From 741f3c6da490b42e0e16a4c74be786933ace26b9 Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Wed, 10 Jul 2024 15:52:27 +0200 Subject: [PATCH 1/3] updated USI example to mzQC v1.0 --- .../pages/worked-examples/USI-example.mzQC.md | 51 +++++++++++++------ .../examples/USI-example.mzQC | 4 +- 2 files changed, 37 insertions(+), 18 deletions(-) diff --git a/docs/pages/worked-examples/USI-example.mzQC.md b/docs/pages/worked-examples/USI-example.mzQC.md index 1b5a4abb..23fbc825 100644 --- a/docs/pages/worked-examples/USI-example.mzQC.md +++ b/docs/pages/worked-examples/USI-example.mzQC.md @@ -4,27 +4,28 @@ title: "USI Example of mzQC" permalink: /examples/USI-example/ --- -Here, we describe a mzQC JSON document to exemplify the use of USI to address the quality of specific spectra by metrics recorded in a table value type. +Here, we describe a mzQC JSON document to exemplify the use of Universal Spectrum Identifiers ([USI](https://doi.org/10.1038%2Fs41592-021-01184-6]) +to address the quality of specific spectra by metrics recorded in a table value type. -Find the complete example file at the bottom of this document or in the example folder. +Find the complete example file at the bottom of this document or in the [examples folder](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples). -We explained the basic structure of an mzQC in previous examples (e.g. individual-runs.mzQC) and here dive directly into the details. +We explained the basic structure of an mzQC in [previous examples](https://hupo-psi.github.io/mzQC/examples/) (e.g. intro_run.mzQC) and here dive directly into the details. The metric values are derived from spectra of a particular run in the CPTAC project, acquired on a Thermo Orbitrap Velos instrument. For purposes of examplification the original run was truncated to the first 10 MS/MS spectra. ``` "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", + "location": "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000966/CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.mzML.gz", + "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.trfr.t3.mzML.gz", "fileFormat": { "accession": "MS:1000584", "name": "mzML format" }, ``` -The metric gauges each considered spectra's TIC in relation to the spectra's peak intensities. +The metric gauges each considered spectra's TIC in relation to the peak intensities. It does so by calculating the (minimal) fraction of peaks neccessary to sum up to half the total intensity of the spectrum itself. -Thus, the metric value will range between 0 and 1, where values closer to 0 will indicate spectra which' TIC is dominated by a few high intensity peaks. +Thus, the metric value will range between 0 and 1, where values closer to 0 will indicate spectra whose TIC is dominated by a few high intensity peaks. ``` "qualityMetrics": [ { @@ -32,25 +33,43 @@ Thus, the metric value will range between 0 and 1, where values closer to 0 will "name": "spectra half-TIC", "value": { ``` -The values for this metric are recorded in a table value type and consist of a column for the spectrum reference and the fractional value ("UO:0000191"). -The spectrum reference is defined by the metric as either the NativeID and/or preferrably the USI in a separate column. -The latter two columns are optional, however at least one has to be present. In our case, as the originating MS-run is available via proteomexchange, and the USI is a more detailed version of NativeID, no NativeID column is given. +The values for this metric are recorded in a table defined by the CV Term [MS:4000068](https://github.com/HUPO-PSI/psi-ms-CV/blob/be1085ed502ef6efc17ec896a03f4154e13428cc/psi-ms.obo#L22927) and consist of a column for the spectrum reference and a second column for the fractional value ("UO:0000191"). +The spectrum reference is defined by the CV as either the NativeID and/or preferrably the USI in a separate column, of which at least one has to be present. +In our case, as the originating MS-run is available via ProteomExchange, and the USI is a more detailed version of NativeID, no NativeID column is given. ``` "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" + "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": [ - 0.1134,0.1628,0.0536,0.102,0.1042,0.0947,0.0784,0.1239,0.2593,0.1214 + 0.1134, + 0.1628, + 0.0536, + 0.102, + 0.1042, + 0.0947, + 0.0784, + 0.1239, + 0.2593, + 0.1214 ] } } ], ``` -As you can see from the values in the fractional value column, +As you can see from the values in the fractional value (UO:0000191) column, most of the first ten spectra cluster around a value of about 10% of the peaks dominating the respective spectras' TIC, with only a few outliers to the 25% and the 5% range. -Each row represents one spectrum that can be directly looked up, in the case of using USI for spectra reference, -[even directly from the web](https://www.proteomicsdb.org/use/?usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:2). +Each row represents one spectrum that can be directly looked up. For USI, +[even directly from the web](https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_05_2Feb12_Cougar_11-10-09:scan:2). ### This is the mzQC file once again, in full: -**[USI-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/USI-example.mzQC)** \ No newline at end of file +**[USI-example.mzQC](https://github.com/HUPO-PSI/mzQC/blob/main/specification_documents/examples/USI-example.mzQC)** \ No newline at end of file diff --git a/specification_documents/examples/USI-example.mzQC b/specification_documents/examples/USI-example.mzQC index 8348792d..00b1eb9e 100644 --- a/specification_documents/examples/USI-example.mzQC +++ b/specification_documents/examples/USI-example.mzQC @@ -10,8 +10,8 @@ "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", + "location": "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000966/CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.mzML.gz", + "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.trfr.t3.mzML.gz", "fileFormat": { "accession": "MS:1000584", "name": "mzML format" From 0429647977892a09ff1b79f3db95e3cf4ad54187 Mon Sep 17 00:00:00 2001 From: Mathias Walzer Date: Tue, 23 Jul 2024 15:56:48 +0100 Subject: [PATCH 2/3] Update USI-example.mzQC fix validation issues --- .../examples/USI-example.mzQC | 84 ++++++++++--------- 1 file changed, 43 insertions(+), 41 deletions(-) diff --git a/specification_documents/examples/USI-example.mzQC b/specification_documents/examples/USI-example.mzQC index 00b1eb9e..8cbb0486 100644 --- a/specification_documents/examples/USI-example.mzQC +++ b/specification_documents/examples/USI-example.mzQC @@ -1,5 +1,5 @@ -{ - "mzQC": { +{"mzQC": + { "creationDate": "2022-03-16T18:58:45Z", "version": "1.0.0", "contactName": "Mathias Walzer", @@ -8,46 +8,48 @@ "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.mzML.gz", - "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.trfr.t3.mzML.gz", - "fileFormat": { - "accession": "MS:1000584", - "name": "mzML format" - }, - "fileProperties": [ - { - "accession": "MS:1000747", - "name": "completion time", - "value": "2012-02-03 11:00:41" + "inputFiles": [ + { + "location": "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000966/CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.mzML.gz", + "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09", + "fileFormat": { + "accession": "MS:1000584", + "name": "mzML format" }, - { - "accession": "MS:1003151", - "name": "SHA-256", - "value": "82ff4545ab8ab85252a4c5bc2c62abbfd04021ef5fefce145386bf27ae663a0f" - }, - { - "accession": "MS:1000031", - "name": "instrument model", - "value": "LTQ Orbitrap Velos" - } - ] - } - ], - "analysisSoftware": [ - { - "accession": "MS:1001058", - "name": "quality estimation by manual validation", - "version": "0", - "uri": "https://dx.doi.org/10.1021/pr201071t" - } - ] + "fileProperties": [ + { + "accession": "MS:1000747", + "name": "completion time", + "value": "2012-02-03 11:00:41" + }, + { + "accession": "MS:1003151", + "name": "SHA-256", + "value": "82ff4545ab8ab85252a4c5bc2c62abbfd04021ef5fefce145386bf27ae663a0f" + }, + { + "accession": "MS:1000031", + "name": "instrument model", + "value": "LTQ Orbitrap Velos" + } + ] + } + ], + "analysisSoftware": [ + { + "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" + } + ] }, "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", @@ -81,14 +83,14 @@ "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" } ] - } + } } From a81543f551d5c3309b6e8875de560dc0af8177b5 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Mon, 29 Jul 2024 17:07:17 +0200 Subject: [PATCH 3/3] Some editing --- .../pages/worked-examples/USI-example.mzQC.md | 75 ----------------- docs/pages/worked-examples/adv_mzqc_usi.md | 65 +++++++++++++++ .../{USI-example.mzQC => adv_mzqc_usi.mzQC} | 80 +++++++++---------- .../examples/intro_run.mzQC | 5 ++ 4 files changed, 110 insertions(+), 115 deletions(-) delete mode 100644 docs/pages/worked-examples/USI-example.mzQC.md create mode 100644 docs/pages/worked-examples/adv_mzqc_usi.md rename specification_documents/examples/{USI-example.mzQC => adv_mzqc_usi.mzQC} (60%) diff --git a/docs/pages/worked-examples/USI-example.mzQC.md b/docs/pages/worked-examples/USI-example.mzQC.md deleted file mode 100644 index b3109650..00000000 --- a/docs/pages/worked-examples/USI-example.mzQC.md +++ /dev/null @@ -1,75 +0,0 @@ ---- -layout: page -title: "USI Example of mzQC" -permalink: /examples/USI-example/ ---- - -Here, we describe a mzQC JSON document to exemplify the use of Universal Spectrum Identifiers ([USI](https://doi.org/10.1038%2Fs41592-021-01184-6]) -to address the quality of specific spectra by metrics recorded in a table value type. - - -Find the complete example file at the bottom of this document or in the [examples folder](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples). - -We explained the basic structure of an mzQC in [previous examples](https://hupo-psi.github.io/mzQC/examples/) (e.g. intro_run.mzQC) and here dive directly into the details. -The metric values are derived from spectra of a particular run in the CPTAC project, acquired on a Thermo Orbitrap Velos instrument. -For purposes of examplification the original run was truncated to the first 10 MS/MS spectra. -``` - "inputFiles": [ - { - "location": "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/09/PXD000966/CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.mzML.gz", - "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.trfr.t3.mzML.gz", - "fileFormat": { - "accession": "MS:1000584", - "name": "mzML format" - }, -``` -The metric gauges each considered spectra's TIC in relation to the peak intensities. -It does so by calculating the (minimal) fraction of peaks neccessary to sum up to half the total intensity of the spectrum itself. -Thus, the metric value will range between 0 and 1, where values closer to 0 will indicate spectra whose TIC is dominated by a few high intensity peaks. -``` - "qualityMetrics": [ - { - "accession": "MS:4000068", - "name": "spectra half-TIC", - "value": { -``` -The values for this metric are recorded in a table defined by the CV Term [MS:4000068](https://github.com/HUPO-PSI/psi-ms-CV/blob/be1085ed502ef6efc17ec896a03f4154e13428cc/psi-ms.obo#L22927) and consist of a column for the spectrum reference and a second column for the fractional value ("UO:0000191"). -The spectrum reference is defined by the CV as either the NativeID and/or preferrably the USI in a separate column, of which at least one has to be present. -In our case, as the originating MS-run is available via ProteomExchange, and the USI is a more detailed version of NativeID, no NativeID column is given. -``` - "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, - 0.102, - 0.1042, - 0.0947, - 0.0784, - 0.1239, - 0.2593, - 0.1214 - ] - } - } - ], -``` -As you can see from the values in the fractional value (UO:0000191) column, -most of the first ten spectra cluster around a value of about 10% of the peaks dominating the respective spectras' TIC, -with only a few outliers to the 25% and the 5% range. -Each row represents one spectrum that can be directly looked up. For USI, -[even directly from the web](https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_05_2Feb12_Cougar_11-10-09:scan:2). - -### This is the mzQC file once again, in full: -**[USI-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/USI-example.mzQC)** \ No newline at end of file diff --git a/docs/pages/worked-examples/adv_mzqc_usi.md b/docs/pages/worked-examples/adv_mzqc_usi.md new file mode 100644 index 00000000..ed1a9c68 --- /dev/null +++ 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/specification_documents/examples/USI-example.mzQC b/specification_documents/examples/adv_mzqc_usi.mzQC similarity index 60% rename from specification_documents/examples/USI-example.mzQC rename to specification_documents/examples/adv_mzqc_usi.mzQC index 8cbb0486..170d3d41 100644 --- a/specification_documents/examples/USI-example.mzQC +++ b/specification_documents/examples/adv_mzqc_usi.mzQC @@ -1,49 +1,49 @@ -{"mzQC": - { +{ + "mzQC": { "creationDate": "2022-03-16T18:58:45Z", "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.mzML.gz", - "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09", - "fileFormat": { - "accession": "MS:1000584", - "name": "mzML format" + "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", + "fileFormat": { + "accession": "MS:1000584", + "name": "mzML format" + }, + "fileProperties": [ + { + "accession": "MS:1000747", + "name": "completion time", + "value": "2012-02-03 11:00:41" }, - "fileProperties": [ - { - "accession": "MS:1000747", - "name": "completion time", - "value": "2012-02-03 11:00:41" - }, - { - "accession": "MS:1003151", - "name": "SHA-256", - "value": "82ff4545ab8ab85252a4c5bc2c62abbfd04021ef5fefce145386bf27ae663a0f" - }, - { - "accession": "MS:1000031", - "name": "instrument model", - "value": "LTQ Orbitrap Velos" - } - ] - } - ], - "analysisSoftware": [ - { - "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" - } - ] + { + "accession": "MS:1003151", + "name": "SHA-256", + "value": "82ff4545ab8ab85252a4c5bc2c62abbfd04021ef5fefce145386bf27ae663a0f" + }, + { + "accession": "MS:1000031", + "name": "instrument model", + "value": "LTQ Orbitrap Velos" + } + ] + } + ], + "analysisSoftware": [ + { + "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" + } + ] }, "qualityMetrics": [ { @@ -67,7 +67,7 @@ 0.1134, 0.1628, 0.0536, - 0.102, + 0.1020, 0.1042, 0.0947, 0.0784, @@ -92,5 +92,5 @@ "version": "v2023-05-23" } ] - } + } } diff --git a/specification_documents/examples/intro_run.mzQC b/specification_documents/examples/intro_run.mzQC index da6b8e13..6fefa8b1 100644 --- 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" } ] }