Commit 8df6c3cb authored by Edlira Nano's avatar Edlira Nano
Browse files

updated examples

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2090 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 62b7eaeb
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......@@ -6,22 +6,23 @@ examples to run masschroq. They are intended to illustrate how masschroq
works and the results it can provide. They are also intended to provide
usage and parameter values support for your further analysis.
The input masschroqML example files are the ones named example_blabla_masschroq.xml.
The input masschroqML example files are the ones named
example_blabla_masschroq.masschroqML.
To run them go into the masschroq_examples directory and simply type:
masschroq example_blabla_masschroq.xml
masschroq example_blabla_masschroq.masschroqML
on the command line.
The mzXML files provided are the LC-MS/MS data files used in these examples.
The following examples are provided :
- example_labelling_dimethylation_masschroq.xml
- example_labelling_dimethylation_masschroq.masschroqML (only in the website archive)
This example analysis the BSA_labeling_mix_light_intermediaire.mzXML
data file produced by a low resolution LTQ spectrometer
in a profile mode and where dimethyl labeling (with light and heavy
dimethyl groups) has been performed.
The quantified entities are the heavy and the light isotopes.
- example_LTQ_and_alignment_masschroq.xml :
- example_LTQ_and_alignment_masschroq.masschroqML :
Here we analyze the BSA_LTQ_1.mzXML and BSA_LTQ_2.mzXML data files
obtained with a low resolution LTQ spectrometer in centroid mode.
The quantification parameters are thereby adapted to LTQ data.
......@@ -38,7 +39,7 @@ The following examples are provided :
you should notice a newly created directory named peplist_xics_traces
containing these traces for each detected peptide in each run.
- example_orbitrap_masschroq.xml
- example_orbitrap_masschroq.masschroqML
In this example we analyze the BSA_Orbitrap.mzXML data file obtained
from a high resolution orbitrap spectrometer. The quantification
parameters are adapted to this spectrometer. Also, an external peptide
......
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<masschroq>
<rawdata>
<data_file format="mzxml" id="samp0" path="BSA_labeling_mix_light_intermediaire.mzXML" type="profile"/>
</rawdata>
<groups>
<group data_ids="samp0" id="G1"/>
</groups>
<protein_list>
<protein desc="conta|P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." id="P1.01"/>
</protein_list>
<peptide_list>
<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.01" seq="TCVADESHAGCEK">
<observed_in data="samp0" scan="744" z="2"/>
<observed_in data="samp0" scan="747" z="2"/>
<observed_in data="samp0" scan="765" z="3"/>
<observed_in data="samp0" scan="1057" z="2"/>
</peptide>
<peptide id="pep1" mh="1072.528" mods="57.04" prot_ids="P1.01" seq="SHCIAEVEK">
<observed_in data="samp0" scan="873" z="3"/>
<observed_in data="samp0" scan="882" z="2"/>
</peptide>
<peptide id="pep2" mh="1068.46" mods="57.04" prot_ids="P1.01" seq="QNCDQFEK">
<observed_in data="samp0" scan="955" z="2"/>
</peptide>
<peptide id="pep3" mh="1494.551" mods="130.07" prot_ids="P1.01" seq="ETYGDMADCCEK">
<observed_in data="samp0" scan="1027" z="2"/>
</peptide>
<peptide id="pep4" mh="1034.491" mods="57.04" prot_ids="P1.01" seq="NECFISHK">
<observed_in data="samp0" scan="1164" z="2"/>
<observed_in data="samp0" scan="1166" z="2"/>
</peptide>
<peptide id="pep5" mh="1291.64" mods="114.08" prot_ids="P1.01" seq="ECCDKPIIEK">
<observed_in data="samp0" scan="1183" z="2"/>
</peptide>
<peptide id="pep6" mh="1138.535" mods="114.08" prot_ids="P1.01" seq="CCTESIVNR">
<observed_in data="samp0" scan="1215" z="2"/>
<observed_in data="samp0" scan="1218" z="2"/>
</peptide>
<peptide id="pep7" mh="1443.661" mods="57.04" prot_ids="P1.01" seq="YICDNQDTISSK">
<observed_in data="samp0" scan="1317" z="2"/>
<observed_in data="samp0" scan="1324" z="2"/>
</peptide>
<peptide id="pep8" mh="886.416" mods="0.0" prot_ids="P1.01" seq="DDSPDIPK">
<observed_in data="samp0" scan="1322" z="2"/>
</peptide>
<peptide id="pep9" mh="1400.682" mods="57.04" prot_ids="P1.01" seq="IQQCPFDEHVK">
<observed_in data="samp0" scan="1489" z="3"/>
</peptide>
<peptide id="pep10" mh="1478.561" mods="114.08" prot_ids="P1.01" seq="ETYGDMADCCEK">
<observed_in data="samp0" scan="1528" z="2"/>
</peptide>
<peptide id="pep11" mh="1163.519" mods="57.04" prot_ids="P1.01" seq="GDIIECADDR">
<observed_in data="samp0" scan="1544" z="2"/>
</peptide>
<peptide id="pep12" mh="1749.719" mods="171.12" prot_ids="P1.01" seq="ECCHGDIIECADDR">
<observed_in data="samp0" scan="1581" z="3"/>
</peptide>
<peptide id="pep13" mh="922.488" mods="0.0" prot_ids="P1.01" seq="AEFVEVTK">
<observed_in data="samp0" scan="1642" z="2"/>
<observed_in data="samp0" scan="1647" z="2"/>
</peptide>
<peptide id="pep14" mh="1927.854" mods="171.12" prot_ids="P1.01" seq="CCAADDKEACFAVEGPK">
<observed_in data="samp0" scan="1674" z="3"/>
<observed_in data="samp0" scan="1676" z="3"/>
</peptide>
<peptide id="pep15" mh="1502.651" mods="114.08" prot_ids="P1.01" seq="EYEATIEECCAK">
<observed_in data="samp0" scan="1683" z="2"/>
</peptide>
<peptide id="pep16" mh="1107.533" mods="57.04" prot_ids="P1.01" seq="EACFAVEGPK">
<observed_in data="samp0" scan="1703" z="2"/>
</peptide>
<peptide id="pep17" mh="1901.889" mods="57.04" prot_ids="P1.01" seq="NECFISHKDDSPDIPK">
<observed_in data="samp0" scan="1707" z="3"/>
<observed_in data="samp0" scan="1713" z="3"/>
</peptide>
<peptide id="pep18" mh="1305.7166" mods="0.0" prot_ids="P1.01" seq="HIVDEPQNIIK">
<observed_in data="samp0" scan="1831" z="2"/>
<observed_in data="samp0" scan="1838" z="2"/>
<observed_in data="samp0" scan="1841" z="3"/>
</peptide>
<peptide id="pep19" mh="2247.999" mods="171.12" prot_ids="P1.01" seq="ECCHGDIIECADDRADIAK">
<observed_in data="samp0" scan="1916" z="3"/>
</peptide>
<peptide id="pep20" mh="1778.836" mods="57.04" prot_ids="P1.01" seq="SQYIQQCPFDEHVK">
<observed_in data="samp0" scan="1926" z="3"/>
<observed_in data="samp0" scan="1932" z="3"/>
</peptide>
<peptide id="pep21" mh="1320.669" mods="0.0" prot_ids="P1.01" seq="SAITPDETYVPK">
<observed_in data="samp0" scan="1952" z="2"/>
<observed_in data="samp0" scan="1962" z="2"/>
</peptide>
<peptide id="pep22" mh="1554.672" mods="57.04" prot_ids="P1.01" seq="DDPHACYSTVFDK">
<observed_in data="samp0" scan="2025" z="3"/>
<observed_in data="samp0" scan="2029" z="2"/>
</peptide>
<peptide id="pep23" mh="927.494" mods="0.0" prot_ids="P1.01" seq="YIYEIAR">
<observed_in data="samp0" scan="2043" z="2"/>
</peptide>
<peptide id="pep24" mh="1639.938" mods="0.0" prot_ids="P1.01" seq="KVPQVSTPTIVEVSR">
<observed_in data="samp0" scan="2093" z="2"/>
<observed_in data="samp0" scan="2103" z="2"/>
<observed_in data="samp0" scan="2145" z="3"/>
</peptide>
<peptide id="pep25" mh="1576.787" mods="57.04" prot_ids="P1.01" seq="IKPDPNTICDEFK">
<observed_in data="samp0" scan="2258" z="2"/>
<observed_in data="samp0" scan="2272" z="2"/>
<observed_in data="samp0" scan="2284" z="3"/>
</peptide>
<peptide id="pep26" mh="1880.94" mods="57.04" prot_ids="P1.01" seq="RPCFSAITPDETYVPK">
<observed_in data="samp0" scan="2270" z="3"/>
<observed_in data="samp0" scan="2273" z="3"/>
<observed_in data="samp0" scan="2287" z="2"/>
<observed_in data="samp0" scan="2288" z="2"/>
</peptide>
<peptide id="pep27" mh="1467.737" mods="0.0" prot_ids="P1.01" seq="FSAITPDETYVPK">
<observed_in data="samp0" scan="2437" z="2"/>
<observed_in data="samp0" scan="2441" z="2"/>
</peptide>
<peptide id="pep28" mh="1163.631" mods="0.0" prot_ids="P1.01" seq="IVNEITEFAK">
<observed_in data="samp0" scan="2507" z="2"/>
<observed_in data="samp0" scan="2521" z="2"/>
</peptide>
<peptide id="pep29" mh="1419.713" mods="57.04" prot_ids="P1.01" seq="SIHTIFGDEICK">
<observed_in data="samp0" scan="2533" z="3"/>
<observed_in data="samp0" scan="2536" z="2"/>
<observed_in data="samp0" scan="2537" z="2"/>
</peptide>
<peptide id="pep30" mh="1014.62" mods="0.0" prot_ids="P1.01" seq="QTAIVEIIK">
<observed_in data="samp0" scan="2723" z="2"/>
</peptide>
<peptide id="pep31" mh="1907.94" mods="57.04" prot_ids="P1.01" seq="IFTFHADICTIPDTEK">
<observed_in data="samp0" scan="2729" z="3"/>
<observed_in data="samp0" scan="2744" z="2"/>
</peptide>
<peptide id="pep32" mh="1415.683" mods="15.99" prot_ids="P1.01" seq="TVMENFVAFVDK">
<observed_in data="samp0" scan="2802" z="2"/>
</peptide>
<peptide id="pep33" mh="2045.0281" mods="0.0" prot_ids="P1.01" seq="RHPYFYAPEIIYYANK">
<observed_in data="samp0" scan="2852" z="3"/>
</peptide>
<peptide id="pep34" mh="1479.796" mods="0.0" prot_ids="P1.01" seq="IGEYGFQNAIIVR">
<observed_in data="samp0" scan="2981" z="2"/>
<observed_in data="samp0" scan="2984" z="2"/>
</peptide>
<peptide id="pep35" mh="1399.693" mods="0.0" prot_ids="P1.01" seq="TVMENFVAFVDK">
<observed_in data="samp0" scan="3299" z="2"/>
</peptide>
<peptide id="pep36" mh="1491.752" mods="0.0" prot_ids="P1.01" seq="FYAPEIIYYANK">
<observed_in data="samp0" scan="3300" z="2"/>
<observed_in data="samp0" scan="3309" z="2"/>
</peptide>
<peptide id="pep37" mh="1567.743" mods="0.0" prot_ids="P1.01" seq="DAFIGSFIYEYSR">
<observed_in data="samp0" scan="3942" z="2"/>
</peptide>
</peptide_list>
<isotope_label_list>
<isotope_label id="iso1">
<mod at="Nter" value="28.0"/>
<mod at="K" value="28.0"/>
</isotope_label>
<isotope_label id="iso2">
<mod at="K" value="32.0"/>
<mod at="Nter" value="32.0"/>
</isotope_label>
</isotope_label_list>
<quantification_methods>
<quantification_method id="quant1">
<xic_extraction xic_type="max">
<mz_range max="0.3" min="0.3"/>
</xic_extraction>
<xic_filters>
<background half_mediane="5" half_min_max="20"/>
</xic_filters>
<peak_detection>
<detection_zivy>
<mean_filter_half_edge>1</mean_filter_half_edge>
<minmax_half_edge>3</minmax_half_edge>
<maxmin_half_edge>2</maxmin_half_edge>
<detection_threshold_on_max>5000</detection_threshold_on_max>
<detection_threshold_on_min>3000</detection_threshold_on_min>
</detection_zivy>
</peak_detection>
</quantification_method>
</quantification_methods>
<quantification>
<quantification_results>
<quantification_result format="tsv" output_file="Result_labelling"/>
</quantification_results>
<quantify id="q1" quantification_method_id="quant1" withingroup="G1">
<peptides_in_peptide_list isotope_label_refs="iso1 iso2" mode="real_or_mean"/>
</quantify>
</quantification>
</masschroq>
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