* updated PSI-MS CV to 4.1.182 and Unimod to 12:08:2024

* updated MBI file format and nativeID cvParam

pwiz/data/common/cv.hpp

@@ -41,8 +41,8 @@
 // [psi-ms.obo]
 #define _PSI_MS_OBO_
 //   format-version: 1.2
-//   data-version: 4.1.163
-//   date: 19:07:2024 07:15
+//   data-version: 4.1.182
+//   date: 11:10:2024 07:15
 //   saved-by: Joshua Klein
 //   auto-generated-by: OBO-Edit 2.3.1
 //   default-namespace: MS
@@ -62,7 +62,7 @@
 //   remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
 //   remark: creator: Joshua Klein <jaklein <-at-> bu.edu>
 //   remark: creator: Chris Bielow <chris.bielow <-at-> fu-berlin.de>
-//   remark: creator: Wout Bittremieux <wbittremieux <-at-> health.ucsd.edu>
+//   remark: creator: Wout Bittremieux <wout.bittremieux <-at-> uantwerpen.be>
 //   remark: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de>
 //   remark: creator: Julian Uszkoreit <julian.uszkoreit <-at-> ruhr-uni-bochum.de>
 //   remark: creator: Mathias Walzer <walzer <-at-> ebi.ac.uk>
@@ -77,7 +77,7 @@
 // [unimod.obo]
 #define _UNIMOD_OBO_
 //   format-version: 1.4
-//   date: 29:02:2024 10:49
+//   date: 12:08:2024 11:33
 //
 // [unit.obo]
 #define _UNIT_OBO_
@@ -3896,8 +3896,11 @@ enum PWIZ_API_DECL CVID
     /// single protein identification statistic: Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group).
     MS_single_protein_identification_statistic = 1001116,
 
-    /// theoretical mass: The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier.
-    MS_theoretical_mass = 1001117,
+    /// theoretical neutral mass: The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier.
+    MS_theoretical_neutral_mass = 1001117,
+
+    /// theoretical mass (theoretical neutral mass): The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier.
+    MS_theoretical_mass = MS_theoretical_neutral_mass,
 
     /// param: b ion: Parameter information, type of product: b ion with charge on the N-terminal side.
     MS_param__b_ion = 1001118,
@@ -4088,6 +4091,12 @@ enum PWIZ_API_DECL CVID
     /// search statistics: The details of the actual run of the search.
     MS_search_statistics = 1001184,
 
+    /// Mobilion MBI format: Mobilion MBI file format.
+    MS_Mobilion_MBI_format = 1001185,
+
+    /// Mobilion MBI nativeID format: Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
+    MS_Mobilion_MBI_nativeID_format = 1001186,
+
     /// modification specificity peptide N-term: As parameter for search engine: apply the modification only at the N-terminus of a peptide.
     MS_modification_specificity_peptide_N_term = 1001189,
 
@@ -7568,8 +7577,11 @@ enum PWIZ_API_DECL CVID
     /// second-pass peptide identification: A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search.
     MS_second_pass_peptide_identification = 1002341,
 
-    /// MZmine: A framework for differential analysis of mass spectrometry data.
-    MS_MZmine = 1002342,
+    /// mzmine: A framework for differential analysis of mass spectrometry data.
+    MS_mzmine = 1002342,
+
+    /// MZmine (mzmine): A framework for differential analysis of mass spectrometry data.
+    MS_MZmine = MS_mzmine,
 
     /// ion stability type: Stability type of the ion.
     MS_ion_stability_type_OBSOLETE = 1002343,
@@ -10853,6 +10865,48 @@ enum PWIZ_API_DECL CVID
     /// electron beam energy: The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD).
     MS_electron_beam_energy = 1003410,
 
+    /// Orbitrap IQ-X: Thermo Scientific Orbitrap IQ-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.
+    MS_Orbitrap_IQ_X = 1003411,
+
+    /// timsTOF Ultra 2: Bruker Daltonics timsTOF Ultra 2.
+    MS_timsTOF_Ultra_2 = 1003412,
+
+    /// Kojak: Kojak open-source crosslinked peptide sequence search engine developed at the Institute for Systems Biology.
+    MS_Kojak = 1003413,
+
+    /// Kojak:score: The Kojak score for an individual peptide sequence, similar to Comet:xcorr.
+    MS_Kojak_score = 1003414,
+
+    /// Kojak:expectation value: The Kojak expectation value for an individual peptide sequence.
+    MS_Kojak_expectation_value = 1003415,
+
+    /// Kojak:matched ions: The number of matched ions for an individual peptide sequence in a Kojak result.
+    MS_Kojak_matched_ions = 1003416,
+
+    /// Kojak:consecutive matched ions: The highest run of consecutive matched ions for an individual peptide sequence in a Kojak result.
+    MS_Kojak_consecutive_matched_ions = 1003417,
+
+    /// Kojak:delta score: The difference between the top Kojak score and the next best Kojak score for a PSM.
+    MS_Kojak_delta_score = 1003418,
+
+    /// Kojak:rank: The rank of an individual peptide from the first pass of the Kojak scoring algorithm. Applies only to sequences in a crosslinked result.
+    MS_Kojak_rank = 1003419,
+
+    /// Kojak:score xlink: The Kojak score for a crosslinked pair of peptide sequences, similar to Comet:xcorr.
+    MS_Kojak_score_xlink = 1003420,
+
+    /// Kojak:expectation value xlink: The Kojak expectation value for a crosslinked pair of peptide sequences.
+    MS_Kojak_expectation_value_xlink = 1003421,
+
+    /// Kojak:matched ions xlink: The number of matched ions for a crosslinked pair of peptide sequences in a Kojak result.
+    MS_Kojak_matched_ions_xlink = 1003422,
+
+    /// Orbitrap Exploris GC 240: Orbitrap Exploris GC 240 Mass Spectrometer.
+    MS_Orbitrap_Exploris_GC_240 = 1003423,
+
+    /// selected fragment theoretical m/z observed intensity spectrum: Spectrum for which the peaks are limited to a subset of known product ions that are important for subsequent identification, whose m/z values are corrected to theoretical values, and intensity values are experimentally derived.
+    MS_selected_fragment_theoretical_m_z_observed_intensity_spectrum = 1003424,
+
     /// Number of Occurrences: The number of times something happened.
     NCIT_Number_of_Occurrences = 103150827,
 
@@ -10928,6 +10982,30 @@ enum PWIZ_API_DECL CVID
     /// environment metric: QC metric related to measurements of the ambient environment, such as the laboratory.
     MS_environment_metric = 4000024,
 
+    /// precursor ion current chromatogram: Representation of the ion current assigned to detected precursors in the series of all MS1 spectra versus time.
+    MS_precursor_ion_current_chromatogram = 4000025,
+
+    /// precursor ion chromatogram (precursor ion current chromatogram): Representation of the ion current assigned to detected precursors in the series of all MS1 spectra versus time.
+    MS_precursor_ion_chromatogram = MS_precursor_ion_current_chromatogram,
+
+    /// fragment ppm deviation median: The median of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied.
+    MS_fragment_ppm_deviation_median = 4000026,
+
+    /// fragment ppm deviation mean: The mean of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied
+    MS_fragment_ppm_deviation_mean = 4000027,
+
+    /// fragment ppm deviation sigma: The standard deviation of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied
+    MS_fragment_ppm_deviation_sigma = 4000028,
+
+    /// area under TIC in MS1: The area under the total ion current chromatogram (MS:1000235) of all MS1 spectra.
+    MS_area_under_TIC_in_MS1 = 4000029,
+
+    /// area under TIC in MS2: The area under the total ion current chromatogram (MS:1000235) of all MS2 spectra.
+    MS_area_under_TIC_in_MS2 = 4000030,
+
+    /// peak area of MS1 vs MS2 signal ratio: The ratio of the area under TIC of MS1 (MS:4000029) divided by the area under the TIC of MS2 (MS:4000030).
+    MS_peak_area_of_MS1_vs_MS2_signal_ratio = 4000031,
+
     /// XIC50 fraction: The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC.
     MS_XIC50_fraction = 4000050,
 
@@ -15887,14 +15965,14 @@ enum PWIZ_API_DECL CVID
     /// DBIA: Desthiobiotinylation of cysteine with DBIA probe.
     UNIMOD_DBIA = 300002062,
 
-    /// Mono_Nγ-propargyl-L-Gln_desthiobiotin: Monomodification of Nγ-propargyl-L-Gln probe with clicked desthiobiotin-azide.
-    UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin = 300002067,
+    /// Mono_Ngamma-propargyl-L-Gln_desthiobiotin: Monomodification of Ngamma-propargyl-L-Gln probe with clicked desthiobiotin-azide.
+    UNIMOD_Mono_Ngamma_propargyl_L_Gln_desthiobiotin = 300002067,
 
-    /// Di_L-Glu_Nγ-propargyl-L-Gln_desthiobiotin: Dimodification of L-Glu and Nγ-propargyl-L-Gln probe with clicked desthiobiotin-azide.
-    UNIMOD_Di_L_Glu_N___propargyl_L_Gln_desthiobiotin = 300002068,
+    /// Di_L-Glu_Ngamma-propargyl-L-Gln_desthiobiotin: Dimodification of L-Glu and Ngamma-propargyl-L-Gln probe with clicked desthiobiotin-azide.
+    UNIMOD_Di_L_Glu_Ngamma_propargyl_L_Gln_desthiobiotin = 300002068,
 
-    /// Di_L-Gln_Nγ-propargyl-L-Gln_desthiobiotin: Dimodification of L-Gln and Nγ-propargyl-L-Gln probe with clicked desthiobiotin-azide.
-    UNIMOD_Di_L_Gln_N___propargyl_L_Gln_desthiobiotin = 300002069,
+    /// Di_L-Gln_Ngamma-propargyl-L-Gln_desthiobiotin: Dimodification of L-Gln and Ngamma-propargyl-L-Gln probe with clicked desthiobiotin-azide.
+    UNIMOD_Di_L_Gln_Ngamma_propargyl_L_Gln_desthiobiotin = 300002069,
 
     /// L-Gln: Monomodification with glutamine.
     UNIMOD_L_Gln = 300002070,
@@ -15935,6 +16013,63 @@ enum PWIZ_API_DECL CVID
     /// Label:13C(2)15N(1): 13C(2) 15N(1) Silac label.
     UNIMOD_Label_13C_2_15N_1_ = 300002088,
 
+    /// DPIA: Desthiobiotinylation of cysteine with DPIA (Desthiobiotin polyethyleneoxide iodoacetamide) probe.
+    UNIMOD_DPIA = 300002106,
+
+    /// Acetoacetyl: Acetoacetylation.
+    UNIMOD_Acetoacetyl = 300002107,
+
+    /// Isovaleryl: Isovalerylation.
+    UNIMOD_Isovaleryl = 300002108,
+
+    /// 2-methylbutyryl: 2-methylbutyrylation.
+    UNIMOD_2_methylbutyryl = 300002109,
+
+    /// Tiglyl: Tiglylation.
+    UNIMOD_Tiglyl = 300002110,
+
+    /// 3-methylglutaryl: 3-methylglutarylation.
+    UNIMOD_3_methylglutaryl = 300002111,
+
+    /// 3-methylglutaconyl: 3-methylglutaconylation.
+    UNIMOD_3_methylglutaconyl = 300002112,
+
+    /// 3-hydroxy-3-methylglutaryl: 3-hydroxy-3-methylglutarylation.
+    UNIMOD_3_hydroxy_3_methylglutaryl = 300002113,
+
+    /// Lactylation: Lactylation(Lac).
+    UNIMOD_Lactylation = 300002114,
+
+    /// Pyruvoyl: Pyruvoylation.
+    UNIMOD_Pyruvoyl = 300002115,
+
+    /// Glyoxylyl: Glyoxylylation.
+    UNIMOD_Glyoxylyl = 300002116,
+
+    /// Itaconatyl: Itaconatylation.
+    UNIMOD_Itaconatyl = 300002117,
+
+    /// Itaconyl: Itaconylation.
+    UNIMOD_Itaconyl = 300002118,
+
+    /// ValGly: UFMylation residue.
+    UNIMOD_ValGly = 300002119,
+
+    /// Pentanoyl: Pentanoylation.
+    UNIMOD_Pentanoyl = 300002120,
+
+    /// Hexanoyl: Hexanoylation.
+    UNIMOD_Hexanoyl = 300002121,
+
+    /// Label:13C(6)15N(2)+TMT6plex: Sixplex Tandem Mass Tag 13C(6) 15N(2) Silac label.
+    UNIMOD_Label_13C_6_15N_2__TMT6plex = 300002122,
+
+    /// Label:13C(6)15N(2)+TMTpro: TMTpro Tandem Mass Tag 13C(6) 15N(2) Silac label.
+    UNIMOD_Label_13C_6_15N_2__TMTpro = 300002123,
+
+    /// 2PCA-triazole-ethanethiol: Cleaved 2PCA clicked to biotin-SS-azide.
+    UNIMOD_2PCA_triazole_ethanethiol = 300002126,
+
     /// unit: A unit of measurement is a standardized quantity of a physical quality.
     UO_unit = 400000000,