updated USI example to mzQC v1.0 (#229)

* updated USI example to mzQC v1.0 * Update USI-example.mzQC fix validation issues * Some editing --------- Co-authored-by: Mathias Walzer <walzer@ebi.ac.uk> Co-authored-by: Wout Bittremieux <wout@bittremieux.be>
HUPO-PSI · Jul 29, 2024 · 11bcff2 · 11bcff2
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diff --git a/docs/pages/worked-examples/USI-example.mzQC.md b/docs/pages/worked-examples/USI-example.mzQC.md
diff --git a/docs/pages/worked-examples/adv_mzqc_usi.md b/docs/pages/worked-examples/adv_mzqc_usi.md
@@ -0,0 +1,65 @@
+---
+layout: page
+title: "Integration of the Universal Spectrum Identifier (USI) in mzQC"
+permalink: /examples/adv_mzqc_usi/
+---
+
+The mzQC format supports various QC metrics that can operate at the level of MS runs or individual spectra.
+One of the powerful features of mzQC is its compatibility with the [Universal Spectrum Identifier (USI)](https://www.psidev.info/usi), also developed by the Proteomics Standards Initiative.
+This compatibility allows mzQC to reference individual spectra explicitly and precisely within a larger dataset.
+
+## Example: Computing the "spectra half-TIC" metric using USI
+
+In this example, we demonstrate the calculation of the "spectra half-TIC" metric for multiple MS/MS spectra.
+The "spectra half-TIC" metric measures the minimal number of the most intense peaks needed to achieve half of the total ion current (TIC) of a spectrum.
+This metric helps in understanding the peak intensity distribution within a spectrum, where a lower value indicates a concentration of intensity in fewer peaks.
+
+For this example, the calculation is limited to the first 10 MS/MS spectra.
+The results are formatted as a tabular metric where one column lists the USIs of the spectra and the other the computed fractional TIC values.
+This example emphasizes the utility of USIs for directly linking QC metrics to specific spectra in public databases like ProteomeXchange.
+
+The JSON representation of the quality metric in the mzQC format includes:
+
+```json
+"qualityMetrics": [
+  {
+    "accession": "MS:4000068",
+    "name": "spectra half-TIC",
+    "description": "The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well.",
+    "value": {
+      "MS:1003063": [
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:2",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:7",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:29",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:31",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:34",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:43",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:45",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:48",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:50",
+        "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:51"
+      ],
+      "UO:0000191": [
+        0.1134,
+        0.1628,
+        0.0536,
+        0.1020,
+        0.1042,
+        0.0947,
+        0.0784,
+        0.1239,
+        0.2593,
+        0.1214
+      ]
+    }
+  }
+]
+```
+
+The table pairs each spectrum's USI with its corresponding "spectra half-TIC" value.
+This format enables clear, unambiguous links between the QC data and the specific spectra, facilitating straightforward validation and further analysis.
+Spectrum references use USIs which provide a robust method to trace back to the exact source data in public repositories, enhancing transparency and reproducibility in proteomic research.
+
+Each spectrum and its TIC contribution can be directly accessed and verified online, ensuring that researchers can easily validate and reproduce findings.
+For instance, the spectrum at USI [`mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:2`](https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:2) can be directly resolved and viewed on PRIDE.
+Additionally, the full mzQC file is available [here](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/adv_mzqc_usi.mzQC).
diff --git a/...ation_documents/examples/USI-example.mzQC → ...tion_documents/examples/adv_mzqc_usi.mzQC b/...ation_documents/examples/USI-example.mzQC → ...tion_documents/examples/adv_mzqc_usi.mzQC
@@ -4,14 +4,14 @@
     "version": "1.0.0",
     "contactName": "Mathias Walzer",
     "contactAddress": "walzer@ebi.ac.uk",
-    "description": "A simple mzQC file containing a metric exemplifying USI incorporation to a metric.",
+    "description": "A simple mzQC file exemplifying integration with the Universal Spectrum Identifier to refer to individual spectra.",
     "runQualities": [
       {
         "metadata": {
           "inputFiles": [
             {
               "location": "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000966/CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.raw",
-              "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.trfr.t3.mzML",
+              "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09",
               "fileFormat": {
                 "accession": "MS:1000584",
                 "name": "mzML format"
@@ -39,6 +39,7 @@
             {
               "accession": "MS:1001058",
               "name": "quality estimation by manual validation",
+              "description": "The quality estimation was done manually.",
               "version": "0",
               "uri": "https://dx.doi.org/10.1021/pr201071t"
             }
@@ -48,6 +49,7 @@
           {
             "accession": "MS:4000068",
             "name": "spectra half-TIC",
+            "description": "The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well.",
             "value": {
               "MS:1003063": [
                 "mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:2",
@@ -65,7 +67,7 @@
                 0.1134,
                 0.1628,
                 0.0536,
-                0.102,
+                0.1020,
                 0.1042,
                 0.0947,
                 0.0784,
@@ -81,13 +83,13 @@
     "controlledVocabularies": [
       {
         "name": "Proteomics Standards Initiative Mass Spectrometry Ontology",
-        "uri": "https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo",
-        "version": "4.1.7"
+        "uri": "https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.157/psi-ms.obo",
+        "version": "4.1.157"
       },
       {
         "name": "Unit Ontology",
-        "uri": "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo",
-        "version": "f9ff25b"
+        "uri": "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/v2023-05-23/unit-ontology.obo",
+        "version": "v2023-05-23"
       }
     ]
   }

diff --git a/specification_documents/examples/intro_run.mzQC b/specification_documents/examples/intro_run.mzQC
@@ -117,6 +117,11 @@
         "name": "Proteomics Standards Initiative Mass Spectrometry Ontology",
         "uri": "https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.130/psi-ms.obo",
         "version": "4.1.130"
+      },
+      {
+        "name": "Unit Ontology",
+        "uri": "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/v2023-05-23/unit-ontology.obo",
+        "version": "v2023-05-23"
       }
     ]
   }