Testing peptides for quantifiability.
/* ############################################################################## # file: tools_quant_helper.cs # # 'msparser' toolkit example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2015 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_csharp/tools_quant_helper.cs $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## */ using System; using System.IO; using System.Collections.Generic; using matrix_science.msparser; namespace MsParserExamples { class tools_quant_helper { private const string QUANT_SCHEMA = @"http://www.matrixscience.com/xmlns/schema/quantitation_2 ../html/xmlns/schema/quantitation_2/quantitation_2.xsd http://www.matrixscience.com/xmlns/schema/quantitation_1 ../html/xmlns/schema/quantitation_1/quantitation_1.xsd", UNIMOD_SCHEMA = @"http://www.unimod.org/xmlns/schema/unimod_2 ../html/xmlns/schema/unimod_2/unimod_2.xsd"; public static int Main(string[] argv) { if (argv.Length == 0) { Console.Error.WriteLine("Usage: {0} <quantitation results.dat>", Path.GetFileName((new tools_quant_helper()).GetType().Assembly.Location)); return 1; } ms_mascotresfile resfile = new ms_mascotresfile(argv[0]); if (!resfile.isValid()) { Console.Error.WriteLine(resfile.getLastErrorString()); return 1; } // the details of loading the quantitation method and peptide summary object // are not relevant to this example (see methods at the end of the file for // implementation). ms_quant_configfile quantConfigFile; ms_quant_method qmethod; ms_peptidesummary pepSum; if (!loadMethod(resfile, out quantConfigFile, out qmethod)) return 1; ms_umod_configfile umodfile = null; if (!loadUmodConfigFile(resfile, out umodfile)) return 1; if (!loadPeptideSummary(resfile, out pepSum)) return 1; ms_quant_helper quantHelper = new ms_quant_helper(pepSum, qmethod, umodfile); if (!quantHelper.isValid()) { Console.WriteLine("ms_quant_helper is not value: {0}", quantHelper.getLastErrorString()); return 1; } List<ms_protein> proteins = pullProteinsFrom(pepSum); Console.WriteLine("File {0} uses {1} and has {2} family proteins", argv[0], qmethod.getName(), proteins.Count); dumpQuantMethod(qmethod); Console.WriteLine(); Dictionary<int, string> peptideQuantStr = new Dictionary<int, string>() { {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_HAS_EXCLUDED_FIXEDMOD, "PEPTIDE_HAS_EXCLUDED_FIXEDMOD"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_HAS_EXCLUDED_LOCAL_FIXEDMOD, "PEPTIDE_HAS_EXCLUDED_LOCAL_FIXEDMOD"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_HAS_EXCLUDED_LOCAL_VARMOD, "PEPTIDE_HAS_EXCLUDED_LOCAL_VARMOD"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_HAS_EXCLUDED_VARMOD, "PEPTIDE_HAS_EXCLUDED_VARMOD"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_HAS_NO_REQUIRED_FIXEDMOD, "PEPTIDE_HAS_NO_REQUIRED_FIXEDMOD"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_HAS_NO_REQUIRED_VARMOD, "PEPTIDE_HAS_NO_REQUIRED_VARMOD"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_HAS_UNMODIFIED_SITE, "PEPTIDE_HAS_UNMODIFIED_SITE"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_IS_QUANTIFIABLE, "PEPTIDE_IS_QUANTIFIABLE"}, {(int) ms_quant_helper.PEPTIDE_QUANTIFIABILITY.PEPTIDE_QUANTIFIABILITY_UNAVAILABLE, "PEPTIDE_QUANTIFIABILITY_UNAVAILABLE"} }; Dictionary<int, string> peptideQualityStr = new Dictionary<int, string>() { {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_EXPECT_ABOVE_THRESHOLD, "PEPTIDE_EXPECT_ABOVE_THRESHOLD"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_CHARGE_BELOW_PRECURSOR_MIN, "PEPTIDE_CHARGE_BELOW_PRECURSOR_MIN"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_HAS_NO_EXCLUSIVE_MODS, "PEPTIDE_HAS_NO_EXCLUSIVE_MODS"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_NOT_UNIQUE, "PEPTIDE_NOT_UNIQUE"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_QUALITY_IS_OK, "PEPTIDE_QUALITY_IS_OK"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_QUALITY_UNAVAILABLE, "PEPTIDE_QUALITY_UNAVAILABLE"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_SCORE_BELOW_HOMOLOGY_THR, "PEPTIDE_SCORE_BELOW_HOMOLOGY_THR"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_SCORE_BELOW_IDENTITY_THR, "PEPTIDE_SCORE_BELOW_IDENTITY_THR"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM, "PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM"}, {(int) ms_quant_helper.PEPTIDE_QUALITY.PEPTIDE_SCORE_BELOW_SCORE_THR, "PEPTIDE_SCORE_BELOW_SCORE_THR"} }; foreach (ms_protein protein in proteins) { Console.WriteLine("Protein {0}::{1}", protein.getDB(), protein.getAccession()); for (int i = 1; i <= protein.getNumPeptides(); i++) { int q = protein.getPeptideQuery(i), p = protein.getPeptideP(i); ms_peptide peptide = pepSum.getPeptide(q, p); if (peptide == null) continue; // Each peptide can be tested for two things: // a) is it quantifiable? // b) is it of high enough quality for quantification // // The two parameters are defined in the quantitation method object // The two tests are orthogonal: the peptide need not pass test (a) // in order to pass test (b), and vice versa. Normally, for // quantitation purposes, you can ignore peptides which fail either test, // so you can continue straight to the next peptide if test (a) fails // Test (a): { string reason; int ok = quantHelper.isPeptideQuantifiable(q, p, protein, i, out reason); Console.WriteLine("\tq{0}_p{1} quantifiable? {2} ({3})", q, p, peptideQuantStr[ok], (string.IsNullOrEmpty(reason) ? "" : reason)); } // Test (b): { string reason; int ok = quantHelper.isPeptideQualityOK(q, p, out reason); Console.WriteLine("\tq{0}_p{1} quality? {2} ({3})", q, p, peptideQualityStr[ok], (string.IsNullOrEmpty(reason) ? "" : reason)); } } } pepSum.getNumberOfHits(); resfile._params(); return 0; } private static void dumpQuantMethod(ms_quant_method qmethod) { { List<string> comps = new List<string>(); for (int i = 0; i < qmethod.getNumberOfComponents(); i++) { comps.Add(qmethod.getComponentByNumber(i).getName()); } Console.WriteLine("Components: [{0}]", string.Join(", ", comps)); } Console.WriteLine("Protein ratio type = {0}", qmethod.getProteinRatioType()); Console.WriteLine("Min. number of peptides = {0}", qmethod.getMinNumPeptides()); if (qmethod.haveQuality()) { var q = qmethod.getQuality(); Console.WriteLine("Quality: min. precursor charge = {0}", q.getMinPrecursorCharge()); Console.WriteLine("Quality: pep. threshold type = {0}", q.getPepThresholdType()); Console.WriteLine("Quality: pep. threshold value = {0}", q.getPepThresholdValue()); } else { Console.WriteLine("Quality: no restrictions"); } if (qmethod.haveNormalisation()) { var q = qmethod.getNormalisation(); Console.WriteLine("Normalisation = {0}", q.getMethod()); } else { Console.WriteLine("Normalisation: none"); } if (qmethod.haveOutliers()) { var q = qmethod.getOutliers(); Console.WriteLine("Outliers = {0}", q.getMethod()); } else { Console.WriteLine("Outliers: none"); } } private static List<ms_protein> pullProteinsFrom(ms_peptidesummary pepsum) { List<ms_protein> proteins = new List<ms_protein>(); for (int i = 1; i <= pepsum.getNumberOfHits(); i++) { ms_protein hit = pepsum.getHit(i); proteins.Add(hit); int j = 0; ms_protein protein; while((protein = pepsum.getNextFamilyProtein(i, ++j)) != null) { proteins.Add(protein); } } return proteins; } private static bool loadPeptideSummary(ms_mascotresfile resfile, out ms_peptidesummary pepSum)//, out ms_peptidesummary pepsum) { // set pepsum to null so we can return out with false if the method fails pepSum = null; ms_mascotoptions opts = new ms_mascotoptions(); uint flags, flags2, minpeplen; int maxhits; double minprob, iisb; bool usePepsum; resfile.get_ms_mascotresults_params(opts, out flags, out minprob, out maxhits, out iisb, out minpeplen, out usePepsum, out flags2); if (!usePepsum) { Console.Error.WriteLine("Results file cannot be opened as a peptide summary"); return false; } pepSum = new ms_peptidesummary(resfile, flags, minprob, maxhits, "", iisb, (int) minpeplen, "", flags2); if (!resfile.isValid()) { Console.Error.WriteLine(resfile.getLastErrorString()); return false; } return true; } private static bool loadUmodConfigFile(ms_mascotresfile resfile, out ms_umod_configfile umodfile) { umodfile = new ms_umod_configfile(); umodfile.setSchemaFileName(UNIMOD_SCHEMA); if (!resfile.getUnimod(umodfile)) { Console.Error.WriteLine("Result file does not have a Unimod section"); return false; } if (!umodfile.isValid()) { Console.Error.WriteLine("Unimod file is not value: {0}", umodfile.getLastErrorString()); return false; } string str = umodfile.validateDocument(); if (str.Length > 0) { Console.Error.WriteLine("Unimod file does not validate: {0}", str); return false; } return true; } private static bool loadMethod(ms_mascotresfile resfile, out ms_quant_configfile quantConfigFile, out ms_quant_method qmethod) { // set the out values to null so we can return false without defining them quantConfigFile = null; qmethod = null; string quantMethodName = resfile._params().getQUANTITATION(); if (quantMethodName == null || quantMethodName.Length == 0 || quantMethodName.Equals("none", StringComparison.OrdinalIgnoreCase)) { Console.Error.WriteLine("File has no quantitation method"); return false; } quantConfigFile = new ms_quant_configfile(); quantConfigFile.setSchemaFileName(QUANT_SCHEMA); if (!resfile.getQuantitation(quantConfigFile)) { Console.Error.WriteLine("File has no quantitation method: {0}", resfile.getLastErrorString()); return false; } if (!quantConfigFile.isValid()) { Console.Error.WriteLine("Quantitation file is not valid: {0}", quantConfigFile.getLastErrorString()); return false; } string str = quantConfigFile.validateDocument(); if (str.Length > 0) { Console.Error.WriteLine("Quantitation file does not validate: {0}", str); return false; } qmethod = quantConfigFile.getMethodByName(quantMethodName); if (qmethod == null) { Console.Error.WriteLine("Quantitation file has no method called: '{0}'", quantMethodName); return false; } return true; } } } /* tools_quant_helper.exe ..\data\F981133.dat Will give the following output: File ..\data\F981133.dat uses SILAC K+6 R+6 multiplex and has 22 family proteins Components: [light, heavy] Protein ratio type = weighted Min. number of peptides = 2 Quality: min. precursor charge = 1 Quality: pep. threshold type = at least homology Quality: pep. threshold value = 0.05 Normalisation: none Outliers = auto Protein 1::K2C1_PANTR q18_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q18_p1 quality? PEPTIDE_QUALITY_IS_OK () q28_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q28_p1 quality? PEPTIDE_QUALITY_IS_OK () q33_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q33_p2 quality? PEPTIDE_QUALITY_IS_OK () q38_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q38_p1 quality? PEPTIDE_QUALITY_IS_OK () q39_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q39_p1 quality? PEPTIDE_QUALITY_IS_OK () q40_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q40_p1 quality? PEPTIDE_QUALITY_IS_OK () q55_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q55_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::TRYP_PIG q1_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q1_p1 quality? PEPTIDE_QUALITY_IS_OK () q2_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q2_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q3_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q3_p1 quality? PEPTIDE_QUALITY_IS_OK () q9_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q9_p1 quality? PEPTIDE_QUALITY_IS_OK () q72_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q72_p1 quality? PEPTIDE_QUALITY_IS_OK () q73_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q73_p1 quality? PEPTIDE_QUALITY_IS_OK () q74_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q74_p1 quality? PEPTIDE_QUALITY_IS_OK () q75_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q75_p1 quality? PEPTIDE_QUALITY_IS_OK () q76_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q76_p1 quality? PEPTIDE_QUALITY_IS_OK () q77_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q77_p1 quality? PEPTIDE_QUALITY_IS_OK () q78_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q78_p1 quality? PEPTIDE_QUALITY_IS_OK () q81_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q81_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q82_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q82_p1 quality? PEPTIDE_QUALITY_IS_OK () q90_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q90_p1 quality? PEPTIDE_QUALITY_IS_OK () q91_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q91_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::IGG2B_MOUSE q12_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q12_p1 quality? PEPTIDE_QUALITY_IS_OK () q57_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q57_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q58_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q58_p1 quality? PEPTIDE_QUALITY_IS_OK () q62_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q62_p1 quality? PEPTIDE_QUALITY_IS_OK () q66_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q66_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::ALBU_BOVIN q16_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q16_p1 quality? PEPTIDE_QUALITY_IS_OK () q30_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q30_p1 quality? PEPTIDE_QUALITY_IS_OK () q46_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q46_p1 quality? PEPTIDE_QUALITY_IS_OK () q49_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q49_p1 quality? PEPTIDE_QUALITY_IS_OK () q50_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q50_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::ENPL_MOUSE q4_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q4_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q19_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q19_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q20_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q20_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q24_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q24_p2 quality? PEPTIDE_QUALITY_IS_OK () q26_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q26_p2 quality? PEPTIDE_QUALITY_IS_OK () q41_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q41_p1 quality? PEPTIDE_QUALITY_IS_OK () q42_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q42_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::NUCL_MOUSE q5_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q5_p1 quality? PEPTIDE_QUALITY_IS_OK () q6_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q6_p1 quality? PEPTIDE_QUALITY_IS_OK () q7_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q7_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q8_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q8_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q44_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q44_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q45_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q45_p1 quality? PEPTIDE_QUALITY_IS_OK () q92_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q92_p1 quality? PEPTIDE_QUALITY_IS_OK () q93_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q93_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::EPHB2_HUMAN q13_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q13_p1 quality? PEPTIDE_QUALITY_IS_OK () q21_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q21_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q53_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q53_p1 quality? PEPTIDE_QUALITY_IS_OK () q88_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q88_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::K2C1_RAT q33_p4 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q33_p4 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q38_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q38_p1 quality? PEPTIDE_QUALITY_IS_OK () q39_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q39_p1 quality? PEPTIDE_QUALITY_IS_OK () q40_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q40_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::K2C75_BOVIN q28_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q28_p1 quality? PEPTIDE_QUALITY_IS_OK () q38_p4 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q38_p4 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q40_p6 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q40_p6 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::HNRPU_HUMAN q32_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q32_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q34_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q34_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q51_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q51_p1 quality? PEPTIDE_QUALITY_IS_OK () q52_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q52_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::SFPQ_HUMAN q14_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q14_p1 quality? PEPTIDE_QUALITY_IS_OK () q15_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q15_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q22_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q22_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q69_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q69_p1 quality? PEPTIDE_QUALITY_IS_OK () q70_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q70_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::CAPR1_MOUSE q23_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q23_p1 quality? PEPTIDE_QUALITY_IS_OK () q36_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q36_p1 quality? PEPTIDE_QUALITY_IS_OK () q37_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q37_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::K2C1B_HUMAN q18_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q18_p2 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q38_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q38_p1 quality? PEPTIDE_QUALITY_IS_OK () q40_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q40_p1 quality? PEPTIDE_QUALITY_IS_OK () q53_p3 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q53_p3 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::ENPL_ARATH q24_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q24_p2 quality? PEPTIDE_QUALITY_IS_OK () q26_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q26_p2 quality? PEPTIDE_QUALITY_IS_OK () q41_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q41_p2 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q42_p10 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q42_p10 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q67_p10 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q67_p10 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::VIME_CRIGR q17_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q17_p1 quality? PEPTIDE_QUALITY_IS_OK () q35_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q35_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::BCAR1_MOUSE q10_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q10_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q11_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q11_p1 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q63_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q63_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::HTPG_ALKEH q24_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q24_p1 quality? PEPTIDE_QUALITY_IS_OK () q26_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q26_p1 quality? PEPTIDE_QUALITY_IS_OK () q67_p9 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q67_p9 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::FAK1_MOUSE q29_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q29_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::HTPG_BDEBA q24_p3 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q24_p3 quality? PEPTIDE_QUALITY_IS_OK () q26_p3 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q26_p3 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::K2C8_MOUSE q33_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q33_p1 quality? PEPTIDE_QUALITY_IS_OK () Protein 1::TRY1_RAT q72_p10 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q72_p10 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q73_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q73_p2 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q74_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q74_p2 quality? PEPTIDE_QUALITY_IS_OK () q75_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q75_p2 quality? PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM (Peptide score is below identity threshold (no homology threshold)) q76_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q76_p2 quality? PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM (Peptide score is below identity threshold (no homology threshold)) q78_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q78_p2 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q81_p4 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q81_p4 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q82_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q82_p2 quality? PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM (Peptide score is below identity threshold (no homology threshold)) Protein 1::IGKC_MOUSE q47_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q47_p1 quality? PEPTIDE_QUALITY_IS_OK () q48_p1 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q48_p1 quality? PEPTIDE_QUALITY_IS_OK () */
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