InSilicoSpectro
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lib/InSilicoSpectro/InSilico/MassCalculator.pm view on Meta::CPAN
m_0:m_1:m_2:m_3:m_4: ... :m_n:m_(n+1),
where m_0 is the N-terminal site modification, m_i is a_i modification, and
m_(n+1) is the C-terminal site modification. For instance, a peptide
DEMSCGHTK
might be modified according to
ACET_nterm:::Oxidation::Cys_CAM::Oxidation:::
which means that there is an N-terminal acetylation, the methionine and the
histidine are oxidized, and the cysteine is carboxyamidomethylated; no
C-terminal modification. We see that in this notation empty positions between
colons are possible to denote the absence of modification. The modification
identifiers come from the configuration file.
In the above string notation it is possible to define variable modifications,
see function variablePeptide.
lib/InSilicoSpectro/InSilico/ModRes.pm view on Meta::CPAN
#or, if the ohenyx system is not installed
InSilicoSpectro::InSilico::ModRes::init("some/path/to/defatultdef.xml");
#print all the modifications
foreach (InSilicoSpectro::InSilico::ModRes::getList()){
$_->print();
}
#given a swissprot FT valkue, return the related modres
foreach ('PHOSPHORYLATION', 'ACETYLATION (IN ISOFORM SHORT))', 'PHOSPHORYLATION', 'ACETYLATION', 'SULFATION'){
print "$_ => ".InSilicoSpectro::InSilico::ModRes::getModifFromSprotFT($_)->get('name')."\n";
}
=head1 DESCRIPTION
Manage all what is related to residue modifications (masses, positions, SwissProt annotations...)
=head1 FUNCTIONS
=head2 Initialization
lib/InSilicoSpectro/config/insilicodef.xml view on Meta::CPAN
<oneInternFragType name="immo">
<residues>HFILYPV</residues>
<delta monoisotopic="-26.9871" average="-26.9871"/>
</oneInternFragType>
</internalFragType>
</fragTypeDefSet>
</fragTypeDescriptions>
<modRes>
<oneModRes type="ptm" name="ACET_nterm">
<description>Acetylation_nterm</description>
<site>
<residue>^NKHFW</residue>
<nterm/>
</site>
<residues aa="^NKHFW" nterm="yes"/>
<delta monoisotopic="42.0106" average="42.0373"/>
<sprotFT><![CDATA[(N-acetylalanine|N-acetylaspartate|N-acetylcysteine|N-acetylglutamate|N-acetylglycine|N-acetylmethionine|N-acetylproline|N-acetylserine|N-acetylthreonine|N-acetyltyrosine|N-acetylvaline).*]]></sprotFT>
</oneModRes>
<oneModRes type="ptm" name="ACET_core">
<description>Acetylation_core</description>
<site>
<residue>KR</residue>
</site>
<residues aa="KR"/>
<delta monoisotopic="42.0106" average="42.0373"/>
<sprotFT><![CDATA[(N2-acetylarginine|N6-acetyllysine).*]]></sprotFT>
</oneModRes>
<oneModRes type="ptm" name="PHOS">
<description>Phosphorylation</description>
scripts/peptSpectra/example.idr.xml view on Meta::CPAN
<idl:OnePeptideData name="spectrumNbPeaks" value="69"/>
<idl:OnePeptideData name="spectrumGaussianParam" value="-22.750:7.631:0.018(17306)"/>
</idl:ExtraPeptideData>
</idl:PeptideMatch>
</idl:DBMatch>
<idl:DBMatch>
<idl:AC>Q14766_WOSIG0</idl:AC>
<idl:ID>LTB1L_HUMAN</idl:ID>
<idl:SeqVersion></idl:SeqVersion>
<idl:SeqLength>1572</idl:SeqLength>
<idl:SeqString start="0" length="1572">RLRRITYVVHPGPGLAAGALPLSGPPASSRTFNVALNARYSRSSAAAGAPSRASPGVPSERTRRTSKPGGAALQGLRPPPPPPPEPARPAVPGGQLHPNPGGHPAAAPFTKQGRQVVRSKVPQETQSGGGSRLQVHQKQQLQGVNVCGGRCCHGWSKAPGSQRCTKPSCVPPCQNGGMCLRPQLCVCKPGTKGKACETIAAQD...
<idl:SeqMass>170696.592</idl:SeqMass>
<idl:SeqPI>5.302</idl:SeqPI>
<idl:OrigDatabase></idl:OrigDatabase>
<idl:OrigAC>Q14766</idl:OrigAC>
<idl:OrigRelease></idl:OrigRelease>
<idl:OrigSeqVersion></idl:OrigSeqVersion>
<idl:MatchDescr><![CDATA[Latent transforming growth factor beta binding protein, isoform 1L precursor (LTBP-1) (Transforming growth factor beta-1 binding protein 1) (TGF-beta1-BP-1)]]></idl:MatchDescr>
<idl:score>6.583</idl:score>
<idl:coverage>0.011</idl:coverage>
<idl:ExtraDBMatchData>
scripts/peptSpectra/mascot2pept.pl view on Meta::CPAN
'1+' => '1',
'2+' => '2',
'2+and3+' => '2,3',
'2+,and3+' => '2,3',
'3+' => '3',
'4+' => '4'
);
# Modifications conversion (Macot mod_file to InSilicoSpectro insilicodef.xml)
my %modifConv = (
'Acetyl (K)' => 'ACET_core',
'Acetyl (N-term)' => 'ACET_nterm',
'Amide (C-term)' => 'AMID',
'Title:Biotin (K)' => 'BIOT',
'Title:Biotin (N-term)' => 'BIOT_nterm',
'Carbamidomethyl (C)' => 'Cys_CAM',
'Carbamyl (K)' => 'CAM_core',
'Carbamyl (N-term)' => 'CAM_nterm',
'Carboxymethyl (C)' => 'Cys_CM',
'Deamidation (NQ)' => 'DEAMID',
'Guanidination (K)' => 'Guanidination',
'ICAT_light' => 'ICAT_light',
'ICAT_heavy' => 'ICAT_heavy',
'iTRAQ (K)' => 'iTRAQ_KY',
'iTRAQ (N-term)' => 'iTRAQ_nterm',
'iTRAQ (Y)' => 'iTRAQ_KY',
'N-Acetyl (Protein)' => 'ACET_nterm',
'N-Formyl (Protein)' => 'FORM',
'O18 (C-term)' => 'O18',
'Oxidation (M)' => 'Oxidation_M',
'Oxidation (HW)' => 'Oxidation_HW',
'Phospho (STY)' => 'PHOS',
'Phospho (Y)' => 'PHOS',
'Propionamide (C)' => 'Cys_PAM',
'Pyro-glu (N-term Q)' => 'PYRR',
'S-pyridylethyl (C)' => 'Cys_PE',
'Sulfation (Y)' => 'SULF_core',
t/InSilico/data/krok.dat view on Meta::CPAN
"GEADAMSLDGGYLYIAGK",
"CACSNHEPYFGYSGAFK",
"SVTDCTSNFCLFQSNSK",
"DQTVIQNTDGNNNEAWAK",
"EDVIWELLNHAQEHFGK",
"AAANFFSASCVPCADQSSFPK",
"MDFELYLGYEYVTALQNLR",
"SVDDYQECYLAMVPSHAVVAR",
"TVGGKEDVIWELLNHAQEHFGK",
"KSVDDYQECYLAMVPSHAVVAR",
"WSGFSGGAIECETAENTEECIAK",
"AISNNEADAVTLDGGLVYEAGLKPNNLKPVVAEFHGTK",
"AWAVAR",
"AACLLPK",
"AEFAEVSK",
"YLYEIAR",
"LCTVATLR",
"DDNPNLPR",
"FQNALLVR",
"TYETTLEK",
"SLHTLFGDK",
t/InSilico/insilicodef-test.xml view on Meta::CPAN
<oneInternFragType name="immo">
<residues>HFILYPV</residues>
<delta monoisotopic="-26.9871" average="-26.9871"/>
</oneInternFragType>
</internalFragType>
</fragTypeDefSet>
</fragTypeDescriptions>
<modRes>
<oneModRes type="ptm" name="ACET_nterm">
<description>Acetylation_nterm</description>
<site>
<residue>^NKHFW</residue>
<nterm/>
</site>
<residues aa="^NKHFW" nterm="yes"/>
<delta monoisotopic="42.0106" average="42.0373"/>
<sprotFT><![CDATA[(N-acetylalanine|N-acetylaspartate|N-acetylcysteine|N-acetylglutamate|N-acetylglycine|N-acetylmethionine|N-acetylproline|N-acetylserine|N-acetylthreonine|N-acetyltyrosine|N-acetylvaline).*]]></sprotFT>
</oneModRes>
<oneModRes type="ptm" name="ACET_core">
<description>Acetylation_core</description>
<site>
<residue>KR</residue>
</site>
<residues aa="KR"/>
<delta monoisotopic="42.0106" average="42.0373"/>
<sprotFT><![CDATA[(N2-acetylarginine|N6-acetyllysine).*]]></sprotFT>
</oneModRes>
<oneModRes type="ptm" name="PHOS">
<description>Phosphorylation</description>
t/InSilico/testModRes.pl view on Meta::CPAN
if ($test == 1) {
print "******* list of all modif *********\n";
foreach (InSilicoSpectro::InSilico::ModRes::getList()) {
$_->print();
print "=> ".$_->get('sprotFT')."\n";
}
}
if ($test == 2) {
print "******* given a FT, return the modif name *********\n";
foreach ('PHOSPHORYLATION', 'N-acetylalanine', 'Phosphoserine (by PKC)]', 'ACETYLATION', 'SULFATION') {
my $m=InSilicoSpectro::InSilico::ModRes::getModifFromSprotFT($_);
print "$_ => ".((defined $m)?($m->get('name')):'unknown')."\n";
}
}
if ($test == 3) {
foreach ('PHOS', 'ACET_nterm', 'Oxidation', 'BIOT') {
my $mr=InSilicoSpectro::InSilico::ModRes::getFromDico($_) || die "no modif for name=[$_]";
print "modif ".$mr->{name}."\n";
foreach my $seq (qw/LADELAKLVDVLEDK LDSVIEFSIPDSLLIR FASFEAQGALANIAVDK ETSGNLEQLLLAVVK SLEEIYLFSLPIK QNLFQEAEEFLYR TENLLGSYFPK VVLAYEPVWAIGTGK SPAGLQVLNDYLADK LISWYDNEFGYSNR SICTTVLELLDK /) {
my @pos=$mr->seq2pos($seq);
print "$seq -> [@pos]\n";
}
print "\n";
}
}
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="510.65"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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</mzArrayBinary>
<intenArrayBinary>
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</intenArrayBinary>
</spectrum>
<spectrum id="129">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="129"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="661.65"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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<intenArrayBinary>
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</intenArrayBinary>
</spectrum>
<spectrum id="144">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="144"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="358.45"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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<intenArrayBinary>
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</spectrum>
<spectrum id="222">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="222"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="565.72"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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<intenArrayBinary>
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</spectrum>
<spectrum id="282">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="282"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="539.27"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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</spectrum>
<spectrum id="288">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="288"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="558.06"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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</spectrum>
<spectrum id="378">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="378"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="760.18"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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</spectrum>
<spectrum id="390">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="390"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="557.45"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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</spectrum>
<spectrum id="492">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="492"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="334.85"/>
</ionSelection>
<activation>
<cvParam cvLabel="psi" accession="" name="method" value="CID"/>
<cvParam cvLabel="psi" accession="" name="energy" value="28.00"/>
</activation>
</precursor>
</precursorList>
</acqDesc>
<mzArrayBinary>
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</spectrum>
<spectrum id="495">
<acqDesc>
<acqSettings>
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
<acquisition acqNumber="495"/>
t/Spectra/myo_ms2_1.04.xml view on Meta::CPAN
<cvParam cvLabel="psi" accession="" name="mz" value="501.91"/>
</ionSelection>
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