Mercurial > repos > tomnl > mspurity_spectralmatching

comparison spectralMatching.xml @ 12:e131f2fb0f97 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:48:31 -0400
parents 103d2613b3a7
children 8dd98b0f83af
comparison
equal deleted inserted replaced
11:103d2613b3a7 12:e131f2fb0f97
16 </stdio> 16 </stdio>
17 <command interpreter="Rscript"><![CDATA[ 17 <command interpreter="Rscript"><![CDATA[
18 spectralMatching.R 18 spectralMatching.R
19 --outDir=. 19 --outDir=.
20 --cores=\${GALAXY_SLOTS:-4} 20 --cores=\${GALAXY_SLOTS:-4}
21 21
22 22 #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData'
23 #if $Query.q_dbPth_con.q_dbPth_select == 'userdb' 23 --q_defaultDb
24 #else if $Query.q_dbPth_con.q_dbPth_select == 'sqlite'
24 --q_dbPth=$Query.q_dbPth_con.q_dbPth 25 --q_dbPth=$Query.q_dbPth_con.q_dbPth
25 #else 26 #end if
26 --q_defaultDb 27
27 #end if 28 #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData'
28 29 --l_defaultDb
29 #if $Library.l_dbPth_con.l_dbPth_select == 'userdb' 30 #else if $Library.l_dbPth_con.l_dbPth_select == 'userdb_sqlite'
30 --l_dbPth=$Library.l_dbPth_con.l_dbPth 31 --l_dbPth=$Library.l_dbPth_con.l_dbPth
31 #else 32 #end if
32 --l_defaultDb 33
33 #end if 34 --l_dbType=$Library.l_dbPth_con.l_dbPth_select
34 35 --q_dbType=$Query.q_dbPth_con.q_dbPth_select
36
37
35 --q_ppmPrec=$Query.q_filters.q_ppmPrec 38 --q_ppmPrec=$Query.q_filters.q_ppmPrec
36 --l_ppmPrec=$Library.l_filters.l_ppmPrec 39 --l_ppmPrec=$Library.l_filters.l_ppmPrec
37 40
38 --q_ppmProd=$Query.q_filters.q_ppmProd 41 --q_ppmProd=$Query.q_filters.q_ppmProd
39 --l_ppmProd=$Library.l_filters.l_ppmProd 42 --l_ppmProd=$Library.l_filters.l_ppmProd
40 43
41 44
42 #if $Query.q_filters.q_raThres_cond.q_raThres_bool 45 #if $Query.q_filters.q_raThres_cond.q_raThres_bool
43 --q_raThres=$Query.q_filters.q_raThres_cond.q_raThres 46 --q_raThres=$Query.q_filters.q_raThres_cond.q_raThres
44 #end if 47 #end if
45 48
46 #if $Library.l_filters.l_raThres_cond.l_raThres_bool 49 #if $Library.l_filters.l_raThres_cond.l_raThres_bool
47 --l_raThres=$Library.l_filters.l_raThres_cond.l_raThres 50 --l_raThres=$Library.l_filters.l_raThres_cond.l_raThres
48 #end if 51 #end if
49 52
50 #if $Query.q_filters.q_polarity_cond.q_polarity_bool 53 #if $Query.q_filters.q_polarity_cond.q_polarity_bool
51 --q_polarity=$Query.q_filters.q_polarity_cond.q_polarity 54 --q_polarity=$Query.q_filters.q_polarity_cond.q_polarity
52 #end if 55 #end if
53 56
54 #if $Library.l_filters.l_polarity_cond.l_polarity_bool 57 #if $Library.l_filters.l_polarity_cond.l_polarity_bool
55 --l_polarity=$Library.l_filters.l_polarity_cond.l_polarity 58 --l_polarity=$Library.l_filters.l_polarity_cond.l_polarity
56 #end if 59 #end if
57 60
58 #if $Query.q_filters.q_purity_cond.q_purity_bool 61 #if $Query.q_filters.q_purity_cond.q_purity_bool
59 --q_purity=$Query.q_filters.q_purity_cond.q_purity 62 --q_purity=$Query.q_filters.q_purity_cond.q_purity
60 #end if 63 #end if
61 64
62 #if $Library.l_filters.l_purity_cond.l_purity_bool 65 #if $Library.l_filters.l_purity_cond.l_purity_bool
63 --l_purity=$Library.l_filters.l_purity_cond.l_purity 66 --l_purity=$Library.l_filters.l_purity_cond.l_purity
64 #end if 67 #end if
65 68
66 #if $Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups_bool 69 #if $Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups_bool
67 --q_xcmsGroups=$Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups 70 --q_xcmsGroups=$Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups
68 #end if 71 #end if
69 72
70 #if $Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups_bool 73 #if $Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups_bool
71 --l_xcmsGroups=$Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups 74 --l_xcmsGroups=$Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups
72 #end if 75 #end if
73 76
74 #if $Query.q_filters.q_pids_cond.q_pids_bool 77 #if $Query.q_filters.q_pids_cond.q_pids_bool
75 --q_pids=$Query.q_filters.q_pids_cond.q_pids 78 --q_pids=$Query.q_filters.q_pids_cond.q_pids
76 #end if 79 #end if
77 80
78 #if $Library.l_filters.l_pids_cond.l_pids_bool 81 #if $Library.l_filters.l_pids_cond.l_pids_bool
79 --l_pids=$Library.l_filters.l_pids_cond.l_pids 82 --l_pids=$Library.l_filters.l_pids_cond.l_pids
80 #end if 83 #end if
81 84
82 #if $Query.q_filters.q_rtrange_cond.q_rtrange_bool 85 #if $Query.q_filters.q_rtrange_cond.q_rtrange_bool
83 --q_rtrangeMin=$Query.q_filters.q_rtrange_cond.q_rtrangeMin 86 --q_rtrangeMin=$Query.q_filters.q_rtrange_cond.q_rtrangeMin
84 --q_rtrangeMax=$Query.q_filters.q_rtrange_cond.q_rtrangeMax 87 --q_rtrangeMax=$Query.q_filters.q_rtrange_cond.q_rtrangeMax
85 #end if 88 #end if
86 89
87 #if $Library.l_filters.l_rtrange_cond.l_rtrange_bool 90 #if $Library.l_filters.l_rtrange_cond.l_rtrange_bool
88 --l_rtrangeMin=$Library.l_filters.l_rtrange_cond.l_rtrangeMin 91 --l_rtrangeMin=$Library.l_filters.l_rtrange_cond.l_rtrangeMin
89 --l_rtrangeMax=$Library.l_filters.l_rtrange_cond.l_rtrangeMax 92 --l_rtrangeMax=$Library.l_filters.l_rtrange_cond.l_rtrangeMax
90 #end if 93 #end if
91 94
92 #if $Query.q_filters.q_accessions_cond.q_accessions_bool 95 #if $Query.q_filters.q_accessions_cond.q_accessions_bool
93 --q_accessions=$Query.q_filters.q_accessions_cond.q_accessions 96 --q_accessions=$Query.q_filters.q_accessions_cond.q_accessions
94 #end if 97 #end if
95 98
96 #if $Library.l_filters.l_accessions_cond.l_accessions_bool 99 #if $Library.l_filters.l_accessions_cond.l_accessions_bool
97 --l_accessions=$Library.l_filters.l_accessions_cond.l_accessions 100 --l_accessions=$Library.l_filters.l_accessions_cond.l_accessions
98 #end if 101 #end if
99 102
100 103
101 #if $Query.q_filters.q_sources_cond.q_sources_bool 104 #if $Query.q_filters.q_sources_cond.q_sources_bool
102 --q_sources=$Query.q_filters.q_sources_cond.q_sources 105 --q_sources=$Query.q_filters.q_sources_cond.q_sources
103 --q_sourcesUser=$Query.q_filters.q_sources_cond.q_sourcesUser 106 --q_sourcesUser=$Query.q_filters.q_sources_cond.q_sourcesUser
104 #end if 107 #end if
105 108
106 #if $Library.l_filters.l_sources_cond.l_sources_bool 109 #if $Library.l_filters.l_sources_cond.l_sources_bool
107 --l_sources=$Library.l_filters.l_sources_cond.l_sources 110 --l_sources=$Library.l_filters.l_sources_cond.l_sources
108 --l_sourcesUser=$Library.l_filters.l_sources_cond.l_sourcesUser 111 --l_sourcesUser=$Library.l_filters.l_sources_cond.l_sourcesUser
109 #end if 112 #end if
110 113
111 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool 114 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool
112 --q_instrumentTypes=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes 115 --q_instrumentTypes=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes
113 --q_instrumentTypesUser=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser 116 --q_instrumentTypesUser=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser
114 #end if 117 #end if
115 118
116 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool 119 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool
117 --l_instrumentTypes=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes 120 --l_instrumentTypes=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes
118 --l_instrumentTypesUser=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser 121 --l_instrumentTypesUser=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser
119 #end if 122 #end if
120 123
121 #if $Query.q_filters.q_instruments_cond.q_instruments_bool 124 #if $Query.q_filters.q_instruments_cond.q_instruments_bool
122 --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments 125 --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments
123 #end if 126 #end if
124 127
125 #if $Library.l_filters.l_instruments_cond.l_instruments_bool 128 #if $Library.l_filters.l_instruments_cond.l_instruments_bool
126 --l_instruments=$Library.l_filters.l_instruments_cond.l_instruments 129 --l_instruments=$Library.l_filters.l_instruments_cond.l_instruments
127 #end if 130 #end if
128 131
129 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool 132 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool
130 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes 133 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes
131 #end if 134 #end if
132 135
133 #if $Library.l_filters.l_spectraTypes_cond.l_spectraTypes_bool 136 #if $Library.l_filters.l_spectraTypes_cond.l_spectraTypes_bool
134 --l_spectraTypes=$Library.l_filters.l_spectraTypes_cond.l_spectraTypes 137 --l_spectraTypes=$Library.l_filters.l_spectraTypes_cond.l_spectraTypes
135 #end if 138 #end if
136 139
137 #if $Query.q_filters.q_spectraFilter 140 #if $Query.q_filters.q_spectraFilter
138 --q_spectraFilter 141 --q_spectraFilter
139 #end if 142 #end if
140 143
141 #if $Library.l_filters.l_spectraFilter 144 #if $Library.l_filters.l_spectraFilter
142 --l_spectraFilter 145 --l_spectraFilter
143 #end if 146 #end if
144 147
145 #if $General.rttol_cond.rttol_bool 148 #if $General.rttol_cond.rttol_bool
146 --rttol=$General.rttol_cond.rttol 149 --rttol=$General.rttol_cond.rttol
147 #end if 150 #end if
148 151
149 --raW=$General.raW 152 --raW=$General.raW
150 --mzW=$General.mzW 153 --mzW=$General.mzW
151 154
152 #if $General.updateDb_cond.updateDb 155 #if $General.updateDb_cond.updateDb
153 --updateDb 156 --updateDb
154 #if $General.updateDb_cond.copyDb 157 #if $General.updateDb_cond.copyDb
155 --copyDb 158 --copyDb
156 #end if 159 #end if
157 #end if 160 #end if
158 161
159 #if $General.usePrecursors 162 #if $General.usePrecursors
160 --usePrecursors 163 --usePrecursors
161 #end if 164 #end if
162 165
163 166
164 167
165 ]]></command> 168 ]]></command>
166 <inputs> 169 <inputs>
167 170
168 171
169 172
170 <section name="Query" title="Query spectra input and filters" expanded="True"> 173 <section name="Query" title="Query spectra input and filters" expanded="True">
171 <expand macro="sm_input" ql='Query' ql_shrt = "q" user="True" mspuritydatalib="False" msp="False" 174 <expand macro="sm_input" ql='Query' ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
172 help="Query SQLite database - in the standard XCMS msPurity workflow - the output 175 help="Query SQLite database - in the standard XCMS msPurity workflow - the output
173 of msPurity.createDatabase should be used here. However any SQLite database 176 of msPurity.createDatabase should be used here. However any SQLite database
174 following the schema of xxx can be used as input"/> 177 following the schema of xxx can be used as input"/>
175 <expand macro="filters" ql="Query" ql_shrt="q"/> 178 <expand macro="filters" ql="Query" ql_shrt="q"/>
176 </section> 179 </section>
177 180
178 <section name="Library" title="Library spectra input and filters" expanded="True"> 181 <section name="Library" title="Library spectra input and filters" expanded="True">
179 <expand macro="sm_input" ql='Library' ql_shrt = "l" user="False" mspuritydatalib="True" msp="False" 182 <expand macro="sm_input" ql='Library' ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
180 help="Library SQLite database - in the standard XCMS msPurity workflow - a default 183 help="Library SQLite database - in the standard XCMS msPurity workflow - a default
181 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite 184 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite
182 database following the schema of xxx can be used as input"/> 185 database following the schema of xxx can be used as input"/>
183 <expand macro="filters" ql="Library" ql_shrt="l"/> 186 <expand macro="filters" ql="Library" ql_shrt="l"/>
184 </section> 187 </section>
185 188
186 <section name="General" title="General arguments" expanded="False"> 189 <section name="General" title="General arguments" expanded="False">
187 <conditional name="rttol_cond"> 190 <conditional name="rttol_cond">
188 <param name="rttol_bool" type="boolean" label="Filter on retention time match?" 191 <param name="rttol_bool" type="boolean" label="Filter on retention time match?"
189 help="" /> 192 help="" />
190 <when value="true"> 193 <when value="true">
191 <param name="rttol" type="float" value="30" min="0" 194 <param name="rttol" type="float" value="30" min="0"
192 label="Retention time tolerance (seconds)" 195 label="Retention time tolerance (seconds)"
193 help="Retention time tolerance in seconds to match precursors"/> 196 help="Retention time tolerance in seconds to match precursors"/>
194 </when> 197 </when>
195 <when value="false"> 198 <when value="false">
196 </when> 199 </when>
197 </conditional> 200 </conditional>
198 201
199 202
200 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?" 203 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?"
201 help="If True, spectra will be filtered by similarity of precursors based on 204 help="If True, spectra will be filtered by similarity of precursors based on
202 the library and query ppm defined tolerance" /> 205 the library and query ppm defined tolerance" />
203 206
204 <param name="raW" label="Weighting for relative abundance" 207 <param name="raW" label="Weighting for relative abundance"
205 type="float" value="0.5" 208 type="float" value="0.5"
206 help="Relative abundance weight for spectra (default to 0.5 as determined by 209 help="Relative abundance weight for spectra (default to 0.5 as determined by
207 massbank for ESI data)"/> 210 massbank for ESI data)"/>
208 211
209 <param name="mzW" label="Weighting for mz" 212 <param name="mzW" label="Weighting for mz"
210 type="float" value="2" 213 type="float" value="2"
211 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/> 214 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/>
212 215
213 <conditional name="updateDb_cond"> 216 <conditional name="updateDb_cond">
214 <param name="updateDb" type="boolean" checked="true" 217 <param name="updateDb" type="boolean" checked="true"
215 label="Update database with results?" help="" /> 218 label="Update database with results?" help="" />
216 <when value="true"> 219 <when value="true">
217 <param name="copyDb" type="boolean" checked="true" 220 <param name="copyDb" type="boolean" checked="true"
218 label="Make a copy of the database?" 221 label="Make a copy of the database?"
219 help="A copy will be made of the input SQLite target database and the 222 help="A copy will be made of the input SQLite target database and the
220 results will be added to this copy. When False, the input SQLite 223 results will be added to this copy. When False, the input SQLite
221 database will be updated with the matching results. Use False if 224 database will be updated with the matching results. Use False if
222 you want to reduce storage space being used."/> 225 you want to reduce storage space being used."/>
223 </when> 226 </when>
224 <when value="false"> 227 <when value="false">
225 </when> 228 </when>
226 </conditional> 229 </conditional>
227 230
228 231
229 232
230 </section> 233 </section>
231 234
232 235
233 236
234 237
235 </inputs> 238 </inputs>
236 239
237 <outputs> 240 <outputs>
272 ----------- 275 -----------
273 General 276 General
274 ----------- 277 -----------
275 278
276 279
277 Perform spectral matching to spectral libraries for an LC-MS/MS dataset. 280 Perform spectral matching to spectral libraries for an LC-MS/MS dataset.
278 281
279 The spectral matching is performed from a **Query** SQLite spectral-database against a **Library** SQLite spectral-database. 282 The spectral matching is performed from a **Query** SQLite spectral-database against a **Library** SQLite spectral-database.
280 283
281 The SQLite schema of the spectral database here: spectral_database_schema_ 284 The SQLite schema of the spectral database here: spectral_database_schema_
282 285
283 286
284 The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity 287 The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity
285 function createDatabase as part of a msPurity-XCMS data processing workflow. 288 function createDatabase as part of a msPurity-XCMS data processing workflow.
286 289
287 The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources. 290 The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources.
288 The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS. 291 The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS.
289 A larger_database_ can be download and used from the msp2db github repository. 292 A larger_database_ can be download and used from the msp2db github repository.
290 293
291 To create a user generated library SQLite database the following tool can be used to generate a SQLite database 294 To create a user generated library SQLite database the following tool can be used to generate a SQLite database
292 from a collection of MSP files: msp2db_. 295 from a collection of MSP files: msp2db_.
293 296
294 It should be noted though, that as long as the schema of the spectral-database is as described here, then any database can be used 297 It should be noted though, that as long as the schema of the spectral-database is as described here, then any database can be used
295 for either the library or query - even allowing for the same database to be used. 298 for either the library or query - even allowing for the same database to be used.
296 299
297 The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching, 300 The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching,
298 and summarising the results. 301 and summarising the results.
299 302
300 Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing 303 Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing
301 the library source, instrument, retention time, precursor PPM tolerance etc). 304 the library source, instrument, retention time, precursor PPM tolerance etc).
302 305
303 The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar 306 The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar
304 to modified pMatch algorithm described in Zhou et al 2015. 307 to modified pMatch algorithm described in Zhou et al 2015.
305 308
306 The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both 309 The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both
307 the query and library spectra (wq and wl). See below: 310 the query and library spectra (wq and wl). See below:
308 311
309 .. math:: 312 .. math::
310 313
311 w=intensity^x \cdot mz^y 314 w=intensity^x \cdot mz^y
312 315
313 316
314 Where x and y represent weight factors and can be adjusted with the parameters raW and mzW. 317 Where x and y represent weight factors and can be adjusted with the parameters raW and mzW.
315 Defaults to x=0.5 and y=2 as per MassBank for ESI based mass spectrometry data. 318 Defaults to x=0.5 and y=2 as per MassBank for ESI based mass spectrometry data.
316 319
317 The aligned weighted vectors are then matched using dot product cosine, reverse dot product cosine and the composite dot product. 320 The aligned weighted vectors are then matched using dot product cosine, reverse dot product cosine and the composite dot product.
318 See below for dot product cosine equation. 321 See below for dot product cosine equation.
319 322
341 344
342 **Database** 345 **Database**
343 346
344 The updated query database (this will have been updated with the annotation results if updateDb argument used) 347 The updated query database (this will have been updated with the annotation results if updateDb argument used)
345 348
346 **matchedResults** 349
347 350 **xcmsMatchedResults**
348 All matched results from the query spectra to the library spectra. Contains the following columns 351
349 352 If the qeury spectra had XCMS based chromotographic peaks tables (e.g c_peak_groups, c_peaks) in the sqlite database - it will
353 be possible to summarise the matches for each XCMS grouped feature. The dataframe contains the following columns
354
355 * lpid - id in database of library spectra
356 * qpid - id in database of query spectra
350 * dpc - dot product cosine of the match 357 * dpc - dot product cosine of the match
351 * rdpc - reverse dot product cosine of the match 358 * rdpc - reverse dot product cosine of the match
352 * cdpc - composite dot product cosine of the match 359 * cdpc - composite dot product cosine of the match
353 * mcount - number of matching peaks 360 * mcount - number of matching peaks
354 * allcount - total number of peaks across both query and library spectra 361 * allcount - total number of peaks across both query and library spectra
355 * mpercent - percentage of matching peaks across both query and library spectra 362 * mpercent - percentage of matching peaks across both query and library spectra
356 * accession - accession of library match 363 * library_rt - retention time of library spectra
357 * name - name of library match 364 * query_rt - retention time of query spectra
358 * inchikey - inchikey of library match 365 * rtdiff - difference between library and query retention time
359 * lpid - pid in database of library match 366 * library_precursor_mz - library precursor mz
360 * qpid - pid in database of query match 367 * query_precursor_mz - query precursor mz
361 * mid - id of the match 368 * library_precursor_ion_purity - library precursor ion purity
362 369 * query_precursor_ion_purity - query precursor ion purity
363 **xcmsMatchedResults** 370 * library_accession - library accession value (unique string or number given to eith MoNA or Massbank data entires)
364 371 * library_precursor_type - library precursor type (i.e. adduct)
365 If the qeury spectra had XCMS based chromotographic peaks tables (e.g c_peak_groups, c_peaks) in the sqlite database - it will 372 * library_entry_name - Name given to the library spectra
366 be possible to summarise the matches for each XCMS grouped feature. The dataframe contains the following columns 373 * inchikey - inchikey of the matched library spectra
367 374 * library_source_name - source of the spectra (e.g. massbank, gnps)
368 * pid - pid in database of query match 375 * library_compound_name - name of compound spectra was obtained from
369 * grpid - grpid of the XCMS grouped feature for query match 376
370 * mz - derived from XCMS grouped feature 377 **matchedResults**
371 * mzmin - derived from XCMS grouped feature 378
372 * mzmax - derived from XCMS grouped feature 379 All matched results from the query spectra to the library spectra. Contains the same as above
373 * rt - derived from XCMS grouped feature 380 without the XCMS details. This table is useful to observe spectral matching results
374 * rtmin - derived from XCMS grouped feature 381 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.
375 * rtmax - derived from XCMS grouped feature
376 * npeaks - derived from XCMS grouped feature
377 * grp_name - derived from XCMS grouped feature
378 * dpc - dot product cosine of the match
379 * rdpc - reverse dot product cosine of the match
380 * cdpc - composite dot product cosine of the match
381 * mcount - number of matching peaks
382 * allcount - total number of peaks across both query and library spectra
383 * mpercent - percentage of matching peaks across both query and library spectra
384 * accession - accession of library match
385 * name - name of library match
386 * inchikey - inchikey of library match
387 * lpid - pid in database of library match
388 * mid - id of the match
389 382
390 383
391 .. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html 384 .. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html
392 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases 385 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
393 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases 386 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases