FileOrganization: data.xml

File data.xml, 6.4 KB (added by dbrentw, 5 years ago)

Example data.xml for non-LC-MS/MS projects

Line 
1<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
2<!-- NOTE:
3     For non-LC-MS/MS data, there is a single overview scan, corresponding to the first MS1 scan. If this is TIM data (no MS1 scan) then a simulated MS1 scan is created (0.xml)
4         A single archive (.zip) is created for the project, and it contains the data.xml, dataHeader.xml, settings.xml, and the xml for all scans in the project
5-->
6
7
8<!-- XML of Data.java -->
9<data version="1.01">
10        <!-- XML of Annotation.java>
11        <!-- list of annotation objects for this project (in this case Glycan Annotations -->
12    <annotation>
13                <!-- XML of GlycanAnnotation.java (extension of Annotation.java) -->
14        <glycanAnn glycanId="GOG972-T" derivatisationType="perMe" seqGWB="freeEnd--??1D-GlcNAc,p--??1D-GlcNAc,p--??1D-Man,p(--??1D-Man,p(--??1D-Man,p--??1D-Man,p)--??1D-Man,p--??1D-Man,p)--??1D-Man,p--??1D-Man,p--??1D-Man,p--??1D-Glc,p" id="2" selected="true" seq="RES&#xA;1b:x-dglc-HEX-1:5&#xA;2b:x-dglc-HEX-1:5&#xA;3b:x-dman-HEX-1:5&#xA;4b:x-dman-HEX-1:5&#xA;5b:x-dman-HEX-1:5&#xA;6b:x-dman-HEX-1:5&#xA;7b:x-dman-HEX-1:5&#xA;8b:x-dman-HEX-1:5&#xA;9b:x-dman-HEX-1:5&#xA;10b:x-dman-HEX-1:5&#xA;11b:x-dman-HEX-1:5&#xA;12b:x-dglc-HEX-1:5&#xA;13s:n-acetyl&#xA;14s:n-acetyl&#xA;LIN&#xA;1:1o(-1+1)2d&#xA;2:2o(-1+1)3d&#xA;3:3o(-1+1)4d&#xA;4:4o(-1+1)5d&#xA;5:5o(-1+1)6d&#xA;6:4o(-1+1)7d&#xA;7:7o(-1+1)8d&#xA;8:3o(-1+1)9d&#xA;9:9o(-1+1)10d&#xA;10:10o(-1+1)11d&#xA;11:11o(-1+1)12d&#xA;12:2d(2+1)13n&#xA;13:1d(2+1)14n&#xA;" sequenceFormat="GlycoCTCondensed" type="org.grits.toolbox.ms.om.data.GlycanAnnotation">
15                        <!-- key/value pairs of various datatypes. The key and its descriptor can be found in dataHeader.xml -->
16            <booleanProp/>
17            <doubleProp>
18                                <!-- CustomExtraData for this Annotation (see dataHeader.xml for meta-info) -->
19                                <!-- example of a double value associated with this glycan annotation -->
20                <item>
21                    <key>gg.pme+na</key>
22                    <value>2600.2820154800006</value>
23                </item>
24            </doubleProp>
25            <integerProp>
26                                <!-- CustomExtraData for this Annotation (see dataHeader.xml for meta-info) -->
27                                <!-- example of a integer value associated with this glycan annotation -->
28                <item>
29                    <key>gg.n.res</key>
30                    <value>14</value>
31                </item>
32            </integerProp>
33            <stringProp>
34                                <!-- CustomExtraData for this Annotation (see dataHeader.xml for meta-info) -->
35                                <!-- example of a String value associated with this glycan annotation -->
36                <item>
37                    <key>gg.type</key>
38                    <value>N-Glycan</value>
39                </item>
40            </stringProp>
41            <reducingEnd label="freeEnd" type="freeEnd"/>
42        </glycanAnn>
43    </annotation>
44<!-- ******************** ADDITIONAL ROWS REMOVED ************************************* -->
45        <annotation>
46        </annotation>
47    <dataHeader version="1.0">
48<!-- ******************** ADDITIONAL ROWS REMOVED (see dataHeader.xml) ************************************* -->
49    </dataHeader>
50        <!-- list of scans in the MS file -->
51    <scans>
52                <!-- an MS Scan -->
53        <item>
54                        <!-- Key is the scan number -->
55            <key>1</key>
56                        <!-- XML of Scan.java -->
57            <value mostAbundantPeak="2.6915094E7" msLevel="1" numAnnotatedPeaks="111" polarity="true" retentionTime="0.14959999997999998" scanEnd="2000.0" scanNo="1" scanStart="500.0">
58                                <!-- peaks in scan. Note that for direct infusion, MS Profile, and TIM, only precursor peaks are provided for the "overview" scan (1 for DI and Profile, 0 for TIM) -->
59                                <!-- XML of Peak.java -->
60                <peak id="1" intensity="63566.34375" isPrecursor="true" mz="1215.6407470703125" precursorCharge="2" precursorIntensity="145662.296875" precursorMz="1215.6458740234375" relativeIntensity="0.006717616231379128">
61                    <doubleProp/>
62                    <integerProp/>
63                </peak>
64<!-- ******************** ADDITIONAL ROWS REMOVED ************************************* -->
65                <peak id="9" intensity="104233.8671875" isPrecursor="true" mz="871.7009887695312" precursorCharge="4" precursorIntensity="449901.28125" precursorMz="871.7000122070312" relativeIntensity="0.009734870481200246">
66                    <doubleProp/>
67                    <integerProp/>
68                </peak>
69<!-- ******************** ADDITIONAL ROWS REMOVED ************************************* -->
70                <peak id="129" intensity="128594.6171875" isPrecursor="true" mz="1089.0989990234375" precursorCharge="2" precursorIntensity="1549634.125" precursorMz="1089.0999755859375" relativeIntensity="0.010871771404209767">
71                    <doubleProp/>
72                    <integerProp/>
73                </peak>
74<!-- ******************** ADDITIONAL ROWS REMOVED ************************************* -->
75                <peak id="139" intensity="127053.3125" isPrecursor="true" mz="893.8036499023438" precursorCharge="3" precursorIntensity="204697.609375" precursorMz="893.8076782226562" relativeIntensity="0.01495090482682173">
76                    <doubleProp/>
77                    <integerProp/>
78                </peak>
79                <subScan>2</subScan>
80<!-- ******************** ADDITIONAL ROWS REMOVED ************************************* -->
81                <subScan>21</subScan>
82            </value>
83        </item>
84        <item>
85            <key>2</key>
86            <value activationMethode="collision-induced dissociation" mostAbundantPeak="2094.753662109375" msLevel="2" numAnnotatedPeaks="111" parentScan="64" polarity="true" retentionTime="153.44629999998" scanEnd="2000.0" scanNo="71" scanStart="225.0">
87                                <!-- This scan is a precursor, so has a precursor Peak -->
88                                <!-- XML of Peak.java -->                               
89                <precursor id="9" intensity="104233.8671875" isPrecursor="true" mz="871.7009887695312" precursorCharge="4" precursorIntensity="449901.28125" precursorMz="871.7000122070312" relativeIntensity="0.009734870481200246">
90                    <doubleProp/>
91                    <integerProp/>
92                </precursor>
93                <peak id="1" intensity="0.7611268162727356" isPrecursor="false" mz="243.1491241455078" relativeIntensity="3.633490801521245E-4">
94                    <doubleProp/>
95                    <integerProp/>
96                </peak>
97            </value>
98        </item>
99<!-- ******************** ADDITIONAL ROWS REMOVED ************************************* -->
100    </scans>
101</data>