diff --git a/psi-ms.owl b/psi-ms.owl index 2b2c86e..cd28792 100644 --- a/psi-ms.owl +++ b/psi-ms.owl @@ -10,13 +10,13 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + * MS:$sequence(7,0,9999999)$ * PEFF:$sequence(7,0,9999999)$ - 10:11:2024 08:30 + 13:01:2025 17:58 MS 1.2 - Yasset Perez-Riverol + Wout Bittremieux For any queries contact psidev-ms-vocab@lists.sourceforge.net This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. @@ -72389,7 +72389,7 @@ 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 MS:4000028 - Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000179 for the MS1 equivalent. + Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000179 for the MS1 equivalent. fragment ppm deviation sigma @@ -72708,18 +72708,20 @@ - The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. + OBSOLETE. The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. + MS:4000182 MS XIC-Height-Q2 XIC-Height-Q3 XIC-Height-Q4 MS:4000052 - XIC-Height quartile ratios + obsolete XIC-Height quartile ratios + true - The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. + OBSOLETE. The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. PSI:MS @@ -72845,7 +72847,8 @@ - The interval when the respective quarter of the TIC accumulates divided by retention time duration. + OBSOLETE. The interval when the respective quarter of the TIC accumulates divided by retention time duration. + MS:4000183 MS RT-TIC-Q1 RT-TIC-Q2 @@ -72853,12 +72856,13 @@ RT-TIC-Q4 MS:4000054 The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run. - TIC quarters RT fraction + obsolete TIC quarters RT fraction + true - The interval when the respective quarter of the TIC accumulates divided by retention time duration. + OBSOLETE. The interval when the respective quarter of the TIC accumulates divided by retention time duration. PSI:MS @@ -72928,7 +72932,8 @@ - The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. + OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. + MS:4000184 MS RT-MS-Q1 RT-MS-Q2 @@ -72936,12 +72941,13 @@ RT-MS-Q4 MS:4000055 The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type. - MS1 quarter RT fraction + obsolete MS1 quarter RT fraction + true - The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. + OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. PSI:MS @@ -73011,7 +73017,8 @@ - The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. + OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. + MS:4000185 MS RT-MSMS-Q1 RT-MSMS-Q2 @@ -73019,12 +73026,13 @@ RT-MSMS-Q4 MS:4000056 The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. - MS2 quarter RT fraction + obsolete MS2 quarter RT fraction + true - The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. + OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. PSI:MS @@ -73094,19 +73102,21 @@ - The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 + OBSOLETE. The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 + MS:4000186 MS MS1-TIC-Change-Q2 MS1-TIC-Change-Q3 MS1-TIC-Change-Q4 MS:4000057 The metric informs about the dynamic range of the acquisition along the chromatographic separation.This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant. - MS1 TIC-change quartile ratios + obsolete MS1 TIC-change quartile ratios + true - The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 + OBSOLETE. The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 PSI:MS @@ -73170,19 +73180,21 @@ - The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. + OBSOLETE. The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. + MS:4000187 MS MS1-TIC-Q2 MS1-TIC-Q3 MS1-TIC-Q4 MS:4000058 The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples. - MS1 TIC quartile ratios + obsolete MS1 TIC quartile ratios + true - The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. + OBSOLETE. The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. PSI:MS @@ -78899,7 +78911,8 @@ - The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. + OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. + MS:4000188 MS RT-MSMS-Q1 RT-MSMS-Q2 @@ -78907,12 +78920,13 @@ RT-MSMS-Q4 MS:4000181 The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. - identified MS2 quarter RT fraction + obsolete identified MS2 quarter RT fraction + true - The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. + OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. PSI:MS @@ -78942,6 +78956,619 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The log ratio of successive XIC height quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of XIC-Height-Q2 to XIC-Height-Q1, XIC-Height-Q3 to XIC-Height-Q2, XIC-Height max to XIC-Height-Q3. The number of values in the tuple implies the quantile mode. + MS + XIC-Height-Q2 + XIC-Height-Q3 + XIC-Height-Q4 + MS:4000182 + XIC-Height quantile ratios + + + + + The log ratio of successive XIC height quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of XIC-Height-Q2 to XIC-Height-Q1, XIC-Height-Q3 to XIC-Height-Q2, XIC-Height max to XIC-Height-Q3. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + XIC-Height-Q2 + PMID:24494671 + + + + + XIC-Height-Q3 + PMID:24494671 + + + + + XIC-Height-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of values in the tuple implies the quantile mode. + MS + RT-TIC-Q1 + RT-TIC-Q2 + RT-TIC-Q3 + RT-TIC-Q4 + MS:4000183 + The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run. + TIC quantile RT fraction + + + + + The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + RT-TIC-Q1 + PMID:24494671 + + + + + RT-TIC-Q2 + PMID:24494671 + + + + + RT-TIC-Q3 + PMID:24494671 + + + + + RT-TIC-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The interval used for acquisition of quantiles of all MS1 events divided by retention time duration. The number of values in the tuple implies the quantile mode. + MS + RT-MS-Q1 + RT-MS-Q2 + RT-MS-Q3 + RT-MS-Q4 + MS:4000184 + The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type. + MS1 quantile RT fraction + + + + + The interval used for acquisition of quantiles of all MS1 events divided by retention time duration. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + RT-MS-Q1 + PMID:24494671 + + + + + RT-MS-Q2 + PMID:24494671 + + + + + RT-MS-Q3 + PMID:24494671 + + + + + RT-MS-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The interval used for acquisition of quantiles of all MS2 events divided by retention time duration. The number of values in the tuple implies the quantile mode. + MS + RT-MSMS-Q1 + RT-MSMS-Q2 + RT-MSMS-Q3 + RT-MSMS-Q4 + MS:4000185 + The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. + MS2 quantile RT fraction + + + + + The interval used for acquisition of quantiles of all MS2 events divided by retention time duration. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + RT-MSMS-Q1 + PMID:24494671 + + + + + RT-MSMS-Q2 + PMID:24494671 + + + + + RT-MSMS-Q3 + PMID:24494671 + + + + + RT-MSMS-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The log ratios of successive TIC-change quantiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. A value triplet represents the original QuaMeter metrics, the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3. The number of values in the tuple implies the quantile mode. + MS + MS1-TIC-Change-Q2 + MS1-TIC-Change-Q3 + MS1-TIC-Change-Q4 + MS:4000186 + The metric informs about the dynamic range of the acquisition along the chromatographic separation. This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant. + MS1 TIC-change quantile ratios + + + + + The log ratios of successive TIC-change quantiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. A value triplet represents the original QuaMeter metrics, the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + MS1-TIC-Change-Q2 + PMID:24494671 + + + + + MS1-TIC-Change-Q3 + PMID:24494671 + + + + + MS1-TIC-Change-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The log ratios of successive TIC quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. The number of values in the tuple implies the quantile mode. + MS + MS1-TIC-Q2 + MS1-TIC-Q3 + MS1-TIC-Q4 + MS:4000187 + The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples. + MS1 TIC quantile ratios + + + + + The log ratios of successive TIC quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + MS1-TIC-Q2 + PMID:24494671 + + + + + MS1-TIC-Q3 + PMID:24494671 + + + + + MS1-TIC-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The interval used for acquisition of quantiles of all identified MS2 events, after user-defined acceptance criteria are applied, divided by retention time duration. The number of values in the tuple implies the quantile mode. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS + RT-MSMS-Q1 + RT-MSMS-Q2 + RT-MSMS-Q3 + RT-MSMS-Q4 + MS:4000188 + The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. + identified MS2 quantile RT fraction + + + + + The interval used for acquisition of quantiles of all identified MS2 events, after user-defined acceptance criteria are applied, divided by retention time duration. The number of values in the tuple implies the quantile mode. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + PSI:MS + + + + + RT-MSMS-Q1 + PMID:24494671 + + + + + RT-MSMS-Q2 + PMID:24494671 + + + + + RT-MSMS-Q3 + PMID:24494671 + + + + + RT-MSMS-Q4 + PMID:24494671 + + + + @@ -81955,6 +82582,12 @@ + + + + + +