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comparison test-data/test_small.xml @ 0:02e802817d48 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
author iuc
date Sat, 21 Oct 2023 10:29:31 +0000
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1 <?xml version="1.0" encoding="UTF-8"?><batch mzmine_version="3.5.5">
2 <batchstep method="io.github.mzmine.modules.io.import_rawdata_all.AllSpectralDataImportModule" parameter_version="1">
3 <parameter name="File names">
4 <file>/tmp/mzminetest/DOM_a.mzML</file>
5 <file>/tmp/mzminetest/DOM_b.mzXML</file>
6 </parameter>
7 <parameter name="Advanced import" selected="false">
8 <parameter name="Scan filters" selected="false">
9 <parameter name="Scan number"/>
10 <parameter name="Base Filtering Integer"/>
11 <parameter name="Retention time"/>
12 <parameter name="Mobility"/>
13 <parameter name="MS level filter" selected="All MS levels">1</parameter>
14 <parameter name="Scan definition"/>
15 <parameter name="Polarity">Any</parameter>
16 <parameter name="Spectrum type">ANY</parameter>
17 </parameter>
18 <parameter name="Crop MS1 m/z" selected="false"/>
19 <parameter name="MS1 detector (Advanced)" selected="false" selected_item="Centroid">
20 <module name="Factor of lowest signal">
21 <parameter name="Noise factor">3.0</parameter>
22 </module>
23 <module name="Centroid">
24 <parameter name="Noise level">3000.0</parameter>
25 <parameter name="Detect isotope signals below noise level" selected="false">
26 <parameter name="Chemical elements">H,C,N,O,S</parameter>
27 <parameter name="m/z tolerance">
28 <absolutetolerance>0.0015</absolutetolerance>
29 <ppmtolerance>3.0</ppmtolerance>
30 </parameter>
31 <parameter name="Maximum charge of isotope m/z">2</parameter>
32 </parameter>
33 </module>
34 <module name="Exact mass">
35 <parameter name="Noise level">1000.0</parameter>
36 <parameter name="Detect isotope signals below noise level" selected="false">
37 <parameter name="Chemical elements">H,C,N,O,S</parameter>
38 <parameter name="m/z tolerance">
39 <absolutetolerance>0.0015</absolutetolerance>
40 <ppmtolerance>3.0</ppmtolerance>
41 </parameter>
42 <parameter name="Maximum charge of isotope m/z">2</parameter>
43 </parameter>
44 </module>
45 <module name="Local maxima">
46 <parameter name="Noise level"/>
47 </module>
48 <module name="Recursive threshold">
49 <parameter name="Noise level"/>
50 <parameter name="Min m/z peak width"/>
51 <parameter name="Max m/z peak width"/>
52 </module>
53 <module name="Wavelet transform">
54 <parameter name="Noise level"/>
55 <parameter name="Scale level"/>
56 <parameter name="Wavelet window size (%)"/>
57 </module>
58 <module name="Auto">
59 <parameter name="Noise level">1000.0</parameter>
60 <parameter name="Detect isotope signals below noise level" selected="false">
61 <parameter name="Chemical elements">H,C,N,O,S</parameter>
62 <parameter name="m/z tolerance">
63 <absolutetolerance>0.0015</absolutetolerance>
64 <ppmtolerance>3.0</ppmtolerance>
65 </parameter>
66 <parameter name="Maximum charge of isotope m/z">2</parameter>
67 </parameter>
68 </module>
69 </parameter>
70 <parameter name="MS2 detector (Advanced)" selected="false" selected_item="Centroid">
71 <module name="Factor of lowest signal">
72 <parameter name="Noise factor">3.0</parameter>
73 </module>
74 <module name="Centroid">
75 <parameter name="Noise level">3000.0</parameter>
76 <parameter name="Detect isotope signals below noise level" selected="false">
77 <parameter name="Chemical elements">H,C,N,O,S</parameter>
78 <parameter name="m/z tolerance">
79 <absolutetolerance>0.0015</absolutetolerance>
80 <ppmtolerance>3.0</ppmtolerance>
81 </parameter>
82 <parameter name="Maximum charge of isotope m/z">2</parameter>
83 </parameter>
84 </module>
85 <module name="Exact mass">
86 <parameter name="Noise level">1000.0</parameter>
87 <parameter name="Detect isotope signals below noise level" selected="false">
88 <parameter name="Chemical elements">H,C,N,O,S</parameter>
89 <parameter name="m/z tolerance">
90 <absolutetolerance>0.0015</absolutetolerance>
91 <ppmtolerance>3.0</ppmtolerance>
92 </parameter>
93 <parameter name="Maximum charge of isotope m/z">2</parameter>
94 </parameter>
95 </module>
96 <module name="Local maxima">
97 <parameter name="Noise level"/>
98 </module>
99 <module name="Recursive threshold">
100 <parameter name="Noise level"/>
101 <parameter name="Min m/z peak width"/>
102 <parameter name="Max m/z peak width"/>
103 </module>
104 <module name="Wavelet transform">
105 <parameter name="Noise level"/>
106 <parameter name="Scale level"/>
107 <parameter name="Wavelet window size (%)"/>
108 </module>
109 <module name="Auto">
110 <parameter name="Noise level">1000.0</parameter>
111 <parameter name="Detect isotope signals below noise level" selected="false">
112 <parameter name="Chemical elements">H,C,N,O,S</parameter>
113 <parameter name="m/z tolerance">
114 <absolutetolerance>0.0015</absolutetolerance>
115 <ppmtolerance>3.0</ppmtolerance>
116 </parameter>
117 <parameter name="Maximum charge of isotope m/z">2</parameter>
118 </parameter>
119 </module>
120 </parameter>
121 <parameter name="Denormalize fragment scans (traps)">false</parameter>
122 </parameter>
123 <parameter name="Spectral library files">
124 <file>/tmp/mzminetest/GNPS-FAULKNERLEGACY.json</file>
125 <!--<file>D:\Data\lib\HMDB.mgf</file>-->
126 </parameter>
127 </batchstep>
128 <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule" parameter_version="1">
129 <parameter name="Raw data files" type="BATCH_LAST_FILES"/>
130 <parameter name="Scan filters" selected="true">
131 <parameter name="Scan number"/>
132 <parameter name="Base Filtering Integer"/>
133 <parameter name="Retention time"/>
134 <parameter name="Mobility"/>
135 <parameter name="MS level filter" selected="MS1, level = 1">1</parameter>
136 <parameter name="Scan definition"/>
137 <parameter name="Polarity">Any</parameter>
138 <parameter name="Spectrum type">ANY</parameter>
139 </parameter>
140 <parameter name="Scan types (IMS)">All scan types</parameter>
141 <parameter name="Mass detector" selected_item="Auto">
142 <module name="Factor of lowest signal">
143 <parameter name="Noise factor">3.0</parameter>
144 </module>
145 <module name="Centroid">
146 <parameter name="Noise level">3000.0</parameter>
147 <parameter name="Detect isotope signals below noise level" selected="false">
148 <parameter name="Chemical elements">H,C,N,O,S</parameter>
149 <parameter name="m/z tolerance">
150 <absolutetolerance>0.0015</absolutetolerance>
151 <ppmtolerance>3.0</ppmtolerance>
152 </parameter>
153 <parameter name="Maximum charge of isotope m/z">2</parameter>
154 </parameter>
155 </module>
156 <module name="Exact mass">
157 <parameter name="Noise level">1000.0</parameter>
158 <parameter name="Detect isotope signals below noise level" selected="false">
159 <parameter name="Chemical elements">H,C,N,O,S</parameter>
160 <parameter name="m/z tolerance">
161 <absolutetolerance>0.0015</absolutetolerance>
162 <ppmtolerance>3.0</ppmtolerance>
163 </parameter>
164 <parameter name="Maximum charge of isotope m/z">2</parameter>
165 </parameter>
166 </module>
167 <module name="Local maxima">
168 <parameter name="Noise level"/>
169 </module>
170 <module name="Recursive threshold">
171 <parameter name="Noise level"/>
172 <parameter name="Min m/z peak width"/>
173 <parameter name="Max m/z peak width"/>
174 </module>
175 <module name="Wavelet transform">
176 <parameter name="Noise level"/>
177 <parameter name="Scale level"/>
178 <parameter name="Wavelet window size (%)"/>
179 </module>
180 <module name="Auto">
181 <parameter name="Noise level">30000.0</parameter>
182 <parameter name="Detect isotope signals below noise level" selected="false">
183 <parameter name="Chemical elements">H,C,N,O,S</parameter>
184 <parameter name="m/z tolerance">
185 <absolutetolerance>0.0015</absolutetolerance>
186 <ppmtolerance>3.0</ppmtolerance>
187 </parameter>
188 <parameter name="Maximum charge of isotope m/z">2</parameter>
189 </parameter>
190 </module>
191 </parameter>
192 <parameter name="Denormalize fragment scans (traps)">false</parameter>
193 <parameter name="Output netCDF filename (optional)" selected="false"/>
194 </batchstep>
195 <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_massdetection.MassDetectionModule" parameter_version="1">
196 <parameter name="Raw data files" type="BATCH_LAST_FILES"/>
197 <parameter name="Scan filters" selected="true">
198 <parameter name="Scan number"/>
199 <parameter name="Base Filtering Integer"/>
200 <parameter name="Retention time"/>
201 <parameter name="Mobility"/>
202 <parameter name="MS level filter" selected="MSn, level ≥ 2">3</parameter>
203 <parameter name="Scan definition"/>
204 <parameter name="Polarity">Any</parameter>
205 <parameter name="Spectrum type">ANY</parameter>
206 </parameter>
207 <parameter name="Scan types (IMS)">All scan types</parameter>
208 <parameter name="Mass detector" selected_item="Auto">
209 <module name="Factor of lowest signal">
210 <parameter name="Noise factor">3.0</parameter>
211 </module>
212 <module name="Centroid">
213 <parameter name="Noise level">3000.0</parameter>
214 <parameter name="Detect isotope signals below noise level" selected="false">
215 <parameter name="Chemical elements">H,C,N,O,S</parameter>
216 <parameter name="m/z tolerance">
217 <absolutetolerance>0.0015</absolutetolerance>
218 <ppmtolerance>3.0</ppmtolerance>
219 </parameter>
220 <parameter name="Maximum charge of isotope m/z">2</parameter>
221 </parameter>
222 </module>
223 <module name="Exact mass">
224 <parameter name="Noise level">1000.0</parameter>
225 <parameter name="Detect isotope signals below noise level" selected="false">
226 <parameter name="Chemical elements">H,C,N,O,S</parameter>
227 <parameter name="m/z tolerance">
228 <absolutetolerance>0.0015</absolutetolerance>
229 <ppmtolerance>3.0</ppmtolerance>
230 </parameter>
231 <parameter name="Maximum charge of isotope m/z">2</parameter>
232 </parameter>
233 </module>
234 <module name="Local maxima">
235 <parameter name="Noise level"/>
236 </module>
237 <module name="Recursive threshold">
238 <parameter name="Noise level"/>
239 <parameter name="Min m/z peak width"/>
240 <parameter name="Max m/z peak width"/>
241 </module>
242 <module name="Wavelet transform">
243 <parameter name="Noise level"/>
244 <parameter name="Scale level"/>
245 <parameter name="Wavelet window size (%)"/>
246 </module>
247 <module name="Auto">
248 <parameter name="Noise level">3000.0</parameter>
249 <parameter name="Detect isotope signals below noise level" selected="false">
250 <parameter name="Chemical elements">H,C,N,O,S</parameter>
251 <parameter name="m/z tolerance">
252 <absolutetolerance>0.0015</absolutetolerance>
253 <ppmtolerance>3.0</ppmtolerance>
254 </parameter>
255 <parameter name="Maximum charge of isotope m/z">2</parameter>
256 </parameter>
257 </module>
258 </parameter>
259 <parameter name="Denormalize fragment scans (traps)">false</parameter>
260 <parameter name="Output netCDF filename (optional)" selected="false"/>
261 </batchstep>
262 <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_adapchromatogrambuilder.ModularADAPChromatogramBuilderModule" parameter_version="1">
263 <parameter name="Raw data files" type="BATCH_LAST_FILES"/>
264 <parameter name="Scan filters" selected="true">
265 <parameter name="Scan number"/>
266 <parameter name="Base Filtering Integer"/>
267 <parameter name="Retention time">
268 <min>0.5</min>
269 <max>10.0</max>
270 </parameter>
271 <parameter name="Mobility"/>
272 <parameter name="MS level filter" selected="MS1, level = 1">1</parameter>
273 <parameter name="Scan definition"/>
274 <parameter name="Polarity">Any</parameter>
275 <parameter name="Spectrum type">ANY</parameter>
276 </parameter>
277 <parameter name="Minimum consecutive scans">5</parameter>
278 <parameter name="Minimum intensity for consecutive scans">300000.0</parameter>
279 <parameter name="Minimum absolute height">500000.0</parameter>
280 <parameter name="m/z tolerance (scan-to-scan)">
281 <absolutetolerance>0.002</absolutetolerance>
282 <ppmtolerance>10.0</ppmtolerance>
283 </parameter>
284 <parameter name="Suffix">eics</parameter>
285 <parameter name="Allow single scan chromatograms"/>
286 </batchstep>
287 <batchstep method="io.github.mzmine.modules.dataprocessing.featdet_chromatogramdeconvolution.minimumsearch.MinimumSearchFeatureResolverModule" parameter_version="2">
288 <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
289 <parameter name="Suffix">r</parameter>
290 <parameter name="Original feature list">KEEP</parameter>
291 <parameter name="MS/MS scan pairing" selected="true">
292 <parameter name="MS1 to MS2 precursor tolerance (m/z)">
293 <absolutetolerance>0.01</absolutetolerance>
294 <ppmtolerance>10.0</ppmtolerance>
295 </parameter>
296 <parameter name="Retention time filter" selected="Use feature edges" unit="MINUTES">0.05</parameter>
297 <parameter name="Minimum relative feature height" selected="true">0.25</parameter>
298 <parameter name="Minimum required signals" selected="true">1</parameter>
299 <parameter name="Limit by ion mobility edges">true</parameter>
300 <parameter name="Merge MS/MS spectra (TIMS)">false</parameter>
301 <parameter name="Minimum signal intensity (absolute, TIMS)" selected="false">6000.0</parameter>
302 <parameter name="Minimum signal intensity (relative, TIMS)" selected="false">0.01</parameter>
303 </parameter>
304 <parameter name="Dimension">Retention time</parameter>
305 <parameter name="Chromatographic threshold">0.8420000000000001</parameter>
306 <parameter name="Minimum search range RT/Mobility (absolute)">0.05</parameter>
307 <parameter name="Minimum relative height">0.0</parameter>
308 <parameter name="Minimum absolute height">500000.0</parameter>
309 <parameter name="Min ratio of peak top/edge">2.0</parameter>
310 <parameter name="Peak duration range (min/mobility)">
311 <min>0.0</min>
312 <max>1.501</max>
313 </parameter>
314 <parameter name="Minimum scans (data points)">5</parameter>
315 </batchstep>
316 <batchstep method="io.github.mzmine.modules.dataprocessing.align_join.JoinAlignerModule" parameter_version="1">
317 <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
318 <parameter name="Feature list name">Aligned feature list</parameter>
319 <parameter name="m/z tolerance (sample-to-sample)">
320 <absolutetolerance>0.0015</absolutetolerance>
321 <ppmtolerance>5.0</ppmtolerance>
322 </parameter>
323 <parameter name="Weight for m/z">3.0</parameter>
324 <parameter name="Retention time tolerance" unit="MINUTES">0.1</parameter>
325 <parameter name="Weight for RT">1.0</parameter>
326 <parameter name="Mobility tolerance" selected="false">1.0</parameter>
327 <parameter name="Mobility weight">0.0</parameter>
328 <parameter name="Require same charge state">false</parameter>
329 <parameter name="Require same ID">false</parameter>
330 <parameter name="Compare isotope pattern" selected="false">
331 <parameter name="Isotope m/z tolerance">
332 <absolutetolerance>0.001</absolutetolerance>
333 <ppmtolerance>5.0</ppmtolerance>
334 </parameter>
335 <parameter name="Minimum absolute intensity">0.0</parameter>
336 <parameter name="Minimum score">0.0</parameter>
337 </parameter>
338 <parameter name="Compare spectra similarity" selected="false">
339 <parameter name="Spectral m/z tolerance">
340 <absolutetolerance>0.001</absolutetolerance>
341 <ppmtolerance>10.0</ppmtolerance>
342 </parameter>
343 <parameter name="MS level">2</parameter>
344 <parameter name="Compare spectra similarity" selected_item="Weighted cosine similarity">
345 <module name="Weighted cosine similarity">
346 <parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter>
347 <parameter name="Minimum cos similarity">0.65</parameter>
348 <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter>
349 </module>
350 <module name="Composite cosine identity (e.g., GC-EI-MS; similar to NIST search)">
351 <parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter>
352 <parameter name="Minimum cos similarity">0.7</parameter>
353 <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter>
354 </module>
355 </parameter>
356 </parameter>
357 <parameter name="Original feature list">KEEP</parameter>
358 </batchstep>
359 <batchstep method="io.github.mzmine.modules.dataprocessing.group_metacorrelate.corrgrouping.CorrelateGroupingModule" parameter_version="2">
360 <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
361 <parameter name="RT tolerance" unit="MINUTES">0.055000003</parameter>
362 <parameter name="Minimum feature height">0.0</parameter>
363 <parameter name="Intensity threshold for correlation">30000.0</parameter>
364 <parameter name="Min samples filter">
365 <parameter name="Min samples in all">
366 <abs>2</abs>
367 <rel>0.0</rel>
368 </parameter>
369 <parameter name="Min samples in group">
370 <abs>0</abs>
371 <rel>0.0</rel>
372 </parameter>
373 <parameter name="Min %-intensity overlap">0.6</parameter>
374 <parameter name="Exclude gap-filled features">true</parameter>
375 </parameter>
376 <parameter name="Feature shape correlation" selected="true">
377 <parameter name="Min data points">5</parameter>
378 <parameter name="Min data points on edge">2</parameter>
379 <parameter name="Measure">PEARSON</parameter>
380 <parameter name="Min feature shape correlation">0.85</parameter>
381 <parameter name="Min total correlation" selected="false">0.5</parameter>
382 </parameter>
383 <parameter name="Feature height correlation" selected="true">
384 <parameter name="Minimum samples">2</parameter>
385 <parameter name="Measure">PEARSON</parameter>
386 <parameter name="Min correlation">0.7</parameter>
387 </parameter>
388 <parameter name="Suffix (or auto)" selected="false"/>
389 </batchstep>
390 <batchstep method="io.github.mzmine.modules.dataprocessing.id_ion_identity_networking.ionidnetworking.IonNetworkingModule" parameter_version="1">
391 <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
392 <parameter name="m/z tolerance (intra-sample)">
393 <absolutetolerance>0.0015</absolutetolerance>
394 <ppmtolerance>3.0</ppmtolerance>
395 </parameter>
396 <parameter name="Check">ALL FEATURES</parameter>
397 <parameter name="Min height">0.0</parameter>
398 <parameter name="Ion identity library">
399 <parameter name="MS mode">POSITIVE</parameter>
400 <parameter name="Maximum charge">2</parameter>
401 <parameter name="Maximum molecules/cluster">2</parameter>
402 <parameter name="Adducts">
403 <adduct_type selected="false">
404 <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/>
405 </adduct_type>
406 <adduct_type selected="false">
407 <subpart charge="1" mass_difference="-5.4858E-4" mol_formula="" name="e" type="ADDUCT"/>
408 </adduct_type>
409 <adduct_type selected="true">
410 <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/>
411 </adduct_type>
412 <adduct_type selected="true">
413 <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/>
414 </adduct_type>
415 <adduct_type selected="true">
416 <subpart charge="1" mass_difference="38.963158" mol_formula="K" name="K" type="ADDUCT"/>
417 </adduct_type>
418 <adduct_type selected="true">
419 <subpart charge="1" mass_difference="18.033823" mol_formula="NH4" name="NH4" type="ADDUCT"/>
420 </adduct_type>
421 <adduct_type selected="false">
422 <subpart charge="1" mass_difference="-5.4858E-4" mol_formula="" name="e" type="ADDUCT"/>
423 <subpart charge="1" mass_difference="-5.4858E-4" mol_formula="" name="e" type="ADDUCT"/>
424 </adduct_type>
425 <adduct_type selected="true">
426 <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/>
427 <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/>
428 </adduct_type>
429 <adduct_type selected="false">
430 <subpart charge="2" mass_difference="39.96149382" mol_formula="Ca" name="Ca" type="ADDUCT"/>
431 </adduct_type>
432 <adduct_type selected="false">
433 <subpart charge="2" mass_difference="55.93384" mol_formula="Fe" name="Fe" type="ADDUCT"/>
434 </adduct_type>
435 <adduct_type selected="false">
436 <subpart charge="2" mass_difference="47.96953482" mol_formula="Mg" name="Mg" type="ADDUCT"/>
437 </adduct_type>
438 <adduct_type selected="false">
439 <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/>
440 <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/>
441 </adduct_type>
442 <adduct_type selected="false">
443 <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/>
444 <subpart charge="1" mass_difference="18.033823" mol_formula="NH4" name="NH4" type="ADDUCT"/>
445 </adduct_type>
446 <adduct_type selected="false">
447 <subpart charge="1" mass_difference="1.007276" mol_formula="H" name="H" type="ADDUCT"/>
448 <subpart charge="1" mass_difference="38.963158" mol_formula="K" name="K" type="ADDUCT"/>
449 </adduct_type>
450 <adduct_type selected="true">
451 <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/>
452 <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/>
453 <subpart charge="1" mass_difference="22.989218" mol_formula="Na" name="Na" type="ADDUCT"/>
454 </adduct_type>
455 <adduct_type selected="false">
456 <subpart charge="2" mass_difference="39.96149382" mol_formula="Ca" name="Ca" type="ADDUCT"/>
457 <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/>
458 </adduct_type>
459 <adduct_type selected="false">
460 <subpart charge="2" mass_difference="55.93384" mol_formula="Fe" name="Fe" type="ADDUCT"/>
461 <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/>
462 </adduct_type>
463 <adduct_type selected="false">
464 <subpart charge="1" mass_difference="0.0" mol_formula="" name="e" type="ADDUCT"/>
465 </adduct_type>
466 <adduct_type selected="false">
467 <subpart charge="-1" mass_difference="-1.007276" mol_formula="H" name="H" type="ADDUCT"/>
468 <subpart charge="2" mass_difference="47.96953482" mol_formula="Mg" name="Mg" type="ADDUCT"/>
469 </adduct_type>
470 <modification_type selected="true">
471 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
472 </modification_type>
473 <modification_type selected="true">
474 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
475 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
476 </modification_type>
477 <modification_type selected="false">
478 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
479 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
480 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
481 </modification_type>
482 <modification_type selected="false">
483 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
484 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
485 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
486 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
487 </modification_type>
488 <modification_type selected="false">
489 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
490 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
491 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
492 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
493 <subpart charge="0" mass_difference="-18.010565" mol_formula="H2O" name="H2O" type="NEUTRAL_LOSS"/>
494 </modification_type>
495 <modification_type selected="false">
496 <subpart charge="0" mass_difference="-17.026549" mol_formula="NH3" name="NH3" type="NEUTRAL_LOSS"/>
497 </modification_type>
498 <modification_type selected="false">
499 <subpart charge="0" mass_difference="15.99491462" mol_formula="O" name="O" type="CLUSTER"/>
500 </modification_type>
501 <modification_type selected="false">
502 <subpart charge="0" mass_difference="-27.994915" mol_formula="CO" name="CO" type="NEUTRAL_LOSS"/>
503 </modification_type>
504 <modification_type selected="false">
505 <subpart charge="0" mass_difference="-43.989829" mol_formula="CO2" name="CO2" type="NEUTRAL_LOSS"/>
506 </modification_type>
507 <modification_type selected="false">
508 <subpart charge="0" mass_difference="-28.031301" mol_formula="C2H4" name="C2H4" type="NEUTRAL_LOSS"/>
509 </modification_type>
510 <modification_type selected="false">
511 <subpart charge="0" mass_difference="46.005479" mol_formula="CHOOH" name="HFA" type="CLUSTER"/>
512 </modification_type>
513 <modification_type selected="false">
514 <subpart charge="0" mass_difference="60.021129" mol_formula="CH3COOH" name="HAc" type="CLUSTER"/>
515 </modification_type>
516 <modification_type selected="false">
517 <subpart charge="0" mass_difference="32.026215" mol_formula="CH3OH" name="MeOH" type="CLUSTER"/>
518 </modification_type>
519 <modification_type selected="false">
520 <subpart charge="0" mass_difference="41.026549" mol_formula="CH3CN" name="ACN" type="CLUSTER"/>
521 </modification_type>
522 <modification_type selected="false">
523 <subpart charge="0" mass_difference="60.058064" mol_formula="C3H8O" name="IsoProp" type="CLUSTER"/>
524 </modification_type>
525 </parameter>
526 </parameter>
527 <parameter name="Annotation refinement" selected="true">
528 <parameter name="Minimum size" selected="false">3</parameter>
529 <parameter name="Delete small networks without major ion">true</parameter>
530 <parameter name="Delete smaller networks: Link threshold" selected="true">4</parameter>
531 <parameter name="Delete networks without monomer">true</parameter>
532 <parameter name="Delete rows witout ion id">false</parameter>
533 </parameter>
534 </batchstep>
535 <batchstep method="io.github.mzmine.modules.dataprocessing.id_spectral_library_match.SpectralLibrarySearchModule" parameter_version="2">
536 <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
537 <parameter name="Spectral libraries" type="ALL_IMPORTED"/>
538 <parameter name="Scans for matching">MS level ≥ 2 (merged)</parameter>
539 <parameter name="Precursor m/z tolerance">
540 <absolutetolerance>0.01</absolutetolerance>
541 <ppmtolerance>20.0</ppmtolerance>
542 </parameter>
543 <parameter name="Spectral m/z tolerance">
544 <absolutetolerance>0.01</absolutetolerance>
545 <ppmtolerance>20.0</ppmtolerance>
546 </parameter>
547 <parameter name="Remove precursor">true</parameter>
548 <parameter name="Minimum matched signals">4</parameter>
549 <parameter name="Similarity" selected_item="Weighted cosine similarity">
550 <module name="Weighted cosine similarity">
551 <parameter name="Weights">SQRT (mz^0 * I^0.5)</parameter>
552 <parameter name="Minimum cos similarity">0.1</parameter>
553 <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter>
554 </module>
555 <module name="Composite cosine identity (e.g., GC-EI-MS; similar to NIST search)">
556 <parameter name="Weights">MassBank (mz^2 * I^0.5)</parameter>
557 <parameter name="Minimum cos similarity">0.7</parameter>
558 <parameter name="Handle unmatched signals">KEEP ALL AND MATCH TO ZERO</parameter>
559 </module>
560 </parameter>
561 <parameter name="Advanced" selected="false">
562 <parameter name="Retention time tolerance" selected="false"/>
563 <parameter name="CCS tolerance [%]" selected="false">0.05</parameter>
564 <parameter name="13C deisotoping" selected="false">
565 <parameter name="m/z tolerance">
566 <absolutetolerance>0.001</absolutetolerance>
567 <ppmtolerance>5.0</ppmtolerance>
568 </parameter>
569 <parameter name="Monotonic shape">false</parameter>
570 <parameter name="Maximum charge">1</parameter>
571 </parameter>
572 <parameter name="Min matched isotope signals" selected="false">3</parameter>
573 <parameter name="Crop spectra to m/z overlap">false</parameter>
574 </parameter>
575 </batchstep>
576 <batchstep method="io.github.mzmine.modules.io.export_features_gnps.fbmn.GnpsFbmnExportAndSubmitModule" parameter_version="2">
577 <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
578 <parameter name="Filename">
579 <current_file>/tmp/mzminetest/test2_iimn_gnps</current_file>
580 </parameter>
581 <parameter name="Merge MS/MS (experimental)" selected="false">
582 <parameter name="Select spectra to merge">across samples</parameter>
583 <parameter name="m/z merge mode">weighted average (remove outliers)</parameter>
584 <parameter name="intensity merge mode">sum intensities</parameter>
585 <parameter name="Expected mass deviation">
586 <absolutetolerance>0.001</absolutetolerance>
587 <ppmtolerance>5.0</ppmtolerance>
588 </parameter>
589 <parameter name="Cosine threshold (%)">0.7</parameter>
590 <parameter name="Signal count threshold (%)">0.2</parameter>
591 <parameter name="Isolation window offset (m/z)">0.0</parameter>
592 <parameter name="Isolation window width (m/z)">3.0</parameter>
593 </parameter>
594 <parameter name="Filter rows">MS2 OR ION IDENTITY</parameter>
595 <parameter name="Feature intensity">Area</parameter>
596 <parameter name="CSV export">SIMPLE</parameter>
597 <parameter name="Submit to GNPS" selected="false">
598 <parameter name="Meta data file" selected="false"/>
599 <parameter name="Export ion identity networks">true</parameter>
600 <parameter name="Presets">HIGHRES</parameter>
601 <parameter name="Job title"/>
602 <parameter name="Email"/>
603 <parameter name="Username"/>
604 <parameter name="Password"/>
605 <parameter name="Open website">true</parameter>
606 </parameter>
607 <parameter name="Open folder">false</parameter>
608 </batchstep>
609 <batchstep method="io.github.mzmine.modules.io.export_features_sirius.SiriusExportModule" parameter_version="1">
610 <parameter name="Feature lists" type="BATCH_LAST_FEATURELISTS"/>
611 <parameter name="Filename">
612 <current_file>D:\tmp\export_mzmine3\test2_sirius.MGF</current_file>
613 <last_file>D:\tmp\new_sirius\merged_new_sirius.mgf</last_file>
614 <last_file>D:\tmp\test\merged_new_sirius.mgf</last_file>
615 </parameter>
616 <parameter name="Merge MS/MS" selected="false">
617 <parameter name="Select spectra to merge">across samples</parameter>
618 <parameter name="m/z merge mode">weighted average (remove outliers)</parameter>
619 <parameter name="intensity merge mode">sum intensities</parameter>
620 <parameter name="Expected mass deviation">
621 <absolutetolerance>0.001</absolutetolerance>
622 <ppmtolerance>5.0</ppmtolerance>
623 </parameter>
624 <parameter name="Cosine threshold (%)">0.7</parameter>
625 <parameter name="Signal count threshold (%)">0.2</parameter>
626 <parameter name="Isolation window offset (m/z)">0.0</parameter>
627 <parameter name="Isolation window width (m/z)">3.0</parameter>
628 </parameter>
629 <parameter name="m/z tolerance">
630 <absolutetolerance>0.002</absolutetolerance>
631 <ppmtolerance>5.0</ppmtolerance>
632 </parameter>
633 <parameter name="Only rows with annotation">false</parameter>
634 <parameter name="Exclude multiple charge">false</parameter>
635 <parameter name="Exclude multimers">false</parameter>
636 </batchstep>
637 </batch>