1use std::collections::HashSet;
2
3use crate::params::{ControlledVocabulary, ParamList, Param};
4use crate::impl_param_described;
5
6#[derive(Debug, Clone, Default, PartialEq, Eq)]
11#[cfg_attr(feature = "serde", derive(serde::Serialize, serde::Deserialize))]
12pub struct Software {
13 pub id: String,
15 pub version: String,
17 pub params: ParamList,
19}
20
21bitflags::bitflags! {
22 #[doc="A bit mask encoding the different kinds of software."]
23 #[derive(Debug, Clone, Copy, PartialEq)]
24 pub struct SoftwareType: u8 {
25 const None = 0;
26 const Analysis = 0b00000001;
27 const DataProcessing = 0b00000010;
28 const Acquisition = 0b00000100;
29 }
30}
31
32#[allow(unused)]
33impl SoftwareType {
34 pub const fn is_analysis(&self) -> bool {
36 self.contains(Self::Analysis)
37 }
38
39 pub const fn is_data_processing(&self) -> bool {
41 self.contains(Self::DataProcessing)
42 }
43
44 pub const fn is_acquisition(&self) -> bool {
46 self.contains(Self::Acquisition)
47 }
48}
49
50impl From<u8> for SoftwareType {
51 fn from(value: u8) -> Self {
52 Self::from_bits_retain(value)
53 }
54}
55
56impl Software {
57 pub fn new(id: String, version: String, params: ParamList) -> Self {
58 Self {
59 id,
60 version,
61 params,
62 }
63 }
64
65 pub fn find_software_term(&self) -> Option<SoftwareTerm> {
67 self.params
68 .iter()
69 .flat_map(|p| {
70 if let Some(i) = p.accession {
71 SoftwareTerm::from_accession(i)
72 } else {
73 None
74 }
75 })
76 .next()
77 }
78
79 pub fn is_analysis(&self) -> bool {
81 self.find_software_term().map(|s| s.flags().is_analysis()).unwrap_or(false)
82 }
83
84 pub fn is_data_processing(&self) -> bool {
86 self.find_software_term().map(|s| s.flags().is_data_processing()).unwrap_or(false)
87 }
88
89 pub fn is_acquisition(&self) -> bool {
91 self.find_software_term().map(|s| s.flags().is_acquisition()).unwrap_or(false)
92 }
93
94 pub fn find_unique_id<'a>(
96 id_stem: &str,
97 softwares: impl IntoIterator<Item = &'a Self>,
98 ) -> String {
99 let software_ids: HashSet<_> = softwares.into_iter().map(|sw| &sw.id).collect();
100 (0..)
101 .map(|i| format!("{id_stem}_{i}"))
102 .find(|s| !software_ids.contains(s))
103 .unwrap()
104 }
105}
106
107pub fn custom_software_name(name: &str) -> Param {
109 ControlledVocabulary::MS.param_val(1000799, "custom unreleased software tool", name)
110}
111
112impl_param_described!(Software);
113
114crate::cvmap! {
115 #[flag_type=SoftwareType]
116 #[allow(unused, clippy::upper_case_acronyms)]
117 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
118 #[cfg_attr(feature = "serde", derive(serde::Serialize, serde::Deserialize))]
119 pub enum SoftwareTerm {
127 #[term(cv=MS, accession=1000531, name="software", flags={0}, parents={[]})]
128 #[doc="software - Software related to the recording or transformation of spectra."]
129 Software,
130 #[term(cv=MS, accession=1000532, name="Xcalibur", flags={7}, parents={["MS:1000693", "MS:1003961", "MS:1001455", "MS:1001456", "MS:1001457"]})]
131 #[doc="Xcalibur - Thermo Finnigan software for data acquisition and analysis."]
132 Xcalibur,
133 #[term(cv=MS, accession=1000533, name="Bioworks", flags={3}, parents={["MS:1000693", "MS:1001456", "MS:1001457"]})]
134 #[doc="Bioworks - Thermo Finnigan software for data analysis of peptides and proteins."]
135 Bioworks,
136 #[term(cv=MS, accession=1000534, name="MassLynx", flags={7}, parents={["MS:1000694", "MS:1001455", "MS:1001456", "MS:1001457"]})]
137 #[doc="MassLynx - Micromass software for data acquisition and analysis."]
138 MassLynx,
139 #[term(cv=MS, accession=1000535, name="FlexAnalysis", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
140 #[doc="FlexAnalysis - Bruker software for data analysis."]
141 FlexAnalysis,
142 #[term(cv=MS, accession=1000536, name="Data Explorer", flags={7}, parents={["MS:1000691", "MS:1001455", "MS:1001456", "MS:1001457"]})]
143 #[doc="Data Explorer - Applied Biosystems software for data acquisition and analysis."]
144 DataExplorer,
145 #[term(cv=MS, accession=1000537, name="4700 Explorer", flags={7}, parents={["MS:1000691", "MS:1001455", "MS:1001456", "MS:1001457"]})]
146 #[doc="4700 Explorer - Applied Biosystems software for data acquisition and analysis."]
147 _4700Explorer,
148 #[term(cv=MS, accession=1000538, name="massWolf", flags={2}, parents={["MS:1001457"]})]
149 #[doc="massWolf - A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology."]
150 MassWolf,
151 #[term(cv=MS, accession=1000539, name="Voyager Biospectrometry Workstation System", flags={7}, parents={["MS:1000691", "MS:1001455", "MS:1001456", "MS:1001457"]})]
152 #[doc="Voyager Biospectrometry Workstation System - Applied Biosystems MALDI-TOF data acquisition and analysis system."]
153 VoyagerBiospectrometryWorkstationSystem,
154 #[term(cv=MS, accession=1000540, name="FlexControl", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
155 #[doc="FlexControl - Bruker software for data acquisition."]
156 FlexControl,
157 #[term(cv=MS, accession=1000541, name="ReAdW", flags={2}, parents={["MS:1001457"]})]
158 #[doc="ReAdW - A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced 'readraw'."]
159 ReAdW,
160 #[term(cv=MS, accession=1000542, name="MzStar", flags={2}, parents={["MS:1001457"]})]
161 #[doc="MzStar - A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program."]
162 MzStar,
163 #[term(cv=MS, accession=1000551, name="Analyst", flags={7}, parents={["MS:1000690", "MS:1001455", "MS:1001456", "MS:1001457"]})]
164 #[doc="Analyst - SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition."]
165 Analyst,
166 #[term(cv=MS, accession=1000553, name="Trapper", flags={2}, parents={["MS:1001457"]})]
167 #[doc="Trapper - A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology."]
168 Trapper,
169 #[term(cv=MS, accession=1000591, name="MzWiff", flags={2}, parents={["MS:1001457"]})]
170 #[doc="MzWiff - A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program."]
171 MzWiff,
172 #[term(cv=MS, accession=1000600, name="Proteios", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
173 #[doc="Proteios - Database application and analysis platform for proteomics."]
174 Proteios,
175 #[term(cv=MS, accession=1000601, name="ProteinLynx Global Server", flags={3}, parents={["MS:1000694", "MS:1001456", "MS:1001457"]})]
176 #[doc="ProteinLynx Global Server - Waters software for data analysis."]
177 ProteinLynxGlobalServer,
178 #[term(cv=MS, accession=1000615, name="ProteoWizard software", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
179 #[doc="ProteoWizard software - ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb."]
180 ProteoWizardSoftware,
181 #[term(cv=MS, accession=1000650, name="Proteome Discoverer", flags={3}, parents={["MS:1000693", "MS:1003961", "MS:1001456", "MS:1001457"]})]
182 #[doc="Proteome Discoverer - Thermo Scientific software for data analysis of peptides and proteins."]
183 ProteomeDiscoverer,
184 #[term(cv=MS, accession=1000659, name="4000 Series Explorer Software", flags={7}, parents={["MS:1000690", "MS:1001455", "MS:1001456", "MS:1001457"]})]
185 #[doc="4000 Series Explorer Software - SCIEX or Applied Biosystems software for data acquisition and analysis."]
186 _4000SeriesExplorerSoftware,
187 #[term(cv=MS, accession=1000661, name="GPS Explorer", flags={7}, parents={["MS:1000690", "MS:1001455", "MS:1001456", "MS:1001457"]})]
188 #[doc="GPS Explorer - SCIEX or Applied Biosystems software for data acquisition and analysis."]
189 GPSExplorer,
190 #[term(cv=MS, accession=1000662, name="LightSight Software", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
191 #[doc="LightSight Software - SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification."]
192 LightSightSoftware,
193 #[term(cv=MS, accession=1000663, name="ProteinPilot Software", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
194 #[doc="ProteinPilot Software - SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant."]
195 ProteinPilotSoftware,
196 #[term(cv=MS, accession=1000664, name="TissueView Software", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
197 #[doc="TissueView Software - Applied Biosystems|MDS SCIEX software for tissue imaging."]
198 TissueViewSoftware,
199 #[term(cv=MS, accession=1000665, name="MarkerView Software", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
200 #[doc="MarkerView Software - Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling."]
201 MarkerViewSoftware,
202 #[term(cv=MS, accession=1000666, name="MRMPilot Software", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
203 #[doc="MRMPilot Software - Applied Biosystems|MDS SCIEX software for MRM assay development."]
204 MRMPilotSoftware,
205 #[term(cv=MS, accession=1000667, name="BioAnalyst", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
206 #[doc="BioAnalyst - Applied Biosystems|MDS SCIEX software for bio-related data exploration."]
207 BioAnalyst,
208 #[term(cv=MS, accession=1000668, name="Pro ID", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
209 #[doc="Pro ID - Applied Biosystems|MDS SCIEX software for protein identification."]
210 ProID,
211 #[term(cv=MS, accession=1000669, name="Pro ICAT", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
212 #[doc="Pro ICAT - Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT."]
213 ProICAT,
214 #[term(cv=MS, accession=1000670, name="Pro Quant", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
215 #[doc="Pro Quant - Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ."]
216 ProQuant,
217 #[term(cv=MS, accession=1000671, name="Pro BLAST", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
218 #[doc="Pro BLAST - Applied Biosystems|MDS SCIEX software for MS-BLAST identification."]
219 ProBLAST,
220 #[term(cv=MS, accession=1000672, name="Cliquid", flags={0}, parents={["MS:1000690"]})]
221 #[doc="Cliquid - SCIEX Cliquid software for data analysis and quantitation."]
222 Cliquid,
223 #[term(cv=MS, accession=1000673, name="MIDAS Workflow Designer", flags={0}, parents={["MS:1000690"]})]
224 #[doc="MIDAS Workflow Designer - Applied Biosystems|MDS SCIEX software for MRM assay development."]
225 MIDASWorkflowDesigner,
226 #[term(cv=MS, accession=1000674, name="MultiQuant", flags={3}, parents={["MS:1000690", "MS:1001456", "MS:1001457"]})]
227 #[doc="MultiQuant - Applied Biosystems|MDS SCIEX software for MRM-based quantitation."]
228 MultiQuant,
229 #[term(cv=MS, accession=1000678, name="MassHunter Data Acquisition", flags={4}, parents={["MS:1000689", "MS:1001455"]})]
230 #[doc="MassHunter Data Acquisition - Software for data acquisition of 6000 series instruments."]
231 MassHunterDataAcquisition,
232 #[term(cv=MS, accession=1000679, name="MassHunter Easy Access", flags={4}, parents={["MS:1000689", "MS:1001455"]})]
233 #[doc="MassHunter Easy Access - Software for open access data acquisition."]
234 MassHunterEasyAccess,
235 #[term(cv=MS, accession=1000680, name="MassHunter Qualitative Analysis", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
236 #[doc="MassHunter Qualitative Analysis - Software for data analysis of data from 6000 series instruments."]
237 MassHunterQualitativeAnalysis,
238 #[term(cv=MS, accession=1000681, name="MassHunter Quantitative Analysis", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
239 #[doc="MassHunter Quantitative Analysis - Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data."]
240 MassHunterQuantitativeAnalysis,
241 #[term(cv=MS, accession=1000682, name="MassHunter Metabolite ID", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
242 #[doc="MassHunter Metabolite ID - Software for identification of metabolites."]
243 MassHunterMetaboliteID,
244 #[term(cv=MS, accession=1000683, name="MassHunter BioConfirm", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
245 #[doc="MassHunter BioConfirm - Software for protein characterization."]
246 MassHunterBioConfirm,
247 #[term(cv=MS, accession=1000684, name="Genespring MS", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
248 #[doc="Genespring MS - Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data."]
249 GenespringMS,
250 #[term(cv=MS, accession=1000685, name="MassHunter Mass Profiler", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
251 #[doc="MassHunter Mass Profiler - Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data."]
252 MassHunterMassProfiler,
253 #[term(cv=MS, accession=1000686, name="METLIN", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
254 #[doc="METLIN - Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites."]
255 METLIN,
256 #[term(cv=MS, accession=1000687, name="Spectrum Mill for MassHunter Workstation", flags={3}, parents={["MS:1000689", "MS:1001456", "MS:1001457"]})]
257 #[doc="Spectrum Mill for MassHunter Workstation - Software for protein identification and characterization of complex protein digest mixtures."]
258 SpectrumMillForMassHunterWorkstation,
259 #[term(cv=MS, accession=1000688, name="6300 Series Ion Trap Data Analysis Software", flags={7}, parents={["MS:1000689", "MS:1001455", "MS:1001456", "MS:1001457"]})]
260 #[doc="6300 Series Ion Trap Data Analysis Software - Software for data analysis of 6300 series ion trap mass spectrometers."]
261 _6300SeriesIonTrapDataAnalysisSoftware,
262 #[term(cv=MS, accession=1000689, name="Agilent software", flags={0}, parents={["MS:1000531"]})]
263 #[doc="Agilent software - Agilent software for data acquisition and analysis."]
264 AgilentSoftware,
265 #[term(cv=MS, accession=1000690, name="SCIEX software", flags={0}, parents={["MS:1000531"]})]
266 #[doc="SCIEX software - SCIEX or Applied Biosystems software for data acquisition and analysis."]
267 SCIEXSoftware,
268 #[term(cv=MS, accession=1000691, name="Applied Biosystems software", flags={0}, parents={["MS:1000531"]})]
269 #[doc="Applied Biosystems software - Applied Biosystems|MDS SCIEX software for data acquisition and analysis."]
270 AppliedBiosystemsSoftware,
271 #[term(cv=MS, accession=1000692, name="Bruker software", flags={0}, parents={["MS:1000531"]})]
272 #[doc="Bruker software - Bruker software for data acquisition and analysis."]
273 BrukerSoftware,
274 #[term(cv=MS, accession=1000693, name="Thermo Finnigan software", flags={0}, parents={["MS:1000531"]})]
275 #[doc="Thermo Finnigan software - Thermo Finnigan software for data acquisition and analysis."]
276 ThermoFinniganSoftware,
277 #[term(cv=MS, accession=1000694, name="Waters software", flags={0}, parents={["MS:1000531"]})]
278 #[doc="Waters software - Waters software for data acquisition and analysis."]
279 WatersSoftware,
280 #[term(cv=MS, accession=1000706, name="apexControl", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
281 #[doc="apexControl - Bruker software for data acquisition."]
282 ApexControl,
283 #[term(cv=MS, accession=1000707, name="BioTools", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
284 #[doc="BioTools - Bruker software for data analysis."]
285 BioTools,
286 #[term(cv=MS, accession=1000708, name="CLINPROT", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
287 #[doc="CLINPROT - Bruker CLINPROT software."]
288 CLINPROT,
289 #[term(cv=MS, accession=1000709, name="CLINPROT micro", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
290 #[doc="CLINPROT micro - Bruker CLINPROT micro software."]
291 CLINPROTMicro,
292 #[term(cv=MS, accession=1000710, name="CLINPROT robot", flags={0}, parents={["MS:1000692"]})]
293 #[doc="CLINPROT robot - Bruker CLINPROT robot software."]
294 CLINPROTRobot,
295 #[term(cv=MS, accession=1000711, name="ClinProTools", flags={0}, parents={["MS:1000692"]})]
296 #[doc="ClinProTools - Bruker ClinProTools software."]
297 ClinProTools,
298 #[term(cv=MS, accession=1000712, name="Compass", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
299 #[doc="Compass - Bruker Compass software."]
300 Compass,
301 #[term(cv=MS, accession=1000713, name="Compass for HCT/esquire", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
302 #[doc="Compass for HCT/esquire - Bruker Compass for HCT/esquire software."]
303 CompassForHCTEsquire,
304 #[term(cv=MS, accession=1000714, name="Compass for micrOTOF", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
305 #[doc="Compass for micrOTOF - Bruker Compass for micrOTOF software."]
306 CompassForMicrOTOF,
307 #[term(cv=MS, accession=1000715, name="Compass OpenAccess", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
308 #[doc="Compass OpenAccess - Bruker compass OpenAccess software."]
309 CompassOpenAccess,
310 #[term(cv=MS, accession=1000716, name="Compass Security Pack", flags={0}, parents={["MS:1000692"]})]
311 #[doc="Compass Security Pack - Bruker compass Security Pack software."]
312 CompassSecurityPack,
313 #[term(cv=MS, accession=1000717, name="CompassXport", flags={2}, parents={["MS:1000692", "MS:1001457"]})]
314 #[doc="CompassXport - Bruker stand-alone software for data conversion."]
315 CompassXport,
316 #[term(cv=MS, accession=1000718, name="CompassXtract", flags={2}, parents={["MS:1000692", "MS:1001457"]})]
317 #[doc="CompassXtract - Bruker software library for data access."]
318 CompassXtract,
319 #[term(cv=MS, accession=1000719, name="DataAnalysis", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
320 #[doc="DataAnalysis - Bruker software for data analysis."]
321 DataAnalysis,
322 #[term(cv=MS, accession=1000720, name="dpControl", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
323 #[doc="dpControl - Bruker software for data acquisition."]
324 DpControl,
325 #[term(cv=MS, accession=1000721, name="esquireControl", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
326 #[doc="esquireControl - Bruker software for data acquisition."]
327 EsquireControl,
328 #[term(cv=MS, accession=1000722, name="flexImaging", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
329 #[doc="flexImaging - Bruker software for data analysis."]
330 FlexImaging,
331 #[term(cv=MS, accession=1000723, name="GENOLINK", flags={0}, parents={["MS:1000692"]})]
332 #[doc="GENOLINK - Bruker GENOLINK software."]
333 GENOLINK,
334 #[term(cv=MS, accession=1000724, name="GenoTools", flags={0}, parents={["MS:1000692"]})]
335 #[doc="GenoTools - Bruker GenoTools software."]
336 GenoTools,
337 #[term(cv=MS, accession=1000725, name="HCTcontrol", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
338 #[doc="HCTcontrol - Bruker software for data acquisition."]
339 HCTcontrol,
340 #[term(cv=MS, accession=1000726, name="micrOTOFcontrol", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
341 #[doc="micrOTOFcontrol - Bruker software for data acquisition."]
342 MicrOTOFcontrol,
343 #[term(cv=MS, accession=1000727, name="PolyTools", flags={0}, parents={["MS:1000692"]})]
344 #[doc="PolyTools - Bruker PolyTools software."]
345 PolyTools,
346 #[term(cv=MS, accession=1000728, name="ProfileAnalysis", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
347 #[doc="ProfileAnalysis - Bruker software for data analysis."]
348 ProfileAnalysis,
349 #[term(cv=MS, accession=1000729, name="PROTEINEER", flags={0}, parents={["MS:1000692"]})]
350 #[doc="PROTEINEER - Bruker PROTEINEER software."]
351 PROTEINEER,
352 #[term(cv=MS, accession=1000730, name="PROTEINEER dp", flags={0}, parents={["MS:1000692"]})]
353 #[doc="PROTEINEER dp - Bruker PROTEINEER dp software."]
354 PROTEINEERDp,
355 #[term(cv=MS, accession=1000731, name="PROTEINEER fc", flags={0}, parents={["MS:1000692"]})]
356 #[doc="PROTEINEER fc - Bruker PROTEINEER fc software."]
357 PROTEINEERFc,
358 #[term(cv=MS, accession=1000732, name="PROTEINEER spII", flags={0}, parents={["MS:1000692"]})]
359 #[doc="PROTEINEER spII - Bruker PROTEINEER spII software."]
360 PROTEINEERSpII,
361 #[term(cv=MS, accession=1000733, name="PROTEINEER-LC", flags={0}, parents={["MS:1000692"]})]
362 #[doc="PROTEINEER-LC - Bruker PROTEINEER-LC software."]
363 PROTEINEERLC,
364 #[term(cv=MS, accession=1000734, name="ProteinScape", flags={1}, parents={["MS:1000692", "MS:1001456"]})]
365 #[doc="ProteinScape - Bruker ProteinScape software."]
366 ProteinScape,
367 #[term(cv=MS, accession=1000735, name="PureDisk", flags={0}, parents={["MS:1000692"]})]
368 #[doc="PureDisk - BrukerPureDisk software."]
369 PureDisk,
370 #[term(cv=MS, accession=1000736, name="QuantAnalysis", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
371 #[doc="QuantAnalysis - Bruker software for data analysis."]
372 QuantAnalysis,
373 #[term(cv=MS, accession=1000737, name="spControl", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
374 #[doc="spControl - Bruker software for data acquisition."]
375 SpControl,
376 #[term(cv=MS, accession=1000738, name="TargetAnalysis", flags={0}, parents={["MS:1000692"]})]
377 #[doc="TargetAnalysis - Bruker TargetAnalysis software."]
378 TargetAnalysis,
379 #[term(cv=MS, accession=1000739, name="WARP-LC", flags={0}, parents={["MS:1000692", "MS:1001139"]})]
380 #[doc="WARP-LC - Bruker WARP-LC software."]
381 WARPLC,
382 #[term(cv=MS, accession=1000752, name="TOPP software", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
383 #[doc="TOPP software - TOPP (The OpenMS proteomics pipeline) software."]
384 TOPPSoftware,
385 #[term(cv=MS, accession=1000753, name="BaselineFilter", flags={0}, parents={["MS:1000752"]})]
386 #[doc="BaselineFilter - Removes the baseline from profile spectra using a top-hat filter."]
387 BaselineFilter,
388 #[term(cv=MS, accession=1000754, name="DBExporter", flags={0}, parents={["MS:1000752"]})]
389 #[doc="DBExporter - Exports data from an OpenMS database to a file."]
390 DBExporter,
391 #[term(cv=MS, accession=1000755, name="DBImporter", flags={0}, parents={["MS:1000752"]})]
392 #[doc="DBImporter - Imports data to an OpenMS database."]
393 DBImporter,
394 #[term(cv=MS, accession=1000756, name="FileConverter", flags={0}, parents={["MS:1000752"]})]
395 #[doc="FileConverter - Converts between different MS file formats."]
396 FileConverter,
397 #[term(cv=MS, accession=1000757, name="FileFilter", flags={0}, parents={["MS:1000752"]})]
398 #[doc="FileFilter - Extracts or manipulates portions of data from peak, feature or consensus feature files."]
399 FileFilter,
400 #[term(cv=MS, accession=1000758, name="FileMerger", flags={0}, parents={["MS:1000752"]})]
401 #[doc="FileMerger - Merges several MS files into one file."]
402 FileMerger,
403 #[term(cv=MS, accession=1000759, name="InternalCalibration", flags={0}, parents={["MS:1000752"]})]
404 #[doc="InternalCalibration - Applies an internal calibration."]
405 InternalCalibration,
406 #[term(cv=MS, accession=1000760, name="MapAligner", flags={0}, parents={["MS:1000752"]})]
407 #[doc="MapAligner - OBSOLETE Corrects retention time distortions between maps."]
408 MapAligner,
409 #[term(cv=MS, accession=1000761, name="MapNormalizer", flags={0}, parents={["MS:1000752"]})]
410 #[doc="MapNormalizer - Normalizes peak intensities in an MS run."]
411 MapNormalizer,
412 #[term(cv=MS, accession=1000762, name="NoiseFilter", flags={0}, parents={["MS:1000752"]})]
413 #[doc="NoiseFilter - OBSOLETE Removes noise from profile spectra by using different smoothing techniques."]
414 NoiseFilter,
415 #[term(cv=MS, accession=1000763, name="PeakPicker", flags={0}, parents={["MS:1000752"]})]
416 #[doc="PeakPicker - OBSOLETE Finds mass spectrometric peaks in profile mass spectra."]
417 PeakPicker,
418 #[term(cv=MS, accession=1000764, name="Resampler", flags={0}, parents={["MS:1000752"]})]
419 #[doc="Resampler - Transforms an LC/MS map into a resampled map or a png image."]
420 Resampler,
421 #[term(cv=MS, accession=1000765, name="SpectraFilter", flags={0}, parents={["MS:1000752"]})]
422 #[doc="SpectraFilter - OBSOLETE Applies a filter to peak spectra."]
423 SpectraFilter,
424 #[term(cv=MS, accession=1000766, name="TOFCalibration", flags={0}, parents={["MS:1000752"]})]
425 #[doc="TOFCalibration - Applies time of flight calibration."]
426 TOFCalibration,
427 #[term(cv=MS, accession=1000799, name="custom unreleased software tool", flags={0}, parents={["MS:1000531"]})]
428 #[doc="custom unreleased software tool - A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added."]
429 CustomUnreleasedSoftwareTool,
430 #[term(cv=MS, accession=1000817, name="HyStar", flags={0}, parents={["MS:1000692"]})]
431 #[doc="HyStar - Bruker software for hyphenated experiments."]
432 HyStar,
433 #[term(cv=MS, accession=1000871, name="SRM software", flags={0}, parents={["MS:1000531"]})]
434 #[doc="SRM software - Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs."]
435 SRMSoftware,
436 #[term(cv=MS, accession=1000872, name="MaRiMba", flags={0}, parents={["MS:1000871"]})]
437 #[doc="MaRiMba - Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology."]
438 MaRiMba,
439 #[term(cv=MS, accession=1000873, name="peptide attribute calculation software", flags={0}, parents={["MS:1000531"]})]
440 #[doc="peptide attribute calculation software - Software used to predict or calculate numerical attributes of peptides."]
441 PeptideAttributeCalculationSoftware,
442 #[term(cv=MS, accession=1000874, name="SSRCalc", flags={0}, parents={["MS:1000873"]})]
443 #[doc="SSRCalc - Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence."]
444 SSRCalc,
445 #[term(cv=MS, accession=1000922, name="Skyline", flags={0}, parents={["MS:1000871", "MS:1001139"]})]
446 #[doc="Skyline - Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington."]
447 Skyline,
448 #[term(cv=MS, accession=1000923, name="TIQAM", flags={0}, parents={["MS:1000871"]})]
449 #[doc="TIQAM - Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology."]
450 TIQAM,
451 #[term(cv=MS, accession=1000925, name="ATAQS", flags={0}, parents={["MS:1000871"]})]
452 #[doc="ATAQS - Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology."]
453 ATAQS,
454 #[term(cv=MS, accession=1001139, name="quantitation software name", flags={0}, parents={["MS:1000531", "MS:1001129"]})]
455 #[doc="quantitation software name - Quantitation software name."]
456 QuantitationSoftwareName,
457 #[term(cv=MS, accession=1001207, name="Mascot", flags={1}, parents={["MS:1001456"]})]
458 #[doc="Mascot - The name of the Mascot search engine."]
459 Mascot,
460 #[term(cv=MS, accession=1001208, name="SEQUEST", flags={1}, parents={["MS:1001456"]})]
461 #[doc="SEQUEST - The name of the SEQUEST search engine."]
462 SEQUEST,
463 #[term(cv=MS, accession=1001209, name="Phenyx", flags={1}, parents={["MS:1001456"]})]
464 #[doc="Phenyx - The name of the Phenyx search engine."]
465 Phenyx,
466 #[term(cv=MS, accession=1001327, name="Spectronaut", flags={1}, parents={["MS:1001456", "MS:1003207"]})]
467 #[doc="Spectronaut - Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data."]
468 Spectronaut,
469 #[term(cv=MS, accession=1001455, name="acquisition software", flags={0}, parents={["MS:1000531"]})]
470 #[doc="acquisition software - Acquisition software."]
471 AcquisitionSoftware,
472 #[term(cv=MS, accession=1001456, name="analysis software", flags={0}, parents={["MS:1000531"]})]
473 #[doc="analysis software - Analysis software."]
474 AnalysisSoftware,
475 #[term(cv=MS, accession=1001457, name="data processing software", flags={0}, parents={["MS:1000531"]})]
476 #[doc="data processing software - Data processing software."]
477 DataProcessingSoftware,
478 #[term(cv=MS, accession=1001461, name="greylag", flags={1}, parents={["MS:1001456"]})]
479 #[doc="greylag - Greylag identification software."]
480 Greylag,
481 #[term(cv=MS, accession=1001475, name="OMSSA", flags={1}, parents={["MS:1001456"]})]
482 #[doc="OMSSA - Open Mass Spectrometry Search Algorithm was used to analyze the spectra."]
483 OMSSA,
484 #[term(cv=MS, accession=1001476, name="X!Tandem", flags={1}, parents={["MS:1001456"]})]
485 #[doc="X!Tandem - X!Tandem was used to analyze the spectra."]
486 XTandem,
487 #[term(cv=MS, accession=1001477, name="SpectraST", flags={1}, parents={["MS:1001456", "MS:1003207", "MS:1003406"]})]
488 #[doc="SpectraST - Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline."]
489 SpectraST,
490 #[term(cv=MS, accession=1001478, name="Mascot Parser", flags={1}, parents={["MS:1001456"]})]
491 #[doc="Mascot Parser - Mascot Parser was used to analyze the spectra."]
492 MascotParser,
493 #[term(cv=MS, accession=1001483, name="SCIEX TOF/TOF Series Explorer Software", flags={7}, parents={["MS:1000690", "MS:1001455", "MS:1001456", "MS:1001457"]})]
494 #[doc="SCIEX TOF/TOF Series Explorer Software - SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis."]
495 SCIEXTOFTOFSeriesExplorerSoftware,
496 #[term(cv=MS, accession=1001487, name="ProteinExtractor", flags={1}, parents={["MS:1000692", "MS:1001456"]})]
497 #[doc="ProteinExtractor - An algorithm for protein determination/assembly integrated into Bruker's ProteinScape."]
498 ProteinExtractor,
499 #[term(cv=MS, accession=1001488, name="Mascot Distiller", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
500 #[doc="Mascot Distiller - Mascot Distiller."]
501 MascotDistiller,
502 #[term(cv=MS, accession=1001489, name="Mascot Integra", flags={1}, parents={["MS:1001456"]})]
503 #[doc="Mascot Integra - Mascot Integra."]
504 MascotIntegra,
505 #[term(cv=MS, accession=1001490, name="Percolator", flags={1}, parents={["MS:1001456"]})]
506 #[doc="Percolator - Percolator."]
507 Percolator,
508 #[term(cv=MS, accession=1001557, name="Shimadzu Corporation software", flags={0}, parents={["MS:1000531"]})]
509 #[doc="Shimadzu Corporation software - Shimadzu Corporation software."]
510 ShimadzuCorporationSoftware,
511 #[term(cv=MS, accession=1001558, name="MALDI Solutions", flags={7}, parents={["MS:1001455", "MS:1001456", "MS:1001457", "MS:1001557"]})]
512 #[doc="MALDI Solutions - Shimadzu Biotech software for data acquisition, processing, and analysis."]
513 MALDISolutions,
514 #[term(cv=MS, accession=1001561, name="Scaffold", flags={1}, parents={["MS:1001456"]})]
515 #[doc="Scaffold - Scaffold analysis software."]
516 Scaffold,
517 #[term(cv=MS, accession=1001582, name="XCMS", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
518 #[doc="XCMS - Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data."]
519 XCMS,
520 #[term(cv=MS, accession=1001583, name="MaxQuant", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
521 #[doc="MaxQuant - MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data."]
522 MaxQuant,
523 #[term(cv=MS, accession=1001585, name="MyriMatch", flags={1}, parents={["MS:1001456"]})]
524 #[doc="MyriMatch - Tabb Lab software for directly comparing peptides in a database to tandem mass spectra."]
525 MyriMatch,
526 #[term(cv=MS, accession=1001586, name="DirecTag", flags={1}, parents={["MS:1001456"]})]
527 #[doc="DirecTag - Tabb Lab software for generating sequence tags from tandem mass spectra."]
528 DirecTag,
529 #[term(cv=MS, accession=1001587, name="TagRecon", flags={1}, parents={["MS:1001456"]})]
530 #[doc="TagRecon - Tabb Lab software for reconciling sequence tags to a protein database."]
531 TagRecon,
532 #[term(cv=MS, accession=1001588, name="Pepitome", flags={1}, parents={["MS:1001456"]})]
533 #[doc="Pepitome - Tabb Lab software for spectral library searches on tandem mass spectra."]
534 Pepitome,
535 #[term(cv=MS, accession=1001795, name="Empower", flags={3}, parents={["MS:1000694", "MS:1001456", "MS:1001457"]})]
536 #[doc="Empower - Waters Empower software for liquid chromatography and mass spectrometry acquisition."]
537 Empower,
538 #[term(cv=MS, accession=1001796, name="UNIFY", flags={3}, parents={["MS:1000694", "MS:1001456", "MS:1001457"]})]
539 #[doc="UNIFY - Waters UNIFY software for liquid chromatography and mass spectrometry acquisition."]
540 UNIFY,
541 #[term(cv=MS, accession=1001798, name="LECO software", flags={0}, parents={["MS:1000531"]})]
542 #[doc="LECO software - LECO software for data acquisition and analysis."]
543 LECOSoftware,
544 #[term(cv=MS, accession=1001799, name="ChromaTOF software", flags={7}, parents={["MS:1001455", "MS:1001456", "MS:1001457", "MS:1001798"]})]
545 #[doc="ChromaTOF software - Software for acquisition, processing and analysis of data for LECO instruments."]
546 ChromaTOFSoftware,
547 #[term(cv=MS, accession=1001830, name="Progenesis LC-MS", flags={0}, parents={["MS:1001139"]})]
548 #[doc="Progenesis LC-MS - Software from Nonlinear Dynamics for LC-MS label-free workflow."]
549 ProgenesisLCMS,
550 #[term(cv=MS, accession=1001831, name="SILACAnalyzer", flags={0}, parents={["MS:1001139", "MS:1000752"]})]
551 #[doc="SILACAnalyzer - Software for SILAC workflow."]
552 SILACAnalyzer,
553 #[term(cv=MS, accession=1001877, name="ChromaTOF HRT software", flags={7}, parents={["MS:1001455", "MS:1001456", "MS:1001457", "MS:1001798"]})]
554 #[doc="ChromaTOF HRT software - Software for acquisition, processing and analysis of data for LECO instruments."]
555 ChromaTOFHRTSoftware,
556 #[term(cv=MS, accession=1001878, name="MALDI Solutions Microbial Identification", flags={0}, parents={["MS:1001558"]})]
557 #[doc="MALDI Solutions Microbial Identification - Shimadzu Biotech software for data acquisition, processing, and analysis."]
558 MALDISolutionsMicrobialIdentification,
559 #[term(cv=MS, accession=1001886, name="SQID", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
560 #[doc="SQID - Software for data analysis of peptides and proteins."]
561 SQID,
562 #[term(cv=MS, accession=1001912, name="PinPoint", flags={3}, parents={["MS:1000693", "MS:1003961", "MS:1001456", "MS:1001457"]})]
563 #[doc="PinPoint - Thermo Scientific PinPoint SRM analysis software."]
564 PinPoint,
565 #[term(cv=MS, accession=1001914, name="pymzML", flags={2}, parents={["MS:1001457"]})]
566 #[doc="pymzML - Python module to interface mzML Data."]
567 PymzML,
568 #[term(cv=MS, accession=1001946, name="PEAKS Studio", flags={3}, parents={["MS:1001139", "MS:1001456", "MS:1001457"]})]
569 #[doc="PEAKS Studio - PEAKS Studio software for data analysis."]
570 PEAKSStudio,
571 #[term(cv=MS, accession=1001947, name="PEAKS Online", flags={3}, parents={["MS:1001139", "MS:1001456", "MS:1001457"]})]
572 #[doc="PEAKS Online - PEAKS Online software for high throughput data analysis."]
573 PEAKSOnline,
574 #[term(cv=MS, accession=1001948, name="PEAKS Node", flags={3}, parents={["MS:1001139", "MS:1001456", "MS:1001457"]})]
575 #[doc="PEAKS Node - PEAKS Node software for high throughput data analysis."]
576 PEAKSNode,
577 #[term(cv=MS, accession=1001949, name="BSI software", flags={0}, parents={["MS:1000531"]})]
578 #[doc="BSI software - Bioinformatics Solutions Inc. Software for data processing and analysis."]
579 BSISoftware,
580 #[term(cv=MS, accession=1001973, name="DeBunker", flags={1}, parents={["MS:1001456"]})]
581 #[doc="DeBunker - DeBunker software."]
582 DeBunker,
583 #[term(cv=MS, accession=1001977, name="MSQuant", flags={1}, parents={["MS:1001456"]})]
584 #[doc="MSQuant - MSQuant software."]
585 MSQuant,
586 #[term(cv=MS, accession=1001984, name="Ascore software", flags={1}, parents={["MS:1001456"]})]
587 #[doc="Ascore software - Ascore software."]
588 AscoreSoftware,
589 #[term(cv=MS, accession=1002043, name="ProteinProspector", flags={1}, parents={["MS:1001456"]})]
590 #[doc="ProteinProspector - ProteinProspector software for data acquisition and analysis."]
591 ProteinProspector,
592 #[term(cv=MS, accession=1002047, name="MS-GF", flags={1}, parents={["MS:1001456"]})]
593 #[doc="MS-GF - MS-GF software used to re-score the peptide-spectrum matches."]
594 MSGF,
595 #[term(cv=MS, accession=1002048, name="MS-GF+", flags={1}, parents={["MS:1001456"]})]
596 #[doc="MS-GF+ - MS-GF+ software used to analyze the spectra."]
597 MSGFplus,
598 #[term(cv=MS, accession=1002059, name="Microsoft Excel", flags={0}, parents={["MS:1001139"]})]
599 #[doc="Microsoft Excel - Microsoft Excel (can be used for spectral counting)."]
600 MicrosoftExcel,
601 #[term(cv=MS, accession=1002063, name="FindPairs", flags={0}, parents={["MS:1001139"]})]
602 #[doc="FindPairs - Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite."]
603 FindPairs,
604 #[term(cv=MS, accession=1002076, name="PAnalyzer", flags={1}, parents={["MS:1001456"]})]
605 #[doc="PAnalyzer - PAnalyzer software for getting protein evidence categories."]
606 PAnalyzer,
607 #[term(cv=MS, accession=1002123, name="x-Tracker", flags={0}, parents={["MS:1001139"]})]
608 #[doc="x-Tracker - X-Tracker generic tool for quantitative proteomics."]
609 XTracker,
610 #[term(cv=MS, accession=1002124, name="ProteoSuite", flags={0}, parents={["MS:1001139"]})]
611 #[doc="ProteoSuite - ProteoSuite software for the analysis of quantitative proteomics data."]
612 ProteoSuite,
613 #[term(cv=MS, accession=1002129, name="ITRAQAnalyzer", flags={0}, parents={["MS:1001139", "MS:1000752"]})]
614 #[doc="ITRAQAnalyzer - Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment."]
615 ITRAQAnalyzer,
616 #[term(cv=MS, accession=1002131, name="TOPP noise filter", flags={0}, parents={["MS:1000752"]})]
617 #[doc="TOPP noise filter - Noise filter component of the TOPP software."]
618 TOPPNoiseFilter,
619 #[term(cv=MS, accession=1002132, name="TOPP NoiseFilterGaussian", flags={0}, parents={["MS:1002131"]})]
620 #[doc="TOPP NoiseFilterGaussian - Removes noise from profile spectra by using a gaussian smoothing."]
621 TOPPNoiseFilterGaussian,
622 #[term(cv=MS, accession=1002133, name="TOPP NoiseFilterSGolay", flags={0}, parents={["MS:1002131"]})]
623 #[doc="TOPP NoiseFilterSGolay - Removes noise from profile spectra by using a Savitzky-Golay smoothing."]
624 TOPPNoiseFilterSGolay,
625 #[term(cv=MS, accession=1002134, name="TOPP peak picker", flags={0}, parents={["MS:1000752"]})]
626 #[doc="TOPP peak picker - Peak picker component of the TOPP software."]
627 TOPPPeakPicker,
628 #[term(cv=MS, accession=1002135, name="TOPP PeakPickerHiRes", flags={0}, parents={["MS:1002134"]})]
629 #[doc="TOPP PeakPickerHiRes - Finds mass spectrometric peaks in high-resoluted profile mass spectra."]
630 TOPPPeakPickerHiRes,
631 #[term(cv=MS, accession=1002136, name="TOPP PeakPickerWavelet", flags={0}, parents={["MS:1002134"]})]
632 #[doc="TOPP PeakPickerWavelet - Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra."]
633 TOPPPeakPickerWavelet,
634 #[term(cv=MS, accession=1002137, name="TOPP spectra filter", flags={0}, parents={["MS:1000752"]})]
635 #[doc="TOPP spectra filter - Spectra filter component of the TOPP software."]
636 TOPPSpectraFilter,
637 #[term(cv=MS, accession=1002138, name="TOPP SpectraFilterBernNorm", flags={0}, parents={["MS:1002137"]})]
638 #[doc="TOPP SpectraFilterBernNorm - Applies a Bern et al normalization to peak spectra."]
639 TOPPSpectraFilterBernNorm,
640 #[term(cv=MS, accession=1002139, name="TOPP SpectraFilterMarkerMower", flags={0}, parents={["MS:1002137"]})]
641 #[doc="TOPP SpectraFilterMarkerMower - Applies a filter to peak spectra for marked peaks."]
642 TOPPSpectraFilterMarkerMower,
643 #[term(cv=MS, accession=1002140, name="TOPP SpectraFilterNLargest", flags={0}, parents={["MS:1002137"]})]
644 #[doc="TOPP SpectraFilterNLargest - Retains the n largest peaks of a peak spectra."]
645 TOPPSpectraFilterNLargest,
646 #[term(cv=MS, accession=1002141, name="TOPP SpectraFilterNormalizer", flags={0}, parents={["MS:1002137"]})]
647 #[doc="TOPP SpectraFilterNormalizer - Applies a TIC/maximal intensity normalization to peak spectra."]
648 TOPPSpectraFilterNormalizer,
649 #[term(cv=MS, accession=1002142, name="TOPP SpectraFilterParentPeakMower", flags={0}, parents={["MS:1002137"]})]
650 #[doc="TOPP SpectraFilterParentPeakMower - Filters putative unfragmented precursor ions from tandem spectra."]
651 TOPPSpectraFilterParentPeakMower,
652 #[term(cv=MS, accession=1002143, name="TOPP SpectraFilterScaler", flags={0}, parents={["MS:1002137"]})]
653 #[doc="TOPP SpectraFilterScaler - Applies a filter to peak spectra after intensity scaling according to rank."]
654 TOPPSpectraFilterScaler,
655 #[term(cv=MS, accession=1002144, name="TOPP SpectraFilterSqrtMower", flags={0}, parents={["MS:1002137"]})]
656 #[doc="TOPP SpectraFilterSqrtMower - Applies a filter to peak spectra after intensity scaling to the square root."]
657 TOPPSpectraFilterSqrtMower,
658 #[term(cv=MS, accession=1002145, name="TOPP SpectraFilterThresholdMower", flags={0}, parents={["MS:1002137"]})]
659 #[doc="TOPP SpectraFilterThresholdMower - Applies a filter of peaks below a given threshold to peak spectra."]
660 TOPPSpectraFilterThresholdMower,
661 #[term(cv=MS, accession=1002146, name="TOPP SpectraFilterWindowMower", flags={0}, parents={["MS:1002137"]})]
662 #[doc="TOPP SpectraFilterWindowMower - Applies a filter of the largest peaks in a sliding window over a peak spectrum."]
663 TOPPSpectraFilterWindowMower,
664 #[term(cv=MS, accession=1002147, name="TOPP map aligner", flags={0}, parents={["MS:1000752"]})]
665 #[doc="TOPP map aligner - Map aligner component of the TOPP software."]
666 TOPPMapAligner,
667 #[term(cv=MS, accession=1002148, name="TOPP MapAlignerIdentification", flags={0}, parents={["MS:1002147"]})]
668 #[doc="TOPP MapAlignerIdentification - Corrects retention time distortions between maps based on common peptide identifications."]
669 TOPPMapAlignerIdentification,
670 #[term(cv=MS, accession=1002149, name="TOPP MapAlignerPoseClustering", flags={0}, parents={["MS:1002147"]})]
671 #[doc="TOPP MapAlignerPoseClustering - Corrects retention time distortions between maps using a pose clustering approach."]
672 TOPPMapAlignerPoseClustering,
673 #[term(cv=MS, accession=1002150, name="TOPP MapAlignerSpectrum", flags={0}, parents={["MS:1002147"]})]
674 #[doc="TOPP MapAlignerSpectrum - Corrects retention time distortions between maps by spectrum alignment."]
675 TOPPMapAlignerSpectrum,
676 #[term(cv=MS, accession=1002154, name="TOPP DTAExtractor", flags={0}, parents={["MS:1000752"]})]
677 #[doc="TOPP DTAExtractor - Extracts spectra of an MS run file to several files in DTA format."]
678 TOPPDTAExtractor,
679 #[term(cv=MS, accession=1002155, name="TOPP IDMerger", flags={0}, parents={["MS:1000752"]})]
680 #[doc="TOPP IDMerger - Merges several protein/peptide identification files into one file."]
681 TOPPIDMerger,
682 #[term(cv=MS, accession=1002156, name="TOPP IDFileConverter", flags={0}, parents={["MS:1000752"]})]
683 #[doc="TOPP IDFileConverter - Converts identification engine file formats."]
684 TOPPIDFileConverter,
685 #[term(cv=MS, accession=1002157, name="TOPP SpectraMerger", flags={0}, parents={["MS:1000752"]})]
686 #[doc="TOPP SpectraMerger - Merges spectra from an LC/MS map, either by precursor or by RT blocks."]
687 TOPPSpectraMerger,
688 #[term(cv=MS, accession=1002158, name="TOPP MzTabExporter", flags={0}, parents={["MS:1000752"]})]
689 #[doc="TOPP MzTabExporter - Exports various XML formats to an mzTab file."]
690 TOPPMzTabExporter,
691 #[term(cv=MS, accession=1002159, name="TOPP MassTraceExtractor", flags={0}, parents={["MS:1000752"]})]
692 #[doc="TOPP MassTraceExtractor - Annotates mass traces in centroided LC/MS maps."]
693 TOPPMassTraceExtractor,
694 #[term(cv=MS, accession=1002160, name="TOPP PrecursorMassCorrector", flags={0}, parents={["MS:1000752"]})]
695 #[doc="TOPP PrecursorMassCorrector - Correct the precursor entries of tandem MS scans."]
696 TOPPPrecursorMassCorrector,
697 #[term(cv=MS, accession=1002161, name="TOPP HighResPrecursorMassCorrector", flags={0}, parents={["MS:1000752"]})]
698 #[doc="TOPP HighResPrecursorMassCorrector - Performs precursor mz correction on centroided high resolution data."]
699 TOPPHighResPrecursorMassCorrector,
700 #[term(cv=MS, accession=1002162, name="TOPP AdditiveSeries", flags={0}, parents={["MS:1000752"]})]
701 #[doc="TOPP AdditiveSeries - Computes an additive series to quantify a peptide in a set of samples."]
702 TOPPAdditiveSeries,
703 #[term(cv=MS, accession=1002163, name="TOPP Decharger", flags={0}, parents={["MS:1000752"]})]
704 #[doc="TOPP Decharger - Decharges and merges different feature charge variants of the same chemical entity."]
705 TOPPDecharger,
706 #[term(cv=MS, accession=1002164, name="TOPP EICExtractor", flags={0}, parents={["MS:1000752"]})]
707 #[doc="TOPP EICExtractor - Quantifies signals at given positions in (raw or picked) LC/MS maps."]
708 TOPPEICExtractor,
709 #[term(cv=MS, accession=1002165, name="TOPP feature finder", flags={0}, parents={["MS:1000752"]})]
710 #[doc="TOPP feature finder - Feature finder component of the TOPP software."]
711 TOPPFeatureFinder,
712 #[term(cv=MS, accession=1002166, name="TOPP FeatureFinderCentroided", flags={0}, parents={["MS:1002165"]})]
713 #[doc="TOPP FeatureFinderCentroided - Detects two-dimensional features in centroided LC-MS data."]
714 TOPPFeatureFinderCentroided,
715 #[term(cv=MS, accession=1002167, name="TOPP FeatureFinderRaw", flags={0}, parents={["MS:1002165"]})]
716 #[doc="TOPP FeatureFinderRaw - Detects two-dimensional features in uncentroided LC-MS data."]
717 TOPPFeatureFinderRaw,
718 #[term(cv=MS, accession=1002168, name="TOPP FeatureFinderIsotopeWavelet", flags={0}, parents={["MS:1002165"]})]
719 #[doc="TOPP FeatureFinderIsotopeWavelet - Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm."]
720 TOPPFeatureFinderIsotopeWavelet,
721 #[term(cv=MS, accession=1002169, name="TOPP FeatureFinderMetabo", flags={0}, parents={["MS:1002165"]})]
722 #[doc="TOPP FeatureFinderMetabo - Detects two-dimensional features in centroided LC-MS data of metabolites."]
723 TOPPFeatureFinderMetabo,
724 #[term(cv=MS, accession=1002170, name="TOPP FeatureFinderMRM", flags={0}, parents={["MS:1002165"]})]
725 #[doc="TOPP FeatureFinderMRM - Quantifies features LC-MS/MS MRM data."]
726 TOPPFeatureFinderMRM,
727 #[term(cv=MS, accession=1002171, name="TOPP ProteinQuantifier", flags={0}, parents={["MS:1000752"]})]
728 #[doc="TOPP ProteinQuantifier - Computes protein abundances from annotated feature/consensus maps."]
729 TOPPProteinQuantifier,
730 #[term(cv=MS, accession=1002172, name="TOPP ConsensusMapNormalizer", flags={0}, parents={["MS:1000752"]})]
731 #[doc="TOPP ConsensusMapNormalizer - Normalizes maps of one consensus XML file (after linking)."]
732 TOPPConsensusMapNormalizer,
733 #[term(cv=MS, accession=1002173, name="TOPP MapRTTransformer", flags={0}, parents={["MS:1000752"]})]
734 #[doc="TOPP MapRTTransformer - Applies retention time transformations to maps."]
735 TOPPMapRTTransformer,
736 #[term(cv=MS, accession=1002174, name="TOPP feature linker", flags={0}, parents={["MS:1000752"]})]
737 #[doc="TOPP feature linker - Feature linker component of the TOPP software."]
738 TOPPFeatureLinker,
739 #[term(cv=MS, accession=1002175, name="TOPP FeatureLinkerLabeled", flags={0}, parents={["MS:1002174"]})]
740 #[doc="TOPP FeatureLinkerLabeled - Groups corresponding isotope-labeled features in a feature map."]
741 TOPPFeatureLinkerLabeled,
742 #[term(cv=MS, accession=1002176, name="TOPP FeatureLinkerUnlabeled", flags={0}, parents={["MS:1002174"]})]
743 #[doc="TOPP FeatureLinkerUnlabeled - Groups corresponding features from multiple maps."]
744 TOPPFeatureLinkerUnlabeled,
745 #[term(cv=MS, accession=1002177, name="TOPP FeatureLinkerUnlabeledQT", flags={0}, parents={["MS:1002174"]})]
746 #[doc="TOPP FeatureLinkerUnlabeledQT - Groups corresponding features from multiple maps using a quality threshold clustering approach."]
747 TOPPFeatureLinkerUnlabeledQT,
748 #[term(cv=MS, accession=1002178, name="TOPP CompNovo", flags={0}, parents={["MS:1000752"]})]
749 #[doc="TOPP CompNovo - Performs a peptide/protein identification with the CompNovo engine."]
750 TOPPCompNovo,
751 #[term(cv=MS, accession=1002179, name="TOPP CompNovoCID", flags={0}, parents={["MS:1000752"]})]
752 #[doc="TOPP CompNovoCID - Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode."]
753 TOPPCompNovoCID,
754 #[term(cv=MS, accession=1002180, name="TOPP software adaptor", flags={0}, parents={["MS:1000752"]})]
755 #[doc="TOPP software adaptor - Software adaptor to an external program in the TOPP software."]
756 TOPPSoftwareAdaptor,
757 #[term(cv=MS, accession=1002181, name="TOPP InspectAdapter", flags={0}, parents={["MS:1002180"]})]
758 #[doc="TOPP InspectAdapter - Identifies MS2 spectra using the external program Inspect."]
759 TOPPInspectAdapter,
760 #[term(cv=MS, accession=1002182, name="TOPP MascotAdapter", flags={0}, parents={["MS:1002180"]})]
761 #[doc="TOPP MascotAdapter - Identifies MS2 spectra using the external program Mascot."]
762 TOPPMascotAdapter,
763 #[term(cv=MS, accession=1002183, name="TOPP MascotAdapterOnline", flags={0}, parents={["MS:1002180"]})]
764 #[doc="TOPP MascotAdapterOnline - Identifies MS2 spectra using the online version of the external program Mascot."]
765 TOPPMascotAdapterOnline,
766 #[term(cv=MS, accession=1002184, name="TOPP OMSSAAdapter", flags={0}, parents={["MS:1002180"]})]
767 #[doc="TOPP OMSSAAdapter - Identifies MS2 spectra using the external program OMSSA."]
768 TOPPOMSSAAdapter,
769 #[term(cv=MS, accession=1002185, name="TOPP PepNovoAdapter", flags={0}, parents={["MS:1002180"]})]
770 #[doc="TOPP PepNovoAdapter - Identifies MS2 spectra using the external program PepNovo."]
771 TOPPPepNovoAdapter,
772 #[term(cv=MS, accession=1002186, name="TOPP XTandemAdapter", flags={0}, parents={["MS:1002180"]})]
773 #[doc="TOPP XTandemAdapter - Identifies MS2 spectra using the external program XTandem."]
774 TOPPXTandemAdapter,
775 #[term(cv=MS, accession=1002187, name="TOPP SpecLibSearcher", flags={0}, parents={["MS:1000752"]})]
776 #[doc="TOPP SpecLibSearcher - Identifies peptide MS2 spectra by spectral matching with a searchable spectral library."]
777 TOPPSpecLibSearcher,
778 #[term(cv=MS, accession=1002188, name="TOPP ConsensusID", flags={0}, parents={["MS:1000752"]})]
779 #[doc="TOPP ConsensusID - Computes a consensus identification from peptide identifications of several identification engines."]
780 TOPPConsensusID,
781 #[term(cv=MS, accession=1002189, name="TOPP IDConflictResolver", flags={0}, parents={["MS:1000752"]})]
782 #[doc="TOPP IDConflictResolver - Resolves ambiguous annotations of features with peptide identifications."]
783 TOPPIDConflictResolver,
784 #[term(cv=MS, accession=1002190, name="TOPP IDFilter", flags={0}, parents={["MS:1000752"]})]
785 #[doc="TOPP IDFilter - Filters results from protein or peptide identification engines based on different criteria."]
786 TOPPIDFilter,
787 #[term(cv=MS, accession=1002191, name="TOPP IDMapper", flags={0}, parents={["MS:1000752"]})]
788 #[doc="TOPP IDMapper - Assigns protein/peptide identifications to feature or consensus features."]
789 TOPPIDMapper,
790 #[term(cv=MS, accession=1002192, name="TOPP IDPosteriorErrorProbability", flags={0}, parents={["MS:1000752"]})]
791 #[doc="TOPP IDPosteriorErrorProbability - Estimates posterior error probabilities using a mixture model."]
792 TOPPIDPosteriorErrorProbability,
793 #[term(cv=MS, accession=1002193, name="TOPP IDRTCalibration", flags={0}, parents={["MS:1000752"]})]
794 #[doc="TOPP IDRTCalibration - Calibrate Retention times of peptide hits to standards."]
795 TOPPIDRTCalibration,
796 #[term(cv=MS, accession=1002194, name="TOPP PeptideIndexer", flags={0}, parents={["MS:1000752"]})]
797 #[doc="TOPP PeptideIndexer - Refreshes the protein references for all peptide hits."]
798 TOPPPeptideIndexer,
799 #[term(cv=MS, accession=1002195, name="TOPP PrecursorIonSelector", flags={0}, parents={["MS:1000752"]})]
800 #[doc="TOPP PrecursorIonSelector - A tool for precursor ion selection based on identification results."]
801 TOPPPrecursorIonSelector,
802 #[term(cv=MS, accession=1002196, name="TOPP MRMMapper", flags={0}, parents={["MS:1000752"]})]
803 #[doc="TOPP MRMMapper - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)."]
804 TOPPMRMMapper,
805 #[term(cv=MS, accession=1002197, name="TOPP OpenSwath component", flags={0}, parents={["MS:1000752"]})]
806 #[doc="TOPP OpenSwath component - OpenSwath component of the TOPP software."]
807 TOPPOpenSwathComponent,
808 #[term(cv=MS, accession=1002198, name="TOPP OpenSwathAnalyzer", flags={0}, parents={["MS:1002197"]})]
809 #[doc="TOPP OpenSwathAnalyzer - Picks peaks and finds features in an SRM experiment."]
810 TOPPOpenSwathAnalyzer,
811 #[term(cv=MS, accession=1002199, name="TOPP OpenSwathChromatogramExtractor", flags={0}, parents={["MS:1002197"]})]
812 #[doc="TOPP OpenSwathChromatogramExtractor - Extract chromatograms (XIC) from a MS2 map file."]
813 TOPPOpenSwathChromatogramExtractor,
814 #[term(cv=MS, accession=1002200, name="TOPP OpenSwathDecoyGenerator", flags={0}, parents={["MS:1002197"]})]
815 #[doc="TOPP OpenSwathDecoyGenerator - Generates decoys according to different models for a specific TraML."]
816 TOPPOpenSwathDecoyGenerator,
817 #[term(cv=MS, accession=1002201, name="TOPP OpenSwathFeatureXMLToTSV", flags={0}, parents={["MS:1002197"]})]
818 #[doc="TOPP OpenSwathFeatureXMLToTSV - Converts a featureXML to a mProphet tsv (tab separated values)."]
819 TOPPOpenSwathFeatureXMLToTSV,
820 #[term(cv=MS, accession=1002202, name="TOPP OpenSwathRTNormalizer", flags={0}, parents={["MS:1002197"]})]
821 #[doc="TOPP OpenSwathRTNormalizer - Generates a transformation file for retention time space into normalized space."]
822 TOPPOpenSwathRTNormalizer,
823 #[term(cv=MS, accession=1002203, name="TOPP ProteinInference", flags={0}, parents={["MS:1000752"]})]
824 #[doc="TOPP ProteinInference - Infer proteins from a list of (high-confidence) peptides."]
825 TOPPProteinInference,
826 #[term(cv=MS, accession=1002204, name="TOPP FalseDiscoveryRate", flags={0}, parents={["MS:1000752"]})]
827 #[doc="TOPP FalseDiscoveryRate - Estimates the false discovery rate on peptide and protein level using decoy searches."]
828 TOPPFalseDiscoveryRate,
829 #[term(cv=MS, accession=1002205, name="ProteoWizard msconvert", flags={0}, parents={["MS:1000615"]})]
830 #[doc="ProteoWizard msconvert - Converts, filters, and processes mass spectrometry data in variety of formats."]
831 ProteoWizardMsconvert,
832 #[term(cv=MS, accession=1002206, name="ProteoWizard idconvert", flags={0}, parents={["MS:1000615"]})]
833 #[doc="ProteoWizard idconvert - Converts, filters, and processes identifications from shotgun proteomics experiments."]
834 ProteoWizardIdconvert,
835 #[term(cv=MS, accession=1002207, name="ProteoWizard chainsaw", flags={0}, parents={["MS:1000615"]})]
836 #[doc="ProteoWizard chainsaw - Filters and processes protein sequence databases."]
837 ProteoWizardChainsaw,
838 #[term(cv=MS, accession=1002208, name="ProteoWizard msaccess", flags={0}, parents={["MS:1000615"]})]
839 #[doc="ProteoWizard msaccess - Filters, processes, and displays mass spectrometry data in a variety of ways."]
840 ProteoWizardMsaccess,
841 #[term(cv=MS, accession=1002209, name="ProteoWizard SeeMS", flags={0}, parents={["MS:1000615"]})]
842 #[doc="ProteoWizard SeeMS - An interactive GUI application to view and filter mass spectrometry data in a variety of formats."]
843 ProteoWizardSeeMS,
844 #[term(cv=MS, accession=1002210, name="IsobariQ", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
845 #[doc="IsobariQ - A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data."]
846 IsobariQ,
847 #[term(cv=MS, accession=1002220, name="MRMaid", flags={0}, parents={["MS:1000871"]})]
848 #[doc="MRMaid - A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database."]
849 MRMaid,
850 #[term(cv=MS, accession=1002237, name="mzidLib", flags={1}, parents={["MS:1001456"]})]
851 #[doc="mzidLib - A library of Java routines for manipulating mzIdentML files."]
852 MzidLib,
853 #[term(cv=MS, accession=1002238, name="mzidLib:Omssa2Mzid", flags={0}, parents={["MS:1002237"]})]
854 #[doc="mzidLib:Omssa2Mzid - A converter for OMSSA OMX to mzIdentML."]
855 MzidLibOmssa2Mzid,
856 #[term(cv=MS, accession=1002239, name="mzidLib:Tandem2Mzid", flags={0}, parents={["MS:1002237"]})]
857 #[doc="mzidLib:Tandem2Mzid - A converter for Tandem XML to mzIdentML."]
858 MzidLibTandem2Mzid,
859 #[term(cv=MS, accession=1002240, name="mzidLib:Csv2Mzid", flags={0}, parents={["MS:1002237"]})]
860 #[doc="mzidLib:Csv2Mzid - A converter for CSV files (following OMSSA CSV style) to mzIdentML."]
861 MzidLibCsv2Mzid,
862 #[term(cv=MS, accession=1002241, name="mzidLib:ProteoGrouper", flags={0}, parents={["MS:1002237"]})]
863 #[doc="mzidLib:ProteoGrouper - A generic and parameterizable protein inference algorithm for mzIdentML files."]
864 MzidLibProteoGrouper,
865 #[term(cv=MS, accession=1002242, name="mzidLib:Thresholder", flags={0}, parents={["MS:1002237"]})]
866 #[doc="mzidLib:Thresholder - A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files."]
867 MzidLibThresholder,
868 #[term(cv=MS, accession=1002243, name="mzidLib:Perform emPAI on mzid", flags={0}, parents={["MS:1002237"]})]
869 #[doc="mzidLib:Perform emPAI on mzid - A routine for adding emPAI quantitative values to an mzIdentML file."]
870 MzidLibPerformEmPAIOnMzid,
871 #[term(cv=MS, accession=1002244, name="mzidLib:FalseDiscoveryRate", flags={0}, parents={["MS:1002237"]})]
872 #[doc="mzidLib:FalseDiscoveryRate - A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search."]
873 MzidLibFalseDiscoveryRate,
874 #[term(cv=MS, accession=1002245, name="mzidLib:Mzidentml2Csv", flags={0}, parents={["MS:1002237"]})]
875 #[doc="mzidLib:Mzidentml2Csv - A tool for converting mzIdentML files to CSV format."]
876 MzidLibMzidentml2Csv,
877 #[term(cv=MS, accession=1002246, name="mzidLib:CombineSearchEngines", flags={0}, parents={["MS:1002237"]})]
878 #[doc="mzidLib:CombineSearchEngines - A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file."]
879 MzidLibCombineSearchEngines,
880 #[term(cv=MS, accession=1002247, name="mzidLib:InsertMetaDataFromFasta", flags={0}, parents={["MS:1002237"]})]
881 #[doc="mzidLib:InsertMetaDataFromFasta - A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files."]
882 MzidLibInsertMetaDataFromFasta,
883 #[term(cv=MS, accession=1002251, name="Comet", flags={1}, parents={["MS:1001456"]})]
884 #[doc="Comet - Comet open-source sequence search engine developed at the University of Washington."]
885 Comet,
886 #[term(cv=MS, accession=1002261, name="Byonic", flags={1}, parents={["MS:1001456"]})]
887 #[doc="Byonic - Byonic search engine from Protein Metrics."]
888 Byonic,
889 #[term(cv=MS, accession=1002285, name="Trans-Proteomic Pipeline", flags={1}, parents={["MS:1001456"]})]
890 #[doc="Trans-Proteomic Pipeline - A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology."]
891 TransProteomicPipeline,
892 #[term(cv=MS, accession=1002286, name="Trans-Proteomic Pipeline software", flags={1}, parents={["MS:1001456"]})]
893 #[doc="Trans-Proteomic Pipeline software - A software program that is a component of the Trans-Proteomic Pipeline."]
894 TransProteomicPipelineSoftware,
895 #[term(cv=MS, accession=1002287, name="PeptideProphet", flags={0}, parents={["MS:1002286"]})]
896 #[doc="PeptideProphet - A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format."]
897 PeptideProphet,
898 #[term(cv=MS, accession=1002288, name="iProphet", flags={0}, parents={["MS:1002286"]})]
899 #[doc="iProphet - A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format."]
900 IProphet,
901 #[term(cv=MS, accession=1002289, name="ProteinProphet", flags={0}, parents={["MS:1002286"]})]
902 #[doc="ProteinProphet - A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format."]
903 ProteinProphet,
904 #[term(cv=MS, accession=1002290, name="XPRESS", flags={0}, parents={["MS:1002286"]})]
905 #[doc="XPRESS - A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc."]
906 XPRESS,
907 #[term(cv=MS, accession=1002291, name="Libra", flags={0}, parents={["MS:1002286"]})]
908 #[doc="Libra - A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc."]
909 Libra,
910 #[term(cv=MS, accession=1002292, name="PTMProphet", flags={0}, parents={["MS:1002286"]})]
911 #[doc="PTMProphet - A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites."]
912 PTMProphet,
913 #[term(cv=MS, accession=1002333, name="conversion software", flags={2}, parents={["MS:1001457"]})]
914 #[doc="conversion software - Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process."]
915 ConversionSoftware,
916 #[term(cv=MS, accession=1002334, name="ProCon", flags={0}, parents={["MS:1002333"]})]
917 #[doc="ProCon - Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML."]
918 ProCon,
919 #[term(cv=MS, accession=1002335, name="PRIDE Converter2", flags={0}, parents={["MS:1002333"]})]
920 #[doc="PRIDE Converter2 - Java software designed to convert one of several proteomics identification results formats into PRIDE XML."]
921 PRIDEConverter2,
922 #[term(cv=MS, accession=1002336, name="Amanda", flags={1}, parents={["MS:1001456"]})]
923 #[doc="Amanda - Amanda scoring system for PSM identification."]
924 Amanda,
925 #[term(cv=MS, accession=1002337, name="Andromeda", flags={1}, parents={["MS:1001456"]})]
926 #[doc="Andromeda - Andromeda is a peptide search engine."]
927 Andromeda,
928 #[term(cv=MS, accession=1002342, name="mzmine", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
929 #[doc="mzmine - A framework for differential analysis of mass spectrometry data."]
930 Mzmine,
931 #[term(cv=MS, accession=1002344, name="Maltcms", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
932 #[doc="Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers."]
933 Maltcms,
934 #[term(cv=MS, accession=1002381, name="MALDI Solutions LC-MALDI", flags={7}, parents={["MS:1001455", "MS:1001456", "MS:1001457", "MS:1001557"]})]
935 #[doc="MALDI Solutions LC-MALDI - Software for automated LC-MALDI analysis and reporting."]
936 MALDISolutionsLCMALDI,
937 #[term(cv=MS, accession=1002383, name="SCiLS software", flags={0}, parents={["MS:1000531"]})]
938 #[doc="SCiLS software - SCiLS software for data acquisition and analysis."]
939 SCiLSSoftware,
940 #[term(cv=MS, accession=1002384, name="SCiLS Lab", flags={3}, parents={["MS:1002383", "MS:1001456", "MS:1001457"]})]
941 #[doc="SCiLS Lab - SCiLS Lab software."]
942 SCiLSLab,
943 #[term(cv=MS, accession=1002386, name="preprocessing software", flags={2}, parents={["MS:1001457"]})]
944 #[doc="preprocessing software - Preprocessing software."]
945 PreprocessingSoftware,
946 #[term(cv=MS, accession=1002387, name="PIA", flags={1}, parents={["MS:1002414", "MS:1001456"]})]
947 #[doc="PIA - PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis."]
948 PIA,
949 #[term(cv=MS, accession=1002410, name="Anubis", flags={0}, parents={["MS:1000871", "MS:1001139"]})]
950 #[doc="Anubis - Anubis software for selected reaction monitoring data."]
951 Anubis,
952 #[term(cv=MS, accession=1002414, name="postprocessing software", flags={2}, parents={["MS:1001457"]})]
953 #[doc="postprocessing software - Postprocessing software."]
954 PostprocessingSoftware,
955 #[term(cv=MS, accession=1002452, name="Maui", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
956 #[doc="Maui - The Maltcms Graphical User Interface."]
957 Maui,
958 #[term(cv=MS, accession=1002458, name="PeptideShaker", flags={1}, parents={["MS:1001456"]})]
959 #[doc="PeptideShaker - PeptideShaker is a software for the interpretation of proteomics identification results."]
960 PeptideShaker,
961 #[term(cv=MS, accession=1002524, name="PepFinder", flags={2}, parents={["MS:1003961", "MS:1001457"]})]
962 #[doc="PepFinder - Thermo Scientific PepFinder BioPharma analysis software."]
963 PepFinder,
964 #[term(cv=MS, accession=1002543, name="xiFDR", flags={1}, parents={["MS:1001456"]})]
965 #[doc="xiFDR - Target/Decoy based FDR estimation for crosslinking peptide-identifications."]
966 XiFDR,
967 #[term(cv=MS, accession=1002544, name="xi", flags={1}, parents={["MS:1001456"]})]
968 #[doc="xi - Search engine for crosslinked peptides."]
969 Xi,
970 #[term(cv=MS, accession=1002546, name="Skyline mzQuantML converter", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
971 #[doc="Skyline mzQuantML converter - A software package to convert Skyline report to mzQuantML."]
972 SkylineMzQuantMLConverter,
973 #[term(cv=MS, accession=1002574, name="ASAPRatio", flags={0}, parents={["MS:1002286"]})]
974 #[doc="ASAPRatio - A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc."]
975 ASAPRatio,
976 #[term(cv=MS, accession=1002575, name="Tide", flags={1}, parents={["MS:1001456"]})]
977 #[doc="Tide - Tide open-source sequence search program developed at the University of Washington."]
978 Tide,
979 #[term(cv=MS, accession=1002596, name="ProLuCID", flags={1}, parents={["MS:1001456"]})]
980 #[doc="ProLuCID - The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute."]
981 ProLuCID,
982 #[term(cv=MS, accession=1002598, name="DTASelect", flags={1}, parents={["MS:1001456"]})]
983 #[doc="DTASelect - Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches."]
984 DTASelect,
985 #[term(cv=MS, accession=1002645, name="MSDK", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
986 #[doc="MSDK - Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data."]
987 MSDK,
988 #[term(cv=MS, accession=1002661, name="Morpheus", flags={1}, parents={["MS:1001456"]})]
989 #[doc="Morpheus - Morpheus search engine."]
990 Morpheus,
991 #[term(cv=MS, accession=1002673, name="OpenXQuest", flags={0}, parents={["MS:1000752"]})]
992 #[doc="OpenXQuest - Cross-Linking MS search engine."]
993 OpenXQuest,
994 #[term(cv=MS, accession=1002714, name="FLASHDeconv", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
995 #[doc="FLASHDeconv - Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics."]
996 FLASHDeconv,
997 #[term(cv=MS, accession=1002717, name="Waters DATA Convert", flags={3}, parents={["MS:1000694", "MS:1001456", "MS:1001457"]})]
998 #[doc="Waters DATA Convert - Software for processing and exporting Waters MassLynx and waters_connect data."]
999 WatersDATAConvert,
1000 #[term(cv=MS, accession=1002720, name="MSPathFinder", flags={1}, parents={["MS:1001456"]})]
1001 #[doc="MSPathFinder - PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra."]
1002 MSPathFinder,
1003 #[term(cv=MS, accession=1002750, name="NIST MSPepSearch", flags={1}, parents={["MS:1001456"]})]
1004 #[doc="NIST MSPepSearch - Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches."]
1005 NISTMSPepSearch,
1006 #[term(cv=MS, accession=1002826, name="MetaMorpheus", flags={1}, parents={["MS:1001456"]})]
1007 #[doc="MetaMorpheus - MetaMorpheus search engine."]
1008 MetaMorpheus,
1009 #[term(cv=MS, accession=1002869, name="mzR", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
1010 #[doc="mzR - Bioconductor package mzR for reading and writing mass spectrometry data files."]
1011 MzR,
1012 #[term(cv=MS, accession=1002870, name="MSnbase", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
1013 #[doc="MSnbase - Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data."]
1014 MSnbase,
1015 #[term(cv=MS, accession=1002871, name="CAMERA", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
1016 #[doc="CAMERA - Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments."]
1017 CAMERA,
1018 #[term(cv=MS, accession=1002878, name="small molecule analysis software", flags={1}, parents={["MS:1001456"]})]
1019 #[doc="small molecule analysis software - Software for the analysis of small molecules."]
1020 SmallMoleculeAnalysisSoftware,
1021 #[term(cv=MS, accession=1002879, name="Progenesis QI", flags={0}, parents={["MS:1002878"]})]
1022 #[doc="Progenesis QI - Metabolomics analysis software for LC-MS data from Nonlinear Dynamics."]
1023 ProgenesisQI,
1024 #[term(cv=MS, accession=1002880, name="Compound Discoverer", flags={0}, parents={["MS:1003961", "MS:1002878"]})]
1025 #[doc="Compound Discoverer - Metabolomics analysis software from Thermo Fisher Scientific."]
1026 CompoundDiscoverer,
1027 #[term(cv=MS, accession=1002881, name="MyCompoundID", flags={0}, parents={["MS:1002878"]})]
1028 #[doc="MyCompoundID - Metabolite identification tool MyCompoundID."]
1029 MyCompoundID,
1030 #[term(cv=MS, accession=1002901, name="TopPIC", flags={1}, parents={["MS:1001456"]})]
1031 #[doc="TopPIC - TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization."]
1032 TopPIC,
1033 #[term(cv=MS, accession=1002902, name="TopFD", flags={1}, parents={["MS:1001456"]})]
1034 #[doc="TopFD - Top-down mass spectral feature detection."]
1035 TopFD,
1036 #[term(cv=MS, accession=1002903, name="TopMG", flags={1}, parents={["MS:1001456"]})]
1037 #[doc="TopMG - A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra."]
1038 TopMG,
1039 #[term(cv=MS, accession=1002964, name="lipidomics analysis software", flags={0}, parents={["MS:1002878"]})]
1040 #[doc="lipidomics analysis software - Lipidomics analysis software."]
1041 LipidomicsAnalysisSoftware,
1042 #[term(cv=MS, accession=1002965, name="Lipid Data Analyzer", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1043 #[doc="Lipid Data Analyzer - Lipid Data Analyzer software for lipid quantification."]
1044 LipidDataAnalyzer,
1045 #[term(cv=MS, accession=1002967, name="LipidHunter", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1046 #[doc="LipidHunter - Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets."]
1047 LipidHunter,
1048 #[term(cv=MS, accession=1002968, name="LipidXplorer", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1049 #[doc="LipidXplorer - Software for consensual cross-platform lipidomics."]
1050 LipidXplorer,
1051 #[term(cv=MS, accession=1002969, name="LipidMatch", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1052 #[doc="LipidMatch - An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data."]
1053 LipidMatch,
1054 #[term(cv=MS, accession=1002970, name="Greazy", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1055 #[doc="Greazy - Open-source software for automated phospholipid tandem mass spectrometry identification."]
1056 Greazy,
1057 #[term(cv=MS, accession=1002971, name="LipidBlast", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1058 #[doc="LipidBlast - LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library."]
1059 LipidBlast,
1060 #[term(cv=MS, accession=1002972, name="Lipid-Pro", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1061 #[doc="Lipid-Pro - A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms."]
1062 LipidPro,
1063 #[term(cv=MS, accession=1002973, name="LipidFinder", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1064 #[doc="LipidFinder - A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets."]
1065 LipidFinder,
1066 #[term(cv=MS, accession=1002974, name="LipiDex", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1067 #[doc="LipiDex - An integrated software package for high-confidence lipid identification."]
1068 LipiDex,
1069 #[term(cv=MS, accession=1002975, name="LIQUID", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1070 #[doc="LIQUID - An-open source software for identifying lipids in LC-MS/MS-based lipidomics data."]
1071 LIQUID,
1072 #[term(cv=MS, accession=1002976, name="ALEX", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1073 #[doc="ALEX - Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1)."]
1074 ALEX,
1075 #[term(cv=MS, accession=1002977, name="ALEX123", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1076 #[doc="ALEX123 - Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level."]
1077 ALEX123,
1078 #[term(cv=MS, accession=1002978, name="LIMSA", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1079 #[doc="LIMSA - Software tool for the quantitative analysis of mass spectrometric lipidome data."]
1080 LIMSA,
1081 #[term(cv=MS, accession=1002979, name="LOBSTAHS", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1082 #[doc="LOBSTAHS - Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers."]
1083 LOBSTAHS,
1084 #[term(cv=MS, accession=1002980, name="LipidQA", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1085 #[doc="LipidQA - Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species."]
1086 LipidQA,
1087 #[term(cv=MS, accession=1002981, name="Proline", flags={1}, parents={["MS:1001456"]})]
1088 #[doc="Proline - The Proline software suite for mass spectrometry based proteomics."]
1089 Proline,
1090 #[term(cv=MS, accession=1002982, name="PepNovo", flags={1}, parents={["MS:1001456"]})]
1091 #[doc="PepNovo - PepNovo tool for de novo peptide sequencing."]
1092 PepNovo,
1093 #[term(cv=MS, accession=1002983, name="pNovo", flags={1}, parents={["MS:1001456"]})]
1094 #[doc="pNovo - pNovo tool for de novo peptide sequencing and identification using HCD spectra."]
1095 PNovo,
1096 #[term(cv=MS, accession=1002984, name="Novor", flags={1}, parents={["MS:1001456"]})]
1097 #[doc="Novor - Novor real-time peptide de novo sequencing software tool."]
1098 Novor,
1099 #[term(cv=MS, accession=1002987, name="IdentiPy", flags={1}, parents={["MS:1001456"]})]
1100 #[doc="IdentiPy - IdentiPy."]
1101 IdentiPy,
1102 #[term(cv=MS, accession=1002990, name="ms_deisotope", flags={2}, parents={["MS:1001457"]})]
1103 #[doc="ms_deisotope - ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra."]
1104 MsDeisotope,
1105 #[term(cv=MS, accession=1002991, name="python-psims", flags={0}, parents={["MS:1002333"]})]
1106 #[doc="python-psims - python-psims, a library for generating mzML and mzIdentML."]
1107 PythonPsims,
1108 #[term(cv=MS, accession=1003010, name="LPPtiger", flags={2}, parents={["MS:1002964", "MS:1001457"]})]
1109 #[doc="LPPtiger - Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets."]
1110 LPPtiger,
1111 #[term(cv=MS, accession=1003011, name="pFind", flags={1}, parents={["MS:1001456"]})]
1112 #[doc="pFind - Sequence-tag-based search engine pFind."]
1113 PFind,
1114 #[term(cv=MS, accession=1003013, name="i3tms", flags={1}, parents={["MS:1001456"]})]
1115 #[doc="i3tms - i3-tms search engine and data-analysis software."]
1116 I3tms,
1117 #[term(cv=MS, accession=1003014, name="MSFragger", flags={1}, parents={["MS:1001456"]})]
1118 #[doc="MSFragger - A database search-based peptide identification tool."]
1119 MSFragger,
1120 #[term(cv=MS, accession=1003018, name="Philosopher", flags={1}, parents={["MS:1001456"]})]
1121 #[doc="Philosopher - General proteomics processing toolkit for shotgun proteomics."]
1122 Philosopher,
1123 #[term(cv=MS, accession=1003023, name="OpenPepXL", flags={0}, parents={["MS:1000752"]})]
1124 #[doc="OpenPepXL - Cross-Linking MS search engine."]
1125 OpenPepXL,
1126 #[term(cv=MS, accession=1003082, name="MS-DIAL", flags={2}, parents={["MS:1002878", "MS:1001457"]})]
1127 #[doc="MS-DIAL - Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors."]
1128 MSDIAL,
1129 #[term(cv=MS, accession=1003108, name="PatternLab", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
1130 #[doc="PatternLab - PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data."]
1131 PatternLab,
1132 #[term(cv=MS, accession=1003109, name="SIM-XL", flags={1}, parents={["MS:1001456"]})]
1133 #[doc="SIM-XL - Identifying crosslinked peptides in complex protein mixtures"]
1134 SIMXL,
1135 #[term(cv=MS, accession=1003111, name="QUIN-XL", flags={0}, parents={["MS:1001139"]})]
1136 #[doc="QUIN-XL - Quantification of crosslinked peptides in complex protein mixtures"]
1137 QUINXL,
1138 #[term(cv=MS, accession=1003118, name="EPIFANY", flags={1}, parents={["MS:1001456", "MS:1000752"]})]
1139 #[doc="EPIFANY - A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework"]
1140 EPIFANY,
1141 #[term(cv=MS, accession=1003141, name="ProSight", flags={1}, parents={["MS:1003961", "MS:1001456"]})]
1142 #[doc="ProSight - ProSight: Database search engine for top-down proteomics."]
1143 ProSight,
1144 #[term(cv=MS, accession=1003142, name="TDPortal", flags={1}, parents={["MS:1001456"]})]
1145 #[doc="TDPortal - TDPortal: Database search engine for top-down proteomics."]
1146 TDPortal,
1147 #[term(cv=MS, accession=1003145, name="ThermoRawFileParser", flags={2}, parents={["MS:1001457"]})]
1148 #[doc="ThermoRawFileParser - Cross-platform software to convert Thermo RAW files to a number of open formats."]
1149 ThermoRawFileParser,
1150 #[term(cv=MS, accession=1003146, name="pyteomics", flags={1}, parents={["MS:1001456"]})]
1151 #[doc="pyteomics - Python module that helps handling various proteomics data analysis tasks."]
1152 Pyteomics,
1153 #[term(cv=MS, accession=1003162, name="PTX-QC", flags={1}, parents={["MS:1001456"]})]
1154 #[doc="PTX-QC - Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization."]
1155 PTXQC,
1156 #[term(cv=MS, accession=1003164, name="QuaMeter IDFree", flags={1}, parents={["MS:1001456"]})]
1157 #[doc="QuaMeter IDFree - QuaMeter IDFree software for QC metric calculation."]
1158 QuaMeterIDFree,
1159 #[term(cv=MS, accession=1003165, name="iMonDB", flags={1}, parents={["MS:1001456"]})]
1160 #[doc="iMonDB - iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files."]
1161 IMonDB,
1162 #[term(cv=MS, accession=1003202, name="BiblioSpec", flags={1}, parents={["MS:1001456", "MS:1003207"]})]
1163 #[doc="BiblioSpec - A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington"]
1164 BiblioSpec,
1165 #[term(cv=MS, accession=1003207, name="library creation software", flags={0}, parents={["MS:1000531", "MS:1003171"]})]
1166 #[doc="library creation software - Library creation software"]
1167 LibraryCreationSoftware,
1168 #[term(cv=MS, accession=1003232, name="PeakForest", flags={1}, parents={["MS:1001456", "MS:1003207", "MS:1002878"]})]
1169 #[doc="PeakForest - comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB)."]
1170 PeakForest,
1171 #[term(cv=MS, accession=1003253, name="DIA-NN", flags={1}, parents={["MS:1001139", "MS:1001456", "MS:1003207"]})]
1172 #[doc="DIA-NN - A universal software for data-independent acquisition (DIA) proteomics data processing"]
1173 DIANN,
1174 #[term(cv=MS, accession=1003281, name="Casanovo", flags={1}, parents={["MS:1001456"]})]
1175 #[doc="Casanovo - Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/."]
1176 Casanovo,
1177 #[term(cv=MS, accession=1003309, name="Goslin", flags={2}, parents={["MS:1001457", "MS:1002414", "MS:1002964"]})]
1178 #[doc="Goslin - The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature."]
1179 Goslin,
1180 #[term(cv=MS, accession=1003357, name="ANN-SoLo", flags={1}, parents={["MS:1001456"]})]
1181 #[doc="ANN-SoLo - ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart."]
1182 ANNSoLo,
1183 #[term(cv=MS, accession=1003376, name="ChemClipse", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
1184 #[doc="ChemClipse - ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH."]
1185 ChemClipse,
1186 #[term(cv=MS, accession=1003377, name="OpenChrom", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
1187 #[doc="OpenChrom - OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse."]
1188 OpenChrom,
1189 #[term(cv=MS, accession=1003382, name="waters_connect", flags={7}, parents={["MS:1000694", "MS:1001455", "MS:1001456", "MS:1001457"]})]
1190 #[doc="waters_connect - Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing."]
1191 WatersConnect,
1192 #[term(cv=MS, accession=1003386, name="Spectra", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
1193 #[doc="Spectra - Bioconductor package Spectra for mass spectrometry data representation and processing."]
1194 Spectra,
1195 #[term(cv=MS, accession=1003387, name="MetaboAnnotation", flags={3}, parents={["MS:1001456", "MS:1001457"]})]
1196 #[doc="MetaboAnnotation - Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data."]
1197 MetaboAnnotation,
1198 #[term(cv=MS, accession=1003388, name="CompoundDb", flags={3}, parents={["MS:1001456", "MS:1001457", "MS:1003207"]})]
1199 #[doc="CompoundDb - Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries."]
1200 CompoundDb,
1201 #[term(cv=MS, accession=1003399, name="quality control software", flags={2}, parents={["MS:1001457"]})]
1202 #[doc="quality control software - Software that creates or manipulates QC-related data."]
1203 QualityControlSoftware,
1204 #[term(cv=MS, accession=1003400, name="rmzqc", flags={0}, parents={["MS:1003399"]})]
1205 #[doc="rmzqc - An R package for reading, validating, and writing mzQC files."]
1206 Rmzqc,
1207 #[term(cv=MS, accession=1003401, name="jmzqc", flags={0}, parents={["MS:1003399"]})]
1208 #[doc="jmzqc - A Java package for reading, validating, and writing mzQC files."]
1209 Jmzqc,
1210 #[term(cv=MS, accession=1003402, name="pymzqc", flags={0}, parents={["MS:1003399"]})]
1211 #[doc="pymzqc - A Python package for reading, validating, and writing mzQC files."]
1212 Pymzqc,
1213 #[term(cv=MS, accession=1003405, name="mzRecal", flags={2}, parents={["MS:1001457"]})]
1214 #[doc="mzRecal - MS1 recalibration using identified peptides as internal calibrants."]
1215 MzRecal,
1216 #[term(cv=MS, accession=1003406, name="spectrum clustering software", flags={0}, parents={["MS:1000531"]})]
1217 #[doc="spectrum clustering software - Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte."]
1218 SpectrumClusteringSoftware,
1219 #[term(cv=MS, accession=1003407, name="Scout", flags={1}, parents={["MS:1001456"]})]
1220 #[doc="Scout - Identifying crosslinked peptides in complex protein mixtures"]
1221 Scout,
1222 #[term(cv=MS, accession=1003413, name="Kojak", flags={1}, parents={["MS:1001456"]})]
1223 #[doc="Kojak - Kojak open-source crosslinked peptide sequence search engine developed at the Institute for Systems Biology."]
1224 Kojak,
1225 #[term(cv=MS, accession=1003425, name="quantms", flags={1}, parents={["MS:1001456", "MS:1001139"]})]
1226 #[doc="quantms - Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data."]
1227 Quantms,
1228 #[term(cv=MS, accession=1003426, name="xQuest/xProphet", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
1229 #[doc="xQuest/xProphet - A software to identify cross-linked peptides from LC-MS/MS spectra."]
1230 XQuestXProphet,
1231 #[term(cv=MS, accession=1003427, name="PeakView", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
1232 #[doc="PeakView - A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data."]
1233 PeakView,
1234 #[term(cv=MS, accession=1003428, name="Perseus", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
1235 #[doc="Perseus - A software for interpreting protein quantification, interaction and post-translational modification data."]
1236 Perseus,
1237 #[term(cv=MS, accession=1003429, name="FragPipe", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
1238 #[doc="FragPipe - A computational platform for analyzing mass spectrometry-based proteomics data."]
1239 FragPipe,
1240 #[term(cv=MS, accession=1003430, name="OpenMS", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
1241 #[doc="OpenMS - A software for LC-MS data management and analysis."]
1242 OpenMS,
1243 #[term(cv=MS, accession=1003431, name="pLink", flags={1}, parents={["MS:1001139", "MS:1001456"]})]
1244 #[doc="pLink - A tool for the analysis of chemically cross-linked proteins using mass spectrometry."]
1245 PLink,
1246 #[term(cv=MS, accession=1003432, name="pLink2", flags={1}, parents={["MS:1003431", "MS:1001139", "MS:1001456"]})]
1247 #[doc="pLink2 - Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure."]
1248 PLink2,
1249 #[term(cv=MS, accession=1003446, name="SCIEX OS", flags={7}, parents={["MS:1000690", "MS:1001455", "MS:1001456", "MS:1001457"]})]
1250 #[doc="SCIEX OS - SCIEX OS software."]
1251 SCIEXOS,
1252 #[term(cv=MS, accession=1003447, name="SCIEX MS Data Converter", flags={2}, parents={["MS:1000690", "MS:1001457"]})]
1253 #[doc="SCIEX MS Data Converter - A software for converting SCIEX wiff or wiff2 format to mzML."]
1254 SCIEXMSDataConverter,
1255 #[term(cv=MS, accession=1003607, name="timsControl", flags={4}, parents={["MS:1000692", "MS:1001455"]})]
1256 #[doc="timsControl - Bruker software for data acquisition."]
1257 TimsControl,
1258 #[term(cv=MS, accession=1003608, name="MetaboScape", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
1259 #[doc="MetaboScape - Bruker software for untargeted metabolomics and lipidomics data analysis."]
1260 MetaboScape,
1261 #[term(cv=MS, accession=1003609, name="TASQ", flags={3}, parents={["MS:1000692", "MS:1001456", "MS:1001457"]})]
1262 #[doc="TASQ - Bruker software for target screening and quantitation."]
1263 TASQ,
1264 #[term(cv=MS, accession=1003612, name="InstaNovo", flags={1}, parents={["MS:1001456"]})]
1265 #[doc="InstaNovo - InstaNovo is a deep learning based tool using a Transformer architecture for de novo peptide sequencing."]
1266 InstaNovo,
1267 #[term(cv=MS, accession=1003613, name="InstaNovo+", flags={1}, parents={["MS:1001456"]})]
1268 #[doc="InstaNovo+ - InstaNovo+ is a deep learning based tool using a Diffusion architecture for de novo peptide sequencing."]
1269 InstaNovoplus,
1270 #[term(cv=MS, accession=1003801, name="AccurateMassSearch", flags={0}, parents={["MS:1000752"]})]
1271 #[doc="AccurateMassSearch - OpenMS TOPP tool to assemble metabolite features from singleton mass traces."]
1272 AccurateMassSearch,
1273 #[term(cv=MS, accession=1003803, name="Ionoptika software", flags={0}, parents={["MS:1000531"]})]
1274 #[doc="Ionoptika software - Ionoptika software for data acquisition and analysis."]
1275 IonoptikaSoftware,
1276 #[term(cv=MS, accession=1003806, name="NeoSIMS", flags={4}, parents={["MS:1001455", "MS:1003803"]})]
1277 #[doc="NeoSIMS - Ionoptika software for data acquisition."]
1278 NeoSIMS,
1279 #[term(cv=MS, accession=1003807, name="Ionoptika Image Analyser", flags={3}, parents={["MS:1001456", "MS:1001457", "MS:1003803"]})]
1280 #[doc="Ionoptika Image Analyser - Ionoptika software for image data analysis."]
1281 IonoptikaImageAnalyser,
1282 #[term(cv=MS, accession=1003808, name="J105 Ionoptika Mass Imager", flags={3}, parents={["MS:1001456", "MS:1001457", "MS:1003803"]})]
1283 #[doc="J105 Ionoptika Mass Imager - Ionoptika J105 software for mass spectrometry imaging data analysis."]
1284 J105IonoptikaMassImager,
1285 #[term(cv=MS, accession=1003809, name="IoDataConverter", flags={2}, parents={["MS:1001457", "MS:1003803"]})]
1286 #[doc="IoDataConverter - Ionoptika software for converting Ionoptika data formats to imzML or HDF5."]
1287 IoDataConverter,
1288 #[term(cv=MS, accession=1003916, name="SpectroSwiss software", flags={0}, parents={["MS:1000531"]})]
1289 #[doc="SpectroSwiss software - SpectroSwiss software for mass spectrometry data processing and analysis."]
1290 SpectroSwissSoftware,
1291 #[term(cv=MS, accession=1003917, name="Peak-by-Peak", flags={3}, parents={["MS:1003916", "MS:1001456", "MS:1001457"]})]
1292 #[doc="Peak-by-Peak - SpectroSwiss software for Fourier transform mass spectrometry (FTMS) data processing and analysis, providing advanced workflows including the processing of unreduced, transient data."]
1293 PeakByPeak,
1294 #[term(cv=MS, accession=1003961, name="Thermo Scientific software", flags={0}, parents={["MS:1000531"]})]
1295 #[doc="Thermo Scientific software - Thermo Scientific software for data acquisition and analysis."]
1296 ThermoScientificSoftware,
1297 #[term(cv=MS, accession=1003962, name="TraceFinder", flags={7}, parents={["MS:1003961", "MS:1001455", "MS:1001456", "MS:1001457"]})]
1298 #[doc="TraceFinder - Thermo Scientific software for targeted quantitative and screening analysis of LC-MS, GC-MS, and IC-MS data, supporting automated data acquisition, processing, and reporting for diverse workflows."]
1299 TraceFinder,
1300 #[term(cv=MS, accession=1003963, name="FreeStyle", flags={3}, parents={["MS:1003961", "MS:1001456", "MS:1001457"]})]
1301 #[doc="FreeStyle - Thermo Scientific software for interactive qualitative visualization and review of mass spectrometry data, including chromatographic peak detection, spectral library searching, and high-resolution deconvolution."]
1302 FreeStyle,
1303 #[term(cv=MS, accession=1003964, name="Chromeleon CDS", flags={7}, parents={["MS:1003961", "MS:1001455", "MS:1001456", "MS:1001457"]})]
1304 #[doc="Chromeleon CDS - Thermo Scientific enterprise chromatography data system with integrated mass spectrometry instrument control and data processing, supporting GC-MS, LC-MS, and IC-MS platforms with GxP/21 CFR Part 11 compliance."]
1305 ChromeleonCDS,
1306 #[term(cv=MS, accession=1003965, name="Mass Frontier", flags={3}, parents={["MS:1003961", "MS:1001456", "MS:1001457"]})]
1307 #[doc="Mass Frontier - Thermo Scientific software for mass spectral interpretation and structural elucidation of small molecules, featuring the HighChem fragmentation library, fragmentation prediction, and spectral tree searching."]
1308 MassFrontier,
1309 #[term(cv=MS, accession=1003966, name="LipidSearch", flags={3}, parents={["MS:1003961", "MS:1001456", "MS:1001457"]})]
1310 #[doc="LipidSearch - Thermo Scientific software for automated identification of lipid molecular species from LC-MS and LC-MS/MS data using a comprehensive database of predicted lipid ion fragments."]
1311 LipidSearch,
1312 #[term(cv=MS, accession=1003967, name="mzVault", flags={3}, parents={["MS:1003961", "MS:1001456", "MS:1001457"]})]
1313 #[doc="mzVault - Thermo Scientific software for offline storage, searching, and management of high-resolution accurate-mass spectral libraries, including curated mzCloud content and user-generated in-house libraries."]
1314 MzVault,
1315 #[term(cv=MS, accession=1003968, name="SIEVE", flags={3}, parents={["MS:1003961", "MS:1001456", "MS:1001457"]})]
1316 #[doc="SIEVE - Thermo Scientific software for label-free differential expression analysis of LC-MS and GC-MS data, providing chromatographic alignment, feature detection, and statistical comparison for proteomics and metabolomics."]
1317 SIEVE,
1318 #[term(cv=MS, accession=1003969, name="BioPharma Finder", flags={3}, parents={["MS:1003961", "MS:1001456", "MS:1001457"]})]
1319 #[doc="BioPharma Finder - Thermo Scientific software for complex biotherapeutic characterization by LC-MS, supporting intact protein analysis, peptide mapping, oligonucleotide analysis, multi-attribute method workflows, and top-down or middle-down approaches."]
1320 BioPharmaFinder,
1321 #[term(cv=MS, accession=1003977, name="Monocle", flags={2}, parents={["MS:1001457"]})]
1322 #[doc="Monocle - A software program for converting Thermo Scientific RAW file format to mzXML, mzML, or CSV with improved monoisotopic mass estimation. Monocle was originally developed at the Gygi Lab at Harvard Medical School."]
1323 Monocle,
1324 #[term(cv=MS, accession=1003996, name="DeepNovo", flags={1}, parents={["MS:1001456", "MS:1001949"]})]
1325 #[doc="DeepNovo - DeepNovo is a deep-learning based de novo peptide sequencer for DDA."]
1326 DeepNovo,
1327 #[term(cv=MS, accession=1003997, name="DeepNovo-DIA", flags={1}, parents={["MS:1001456", "MS:1001949"]})]
1328 #[doc="DeepNovo-DIA - DeepNovo is a deep-learning based de novo peptide sequencer for DDA and DIA."]
1329 DeepNovoDIA,
1330 #[term(cv=MS, accession=1003998, name="PointNovo", flags={1}, parents={["MS:1001456"]})]
1331 #[doc="PointNovo - PointNovo is neural network based de novo peptide sequencing model."]
1332 PointNovo,
1333 #[term(cv=MS, accession=1003999, name="PGPointNovo", flags={1}, parents={["MS:1001456"]})]
1334 #[doc="PGPointNovo - PGPointNovo is a modification of PointNovo that allows parallel processing and a better optimization strategy."]
1335 PGPointNovo,
1336 #[term(cv=MS, accession=1004000, name="BiATNovo", flags={1}, parents={["MS:1001456"]})]
1337 #[doc="BiATNovo - BiATNovo an attention based bidirectional de novo peptide sequencing software."]
1338 BiATNovo,
1339 #[term(cv=MS, accession=1004001, name="NovoB", flags={1}, parents={["MS:1001456"]})]
1340 #[doc="NovoB - NovoB a transformer based bidirectional de novo peptide sequencing software."]
1341 NovoB,
1342 #[term(cv=MS, accession=1004002, name="PepNet", flags={1}, parents={["MS:1001456"]})]
1343 #[doc="PepNet - PepNet a convolutional neural network de novo peptide sequencing software."]
1344 PepNet,
1345 #[term(cv=MS, accession=1004003, name="π-HelixNovo", flags={1}, parents={["MS:1001456"]})]
1346 #[doc="π-HelixNovo - π-HelixNovo a transformer based de novo peptide sequencing software."]
1347 PiHelixNovo,
1348 #[term(cv=MS, accession=1004004, name="π-PrimeNovo", flags={1}, parents={["MS:1001456"]})]
1349 #[doc="π-PrimeNovo - π-PrimeNovo a non-autoregressive de novo peptide sequencing software."]
1350 PiPrimeNovo,
1351 #[term(cv=MS, accession=1004005, name="PowerNovo", flags={1}, parents={["MS:1001456"]})]
1352 #[doc="PowerNovo - PowerNovo a BERT and transformer ensemble de novo peptide sequencing software."]
1353 PowerNovo,
1354 #[term(cv=MS, accession=1004006, name="pUniFind", flags={1}, parents={["MS:1001456"]})]
1355 #[doc="pUniFind - pUniFind a open modification de novo peptide sequencing and rescoring software."]
1356 PUniFind,
1357 #[term(cv=MS, accession=1004007, name="Sage", flags={1}, parents={["MS:1001456", "MS:1001139"]})]
1358 #[doc="Sage - A database search based peptide identification software with retention time prediction, quantification, rescoring, and false discovery rate control."]
1359 Sage,
1360 #[term(cv=MS, accession=1004009, name="ProteoScape", flags={1}, parents={["MS:1001456", "MS:1000692"]})]
1361 #[doc="ProteoScape - Bruker ProteoScape is a GPU-powered platform delivering parallel computing capabilities and real-time database search results for bottom-up proteomics."]
1362 ProteoScape,
1363 #[term(cv=MS, accession=1004010, name="Stitch", flags={1}, parents={["MS:1001456"]})]
1364 #[doc="Stitch - Template-based assembly of PSMs for de novo protein sequencing."]
1365 Stitch,
1366 #[term(cv=MS, accession=4000151, name="MsQuality", flags={1}, parents={["MS:1001456"]})]
1367 #[doc="MsQuality - MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data."]
1368 MsQuality,
1369 #[term(cv=MS, accession=4000189, name="DIAMetric", flags={1}, parents={["MS:1001456"]})]
1370 #[doc="DIAMetric - DIAMetric is a Data-Independent Acquisition Quality Metric Generator."]
1371 DIAMetric,
1372 }
1373 }
1375
1376#[cfg(test)]
1377mod test {
1378 use crate::params::ParamDescribed;
1379
1380 use super::*;
1381
1382 #[test]
1383 fn cvmap_test() {
1384 assert_eq!(
1385 SoftwareTerm::SCIEXTOFTOFSeriesExplorerSoftware.accession(),
1386 1001483
1387 );
1388 assert_eq!(
1389 SoftwareTerm::SCIEXTOFTOFSeriesExplorerSoftware.name(),
1390 "SCIEX TOF/TOF Series Explorer Software"
1391 );
1392 assert_eq!(
1393 SoftwareTerm::SCIEXTOFTOFSeriesExplorerSoftware.flags(),
1394 SoftwareType::Analysis | SoftwareType::Acquisition | SoftwareType::DataProcessing
1395 );
1396 assert!(
1397 SoftwareTerm::SCIEXTOFTOFSeriesExplorerSoftware.flags().is_analysis(),
1398 );
1399 }
1400
1401 #[test]
1402 fn sw_test() {
1403 let mut sw = Software::new("foo".into(), "v0.1.0".into(), vec![custom_software_name("foo")]);
1404 assert_eq!(sw.id, "foo");
1405 assert_eq!(sw.version, "v0.1.0");
1406 assert!(sw.find_software_term().is_some());
1407 sw.add_param(SoftwareTerm::ANNSoLo.into());
1408 assert!(!sw.is_analysis());
1409 sw.params_mut().reverse();
1410 assert!(sw.is_analysis());
1411 assert!(sw.find_software_term().is_some());
1412
1413
1414 let id = Software::find_unique_id("foo", [sw].iter());
1415 assert_eq!(id, "foo_0");
1416 }
1417}