Testing peptides for quantifiability.
#!/usr/local/bin/perl ############################################################################## # file: tools_quant_helper.pl # # Mascot Parser toolkit example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2012 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_perl/tools_quant_helper.pl $ # $Author: villek@matrixscience.com $ # $Date: 2018-07-30 16:23:53 +0100 $ # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ ############################################################################## use strict; ############################################################################## use msparser; use constant { 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', }; if (not @ARGV) { print STDERR "Usage: $0 <quantitation results.dat>\n"; exit 1; } my $resfile = msparser::ms_mascotresfile->new($ARGV[0]); if (not $resfile->isValid) { print STDERR $resfile->getLastErrorString(), "\n"; exit 1; } # The details of loading the quantitation method and peptide summary object # are not relevant to this example (see end of file for implementation). my ($quant_config_file, $qmethod) = load_method_or_exit($resfile); my $umodfile = load_umod_configfile_or_exit($resfile); my $pepsum = open_peptidesummary_or_exit($resfile); my $quant_helper = msparser::ms_quant_helper->new($pepsum, $qmethod, $umodfile); if (not $quant_helper->isValid) { printf STDERR "ms_quant_helper is not valid: %s\n", $quant_helper->getLastErrorString(); exit 1; } my @proteins = pull_proteins_from($pepsum); printf "File %s uses %s and has %d family proteins\n\n", $ARGV[0], $qmethod->getName(), scalar(@proteins); dump_quant_method($qmethod); print "\n"; # Reverse map of test result values for pretty printing purposes: my (%peptide_quality_str, %peptide_quant_str); do { no strict 'refs'; %peptide_quality_str = map { ${"msparser::ms_quant_helper::$_"} => $_ } qw( PEPTIDE_QUALITY_IS_OK PEPTIDE_CHARGE_BELOW_PRECURSOR_MIN PEPTIDE_SCORE_BELOW_SCORE_THR PEPTIDE_EXPECT_ABOVE_THRESHOLD PEPTIDE_SCORE_BELOW_IDENTITY_THR PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM PEPTIDE_SCORE_BELOW_HOMOLOGY_THR PEPTIDE_HAS_NO_EXCLUSIVE_MODS PEPTIDE_QUALITY_UNAVAILABLE ); %peptide_quant_str = map { ${"msparser::ms_quant_helper::$_"} => $_ } qw( PEPTIDE_IS_QUANTIFIABLE PEPTIDE_HAS_NO_REQUIRED_FIXEDMOD PEPTIDE_HAS_NO_REQUIRED_VARMOD PEPTIDE_HAS_EXCLUDED_FIXEDMOD PEPTIDE_HAS_EXCLUDED_LOCAL_FIXEDMOD PEPTIDE_HAS_EXCLUDED_VARMOD PEPTIDE_HAS_UNMODIFIED_SITE PEPTIDE_HAS_EXCLUDED_LOCAL_VARMOD PEPTIDE_QUANTIFIABILITY_UNAVAILABLE ); }; for my $protein (@proteins) { printf "Protein %d::%s\n", $protein->getDB(), $protein->getAccession(); for my $i (1 .. $protein->getNumPeptides()) { next if $protein->getPeptideDuplicate($i) == $msparser::ms_protein::DUPE_DuplicateSameQuery; my $q = $protein->getPeptideQuery($i); my $p = $protein->getPeptideP($i); my $peptide = $pepsum->getPeptide($q, $p); next if not $peptide; # Each peptide can be tested for two things: # a) is it quantifiable? # b) is it of high enough quality for quantification? # # The test parameters are defined in the quantitation method object. # The two tests are orthogonal: the peptide need not pass test (a) # in order to pass test (b), and vice versa. Normally, for quantitation # purposes, you can ignore peptides which fail either test, so you # can continue straight to the next peptide if test (a) fails. # Test (a): do { my ($ok, $reason) = $quant_helper->isPeptideQuantifiable($q, $p, $protein, $i); printf "\tq%d_p%d quantifiable? %s (%s)\n", $q, $p, $peptide_quant_str{$ok}, (defined $reason ? $reason : '<undef>'); }; # Test (b): do { my ($ok, $reason) = $quant_helper->isPeptideQualityOK($q, $p); printf "\tq%d_p%d quality? %s (%s)\n", $q, $p, $peptide_quality_str{$ok}, (defined $reason ? $reason : '<undef>'); }; } } # Load the quantitation method from the results file or exit with an error. sub load_method_or_exit { my ($resfile) = @_; my $quant_method_name = $resfile->params->getQUANTITATION(); if (not $quant_method_name or lc($quant_method_name) eq 'none') { print STDERR "File has no quantitation method\n"; exit 1; } my $qf = msparser::ms_quant_configfile->new(); $qf->setSchemaFileName(QUANT_SCHEMA); if (not $resfile->getQuantitation($qf)) { printf STDERR "File has no quantitation method (%s)\n", $resfile->getLastErrorString(); exit 1; } if (not $qf->isValid) { printf STDERR "Quantitation file is not valid (%s)\n", $qf->getLastErrorString(); exit 1; } if ('' ne (my $str = $qf->validateDocument())) { printf STDERR "Quantitation file does not validate (%s)\n", $str; exit 1; } my $qmethod = $qf->getMethodByName($quant_method_name); if (not $qmethod) { printf STDERR "Quantitation file has no method called '%s'\n", $quant_method_name; exit 1; } return ($qf, $qmethod); } # Load the Unimod section from the results file or exit with an error. sub load_umod_configfile_or_exit { my ($resfile) = @_; my $umodfile = msparser::ms_umod_configfile->new(); $umodfile->setSchemaFileName(UNIMOD_SCHEMA); if (not $resfile->getUnimod($umodfile)) { print STDERR "Results file does not have a Unimod section\n"; exit 1; } if (not $umodfile->isValid) { printf STDERR "Unimod file is not valid (%s)\n", $umodfile->getLastErrorString(); exit 1; } if ('' ne (my $str = $umodfile->validateDocument())) { printf STDERR "Unimod file does not validate (%s)\n", $str; exit 1; } return $umodfile; } # Load the results file as ms_peptidesummary or exit with an error. sub open_peptidesummary_or_exit { my ($resfile) = @_; my $opts = msparser::ms_mascotoptions->new(); my (undef, $flags, $minprob, $maxhits, $iisb, $minpeplen, $use_pepsum, $flags2) = $resfile->get_ms_mascotresults_params($opts); if (not $use_pepsum) { print STDERR "Results file cannot be opened as a peptide summary\n"; exit 1; } my $pepsum = msparser::ms_peptidesummary->new( $resfile, $flags, $minprob, $maxhits, '', $iisb, $minpeplen, '', $flags2 ); if (not $resfile->isValid) { print STDERR $resfile->getLastErrorString, "\n"; exit 1; } return $pepsum; } # Return a list of all top-level protein hits. sub pull_proteins_from { my ($pepsum) = @_; my @proteins = (); for my $i (1 .. $pepsum->getNumberOfHits()) { my $hit = $pepsum->getHit($i); push @proteins, $hit; my $j = 0; while (my $protein = $pepsum->getNextFamilyProtein($i, ++$j)) { push @proteins, $protein; } } return @proteins; } # Print quantitation method parameters relevant to ms_quant_helper. sub dump_quant_method { my ($qmethod) = @_; do { my @comps = (); for my $i (0 .. $qmethod->getNumberOfComponents()-1) { my $comp = $qmethod->getComponentByNumber($i); $comps[$i] = $comp->getName(); } printf "Components: [%s]\n", join(', ', @comps); }; printf "Protein ratio type = %s\n", $qmethod->getProteinRatioType(); printf "Min. number of peptides = %d\n", $qmethod->getMinNumPeptides(); if ($qmethod->haveQuality()) { my $q = $qmethod->getQuality(); printf "Quality: min. precursor charge = %s\n", $q->getMinPrecursorCharge(); printf "Quality: pep. threshold type = %s\n", $q->getPepThresholdType(); printf "Quality: pep. threshold value = %s\n", $q->getPepThresholdValue(); } else { printf "Quality: no restrictions\n"; } if ($qmethod->haveNormalisation()) { my $q = $qmethod->getNormalisation(); printf "Normalisation = %s\n", $q->getMethod(); } else { printf "Normalisation: none\n"; } if ($qmethod->haveOutliers()) { my $q = $qmethod->getOutliers(); printf "Outliers = %s\n", $q->getMethod(); } else { printf "Outliers: none\n"; } } =pod Running the program as perl -I../bin tools_quant_helper.pl ../data/F981133.dat will give the following output under Mascot 2.5: File ../data/F981133.dat uses SILAC K+6 R+6 multiplex and has 23 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_HUMAN 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::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_p8 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q67_p8 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_ALHEH 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_p7 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q67_p7 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) Protein 1::HTPG_HALHL 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::HSC90_DICDI 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 () q67_p10 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q67_p10 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_QUALITY_IS_OK () q76_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q76_p2 quality? PEPTIDE_QUALITY_IS_OK () q78_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q78_p2 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q81_p3 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q81_p3 quality? PEPTIDE_SCORE_BELOW_HOMOLOGY_THR (Peptide score is below homology threshold) q82_p2 quantifiable? PEPTIDE_IS_QUANTIFIABLE () q82_p2 quality? PEPTIDE_QUALITY_IS_OK () 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 () =cut
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