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: robertog@matrixscience.com $
# $Date: 2024-09-04 10:23:46 +0100 $
# $Revision: 526921a73137894bb1eae0b0fc8ccb4bb52ea662 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
##############################################################################
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 $resfile = msparser::ms_mascotresfilebase::createResfile($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
1.9.6