Commit 6f5d45a5 authored by Edlira Nano's avatar Edlira Nano
Browse files

modified examples

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2104 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 26cda397
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<masschroq>
<rawdata>
<data_file id="samp0" format="mzxml" path="bsa1.mzXML" type="centroid"/>
<data_file id="samp1" format="mzxml" path="bsa2.mzXML" type="profile"/>
<data_file id="samp2" format="mzml" path="/home/user/bsa3.mzml" type="profile"/>
<data_file id="samp3" format="mzml" path="/home/user/bsa4.mzml" type="profile"/>
</rawdata>
<groups>
<group data_ids="samp0 samp1" id="G1"/>
<group data_ids="samp2 samp3" id="G2"/>
</groups>
<peptide_files_list>
<peptide_file data="samp0" path="bsa1_peptides.txt"/>
<peptide_file data="samp1" path="bsa2_peptides.txt"/>
<peptide_file data="samp2" path="bsa3_peptides.txt"/>
<peptide_file data="samp3" path="bsa4_peptides.txt"/>
</peptide_files_list>
<protein_list>
<protein desc="conta|P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." id="P1.1"/>
<protein desc="conta|P02770|ALBU_RAT SERUM ALBUMIN PRECURSOR." id="P1.2"/>
</protein_list>
<peptide_list>
<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1" seq="TCVADESHAGCEK">
<observed_in data="samp0" scan="655" z="2"/>
<observed_in data="samp1" scan="798" z="2"/>
</peptide>
<peptide id="pep1" mh="1103.461" mods="57.04" prot_ids="P1.1" seq="ADESHAGCEK">
<observed_in data="samp3" scan="663" 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="Nter" value="32.0"/>
<mod at="K" value="32.0"/>
</isotope_label>
</isotope_label_list>
<alignments>
<alignment_methods>
<alignment_method id="my_ms2">
<ms2>
<ms2_tendency_halfwindow>10</ms2_tendency_halfwindow>
<ms2_smoothing_halfwindow>5</ms2_smoothing_halfwindow>
<ms1_smoothing_halfwindow>3</ms1_smoothing_halfwindow>
</ms2>
</alignment_method>
<alignment_method id="my_obiwarp">
<obiwarp>
<lmat_precision>1</lmat_precision>
<mz_start>500</mz_start>
<mz_stop>1200</mz_stop>
</obiwarp>
</alignment_method>
</alignment_methods>
<align group_id="G1" method_id="my_ms2" reference_data_id="samp0"/>
<align group_id="G2" method_id="my_obiwarp" reference_data_id="samp2"/>
</alignments>
<quantification_methods>
<quantification_method id="my_qzivy">
<xic_extraction xic_type="sum">
<mz_range max="1.5" min="0.5"/>
</xic_extraction>
<xic_filters>
<anti_spike half="5"/>
<background half_mediane="5" half_min_max="15"/>
<smoothing half="3"/>
</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_method id="my_qmoulon">
<xic_extraction xic_type="max">
<ppm_range max="1.5" min="0.5"/>
</xic_extraction>
<xic_filters>
<background half_mediane="5" half_min_max="15"/>
</xic_filters>
<peak_detection>
<detection_moulon>
<smoothing_point>3</smoothing_point>
<TIC_start>5000</TIC_start>
<TIC_stop>3000</TIC_stop>
</detection_moulon>
</peak_detection>
</quantification_method>
</quantification_methods>
<quantification>
<quantification_results>
<quantification_result output_file="result1" format ="tsv"/>
<quantification_result output_file="result2" format="gnumeric"/>
<quantification_result output_file="result3" format ="xhtmltable"/>
<quantification_result output_file="result4" format ="xml" xic_traces="true"/>
</quantification_results>
<quantification_traces>
<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces" format="tsv"/>
<all_xics_traces output_dir="all_xics_traces" format="tsv"/>
<mz_traces mz_values="634.635 449.754 552.234" output_dir="mz_traces" format="tsv"/>
<mzrt_traces output_dir="mzrt_traces" format="tsv">
<mzrt_values>
<mzrt_value mz="732.317" rt="230.712"/>
<mzrt_value mz="575.256" rt="254.788"/>
</mzrt_values>
</mzrt_traces>
</quantification_traces>
<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
<peptides_in_peptide_list mode="real_or_mean"/>
</quantify>
<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
<peptides_in_peptide_list mode="real_or_mean" isotope_label_refs="iso1 iso2"/>
<mz_list>732.317 449.754 552.234 464.251 381.577 569.771 575.256</mz_list>
<mzrt_list>
<mzrt mz="732.317" rt="230.712"/>
<mzrt mz="575.256" rt="254.788"/>
</mzrt_list>
</quantify>
</quantification>
</masschroq>
scan sequence mh z proteins mods
778 CCTKPESER 1166.4934 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." 114.08
839 NYQEAK 752.3585 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." Ymod
1136 TCVADESHAGCEK 1463.5852 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." 57.04
1585 SHCIAEVEK 1072.5111 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
1935 NECFLSHK 1034.4729 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
1960 ECCDKPLLEK 1291.6019 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
1980 LCVLHEK 898.48236 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2089 CCTESLVNR 1138.4973 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2237 YICDNQDTISSK 1443.6373 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2241 QNCDQFEK 1051.4155 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2278 ETYGDMADCCEK 1478.5223 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2702 QEPERNECFLSHK 1656.7439 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2713 EYEATLEECCAK 1502.61 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2753 ECCHGDLLECADDR 1749.6615 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2867 CCAADDKEACFAVEGPK 1927.797 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
2910 EACFAVEGPK 1107.5137 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
3267 DDPHACYSTVFDK 1554.6533 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
3494 YLYEIAR 927.49396 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
3629 RHPEYAVSVLLR 1439.8123 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
3818 LKPDPNTLCDEFK 1576.7699 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
3821 KVPQVSTPTLVEVSR 1639.9381 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
3870 KQTALVELLK 1142.715 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
4082 RHPEYAVSVLLR 1439.8177 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
4236 RPCFSALTPDETYVPK 1880.9225 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
4253 SLHTLFGDELCK 1419.6945 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
4460 LVNELTEFAK 1163.6317 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
4499 SLHTLFGDELCK 1419.6956 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
4972 RHPYFYAPELLYYANK 2045.0253 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
5084 LFTFHADICTLPDTEK 1907.9092 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
5308 LGEYGFQNALIVR 1479.807 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
5578 HPYFYAPELLYYANK 1888.9224 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
6015 TVMENFVAFVDK 1399.6898 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
6689 MPCTEDYLSLILNR 1724.8433 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
6788 DAFLGSFLYEYSR 1567.748 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
scan sequence mh z proteins
778 CCTKPESER 1166.4934 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
839 NYQEAK 752.3585 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
1136 TCVADESHAGCEK 1463.5852 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
1585 SHCIAEVEK 1072.5111 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
778 CCTKPESER 1166.4934 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." blabla
839 NYQEAK 752.3585 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." 6.66
1136 TCVADESHAGCEK 1463.5852 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." Phospho(ST)-0000010000
1585 SHCIAEVEK 1072.5111 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR." bla bla
1935 NECFLSHK 1034.4729 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
1960 ECCDKPLLEK 1291.6019 3 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
1980 LCVLHEK 898.48236 2 "P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
......
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