Matrix Science header

tools_quant_helper.pl

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: /vol/cvsroot/parser/examples/test_perl/tools_quant_helper.pl,v $
#     $Author: davidc $
#       $Date: 2016/04/12 09:35:37 $
#   $Revision: 1.2 $ 
##############################################################################
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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