86337.0859 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43605.43605.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","IGGGIGFGGLEAMNSMGGFGGVGR","n[230]IGGGIGFGGLEAMNSMGGFGGVGR",1,3,377,400,"MYEF2","","sp|Q9P2K5|MYEF2_HUMAN","Q9P2K5","","Myelin expression factor 2",TRUE,0,0,31483.1602,46732.5,34811.7773,31429.8223,38235.8359,41466.0352,37983.0781,32965.4727,50718.332,32575.7988 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43698.43698.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","AVPVWDVLASGYVSGAAR","n[230]AVPVWDVLASGYVSGAAR",1,3,4670,4687,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,0,24352304,18913.9551,18430.5742,23662.7012,23380.3691,31197.4531,22906.9043,25586.7188,22859.916,24170.2852,23688.5195 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43711.43711.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","AVPVWDVLASGYVSGAAR","n[230]AVPVWDVLASGYVSGAAR",1,3,4670,4687,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,0,0,20426,20898.4668,18721.1504,22153.2617,30320.668,20762.3145,22914.25,20001.4941,25546.123,20352.9941 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43717.43717.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","AVPVWDVLASGYVSGAAR","n[230]AVPVWDVLASGYVSGAAR",1,3,4670,4687,"EPPK1","","sp|P58107|EPIPL_HUMAN","P58107","","Epiplakin",TRUE,1,30402308,17394.6738,16882.2852,18113.1719,20978.8965,32042.8125,20866.4355,26597.0215,21222.6465,24294.4336,15848.207 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.43912.43912.3","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","MSNWQGAIDSCLEALELDPSNTK","M[147]S[316]NWQGAIDSCLEALELDPSNTK",1,3,286,308,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,1,27560010,122582.1953,82481.7656,79387.1484,133003.0625,178821.0625,89622.9766,136408.0781,120745.6406,73213.2656,114462.5547 +"17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.46161.46161.2","17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01.mzML","MSNWQGAIDSCLEALELDPSNTK","n[230]MSNWQGAIDSCLEALELDPSNTK",1,2,286,308,"PPID","","sp|Q08752|PPID_HUMAN","Q08752","","Peptidyl-prolyl cis-trans isomerase D",TRUE,0,0,24850.3398,22807.7891,14892.9639,26095.6797,36738.7422,12269.0049,26776.502,20596.3926,14881.5625,19730.4785 diff --git a/man/MSstatsTMT.Rd b/man/MSstatsTMT.Rd index c2616b7..ebbacc8 100644 --- a/man/MSstatsTMT.Rd +++ b/man/MSstatsTMT.Rd @@ -37,8 +37,11 @@ Authors: \item Ting Huang \email{thuang0703@gmail.com} \item Meena Choi \email{mnchoi67@gmail.com} \item Mateusz Staniak \email{mtst@mstaniak.pl} + \item Tony Wu \email{wu.anthon@northeastern.edu} + \item Deril Raju \email{raju.d@northeastern.edu} \item Sicheng Hao \email{hao.sic@husky.neu.edu} \item Olga Vitek \email{o.vitek@northeastern.edu} } } +\keyword{internal} diff --git a/man/PhilosophertoMSstatsTMTFormat.Rd b/man/PhilosophertoMSstatsTMTFormat.Rd index 0ed82fb..dfa8d15 100644 --- a/man/PhilosophertoMSstatsTMTFormat.Rd +++ b/man/PhilosophertoMSstatsTMTFormat.Rd @@ -75,3 +75,14 @@ If `append = TRUE`, has to be a valid path to a file.} \description{ Convert Philosopher (Fragpipe) output to MSstatsTMT format. } +\examples{ +input_file_path = system.file("raw_data/Philosopher/msstats.csv", + package = "MSstatsTMT") +annotation_file_path = system.file("raw_data/Philosopher/MSstatsTMT_annotation.csv", + package = "MSstatsTMT") +input = data.table::fread(input_file_path) +annotation = data.table::fread(annotation_file_path) +msstats_format = PhilosophertoMSstatsTMTFormat(input, annotation) +head(msstats_format) + +} From 2d14c464d939b4af1135754c998742e5c7a42e56 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 28 Jul 2025 11:43:36 -0400 Subject: [PATCH 2/3] remove rows from annotation --- .../Philosopher/MSstatsTMT_annotation.csv | 32 +------------------ 1 file changed, 1 insertion(+), 31 deletions(-) diff --git a/inst/raw_data/Philosopher/MSstatsTMT_annotation.csv b/inst/raw_data/Philosopher/MSstatsTMT_annotation.csv index 521f500..fc84837 100644 --- a/inst/raw_data/Philosopher/MSstatsTMT_annotation.csv +++ b/inst/raw_data/Philosopher/MSstatsTMT_annotation.csv @@ -58,34 +58,4 @@ Run,Fraction,TechRepMixture,Mixture,Channel,BioReplicate,Condition 17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,130C,CPT0069160003_T,T 17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,131N,pool17_NORM,Norm 17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,131N,pool17_NORM,Norm -17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,131N,pool17_NORM,Norm -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,126,CPT0007870001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,126,CPT0007870001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,126,CPT0007870001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,127N,CPT0001270001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,127N,CPT0001270001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,127N,CPT0001270001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,127C,CPT0077110003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,127C,CPT0077110003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,127C,CPT0077110003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,128N,QC8_QC,QC -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,128N,QC8_QC,QC -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,128N,QC8_QC,QC -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,128C,CPT0077140001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,128C,CPT0077140001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,128C,CPT0077140001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,129N,CPT0001260009_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,129N,CPT0001260009_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,129N,CPT0001260009_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,129C,CPT0076350001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,129C,CPT0076350001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,129C,CPT0076350001_N,N -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,130N,CPT0076330003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,130N,CPT0076330003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,130N,CPT0076330003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,130C,CPT0007860003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,130C,CPT0007860003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,130C,CPT0007860003_T,T -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f01,1,1,plex18,131N,pool18_NORM,Norm -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f02,2,1,plex18,131N,pool18_NORM,Norm -18CPTAC_CCRCC_W_JHU_20180521_LUMOS_f03,3,1,plex18,131N,pool18_NORM,Norm +17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,131N,pool17_NORM,Norm \ No newline at end of file From c52c9e65b7778d7f6d36ab705f266b1b1ac00205 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 28 Jul 2025 11:47:52 -0400 Subject: [PATCH 3/3] add unit tests --- ...est-PDtoMSstatsTMTFormat.R => test-converters.R} | 13 +++++++++++++ 1 file changed, 13 insertions(+) rename tests/testthat/{test-PDtoMSstatsTMTFormat.R => test-converters.R} (69%) diff --git a/tests/testthat/test-PDtoMSstatsTMTFormat.R b/tests/testthat/test-converters.R similarity index 69% rename from tests/testthat/test-PDtoMSstatsTMTFormat.R rename to tests/testthat/test-converters.R index b66ebce..3e45fa8 100644 --- a/tests/testthat/test-PDtoMSstatsTMTFormat.R +++ b/tests/testthat/test-converters.R @@ -26,3 +26,16 @@ test_that("SpectroMinetoMSstatsTMTFormat works", { summaryforMultipleRows = average)) # wrong argument value }) + +test_that("PhilosophertoMSstatsTMTFormat works", { + + input_file_path = system.file("raw_data/Philosopher/msstats.csv", + package = "MSstatsTMT") + annotation_file_path = system.file("raw_data/Philosopher/MSstatsTMT_annotation.csv", + package = "MSstatsTMT") + input = data.table::fread(input_file_path) + annotation = data.table::fread(annotation_file_path) + msstats_format = PhilosophertoMSstatsTMTFormat(input, annotation) + expect_equal(nrow(msstats_format), 550) + +})