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Merge pull request #796 from jonasscheid/feature/dda-precursor-columns
Add optional precursor mass/charge/RT/IM range columns to DDA/DIA template
2 parents 938c540 + 40d44ed commit 14f748e

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‎.gitignore‎

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# Claude Code #
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###############
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.claude/
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CLAUDE.md
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.codacy/
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# Local files for developers are in folder in local-info

‎sdrf-proteomics/metadata-guidelines/sdrf-terms.tsv‎

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@@ -76,6 +76,14 @@ data file comment MS:1000577 minimum, default, human, cell-lines, single-cell, i
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modification parameters comment MS:1001055 dia-acquisition, dda-acquisition Unimod, PSI-MOD Post-translational modifications searched true false false
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precursor mass tolerance comment PRIDE:0000575 dia-acquisition, dda-acquisition pattern: number + ppm/Da Precursor mass tolerance for database search true true false
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fragment mass tolerance comment PRIDE:0000576 dia-acquisition, dda-acquisition pattern: number + ppm/Da Fragment mass tolerance for database search true true false
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precursor min mz comment PRIDE:0000476 dia-acquisition, dda-acquisition numeric (m/z) MS method-defined minimum precursor m/z setting used to acquire the data true true false
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precursor max mz comment PRIDE:0000477 dia-acquisition, dda-acquisition numeric (m/z) MS method-defined maximum precursor m/z setting used to acquire the data true true false
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precursor min charge comment PRIDE:0000472 dia-acquisition, dda-acquisition integer MS method-defined minimum precursor charge state setting used to acquire the data true true false
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precursor max charge comment PRIDE:0000473 dia-acquisition, dda-acquisition integer MS method-defined maximum precursor charge state setting used to acquire the data true true false
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min retention time comment PRIDE:0000474 dia-acquisition, dda-acquisition numeric (minutes) LC method-defined minimum retention time setting used to acquire the data true true false
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max retention time comment PRIDE:0000475 dia-acquisition, dda-acquisition numeric (minutes) LC method-defined maximum retention time setting used to acquire the data true true false
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min ion mobility comment PRIDE:0000841 dia-acquisition, dda-acquisition numeric (1/K0 or Vs/cm2) MS method-defined minimum ion mobility setting used to acquire the data true true false
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max ion mobility comment PRIDE:0000842 dia-acquisition, dda-acquisition numeric (1/K0 or Vs/cm2) MS method-defined maximum ion mobility setting used to acquire the data true true false
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passage number comment to be filled cell-lines integer or range Passage number of the cell line true true false
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cell line source comment to be filled cell-lines free text Repository or source from which the cell line was obtained true true false
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authentication method comment to be filled cell-lines free text Method used to authenticate the cell line identity true true false

‎sdrf-proteomics/templates/dda-acquisition/README.adoc‎

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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000443">PSI-MS (MS:1000443)</a></td>
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<td>NT=orbitrap;AC=MS:1000484</td>
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</tr>
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<tr>
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<td><code>comment[precursor min mz]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined minimum precursor m/z setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000476">PRIDE (PRIDE:0000476)</a></td>
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<td>350, 400</td>
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</tr>
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<tr>
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<td><code>comment[precursor max mz]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined maximum precursor m/z setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000477">PRIDE (PRIDE:0000477)</a></td>
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<td>1600, 2000</td>
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</tr>
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<tr>
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<td><code>comment[precursor min charge]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined minimum precursor charge state setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000472">PRIDE (PRIDE:0000472)</a></td>
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<td>1, 2</td>
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</tr>
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<tr>
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<td><code>comment[precursor max charge]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined maximum precursor charge state setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000473">PRIDE (PRIDE:0000473)</a></td>
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<td>4, 6</td>
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</tr>
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<tr>
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<td><code>comment[min retention time]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>LC method-defined minimum retention time setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000474">PRIDE (PRIDE:0000474)</a></td>
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<td>0, 5</td>
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</tr>
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<tr>
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<td><code>comment[max retention time]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>LC method-defined maximum retention time setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000475">PRIDE (PRIDE:0000475)</a></td>
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<td>120, 90</td>
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</tr>
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<tr>
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<td><code>comment[min ion mobility]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined minimum ion mobility setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000841">PRIDE (PRIDE:0000841)</a></td>
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<td>0.6, 0.7</td>
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</tr>
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<tr>
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<td><code>comment[max ion mobility]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined maximum ion mobility setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000842">PRIDE (PRIDE:0000842)</a></td>
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<td>1.4, 1.6</td>
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</tr>
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</tbody>
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</table>
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|comment[precursor mass tolerance] |OPTIONAL |Mass tolerance for precursor ions in database search |Numeric value with unit |10 ppm, 20 ppm
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|comment[fragment mass tolerance] |OPTIONAL |Mass tolerance for fragment ions in database search |Numeric value with unit |0.02 Da, 20 ppm
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|comment[MS2 mass analyzer] |OPTIONAL |Mass analyzer used for MS2 acquisition |PSI-MS (MS:1000443) |NT=orbitrap;AC=MS:1000484
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|comment[precursor min mz] |OPTIONAL |MS method-defined minimum precursor m/z setting used to acquire the data |PRIDE (PRIDE:0000476) |350, 400
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|comment[precursor max mz] |OPTIONAL |MS method-defined maximum precursor m/z setting used to acquire the data |PRIDE (PRIDE:0000477) |1600, 2000
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|comment[precursor min charge] |OPTIONAL |MS method-defined minimum precursor charge state setting used to acquire the data |PRIDE (PRIDE:0000472) |1, 2
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|comment[precursor max charge] |OPTIONAL |MS method-defined maximum precursor charge state setting used to acquire the data |PRIDE (PRIDE:0000473) |4, 6
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|comment[min retention time] |OPTIONAL |LC method-defined minimum retention time setting used to acquire the data |PRIDE (PRIDE:0000474) |0, 5
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|comment[max retention time] |OPTIONAL |LC method-defined maximum retention time setting used to acquire the data |PRIDE (PRIDE:0000475) |120, 90
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|comment[min ion mobility] |OPTIONAL |MS method-defined minimum ion mobility setting used to acquire the data |PRIDE (PRIDE:0000841) |0.6, 0.7
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|comment[max ion mobility] |OPTIONAL |MS method-defined maximum ion mobility setting used to acquire the data |PRIDE (PRIDE:0000842) |1.4, 1.6
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|===
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endif::[]
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‎sdrf-proteomics/templates/dia-acquisition/README.adoc‎

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<td>Numeric value with unit</td>
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<td>0.02 Da, 20 ppm</td>
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</tr>
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<tr>
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<td><code>comment[precursor min mz]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined minimum precursor m/z setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000476">PRIDE (PRIDE:0000476)</a></td>
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<td>350, 400</td>
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</tr>
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<tr>
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<td><code>comment[precursor max mz]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined maximum precursor m/z setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000477">PRIDE (PRIDE:0000477)</a></td>
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<td>1600, 2000</td>
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</tr>
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<tr>
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<td><code>comment[precursor min charge]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined minimum precursor charge state setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000472">PRIDE (PRIDE:0000472)</a></td>
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<td>1, 2</td>
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</tr>
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<tr>
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<td><code>comment[precursor max charge]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined maximum precursor charge state setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000473">PRIDE (PRIDE:0000473)</a></td>
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<td>4, 6</td>
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</tr>
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<tr>
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<td><code>comment[min retention time]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>LC method-defined minimum retention time setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000474">PRIDE (PRIDE:0000474)</a></td>
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<td>0, 5</td>
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</tr>
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<tr>
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<td><code>comment[max retention time]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>LC method-defined maximum retention time setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000475">PRIDE (PRIDE:0000475)</a></td>
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<td>120, 90</td>
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</tr>
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<tr>
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<td><code>comment[min ion mobility]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined minimum ion mobility setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000841">PRIDE (PRIDE:0000841)</a></td>
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<td>0.6, 0.7</td>
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</tr>
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<tr>
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<td><code>comment[max ion mobility]</code></td>
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<td><span class="optional-badge">OPTIONAL</span></td>
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<td>MS method-defined maximum ion mobility setting used to acquire the data</td>
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<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000842">PRIDE (PRIDE:0000842)</a></td>
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<td>1.4, 1.6</td>
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</tr>
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</tbody>
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</table>
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|comment[precursor mass tolerance] |OPTIONAL |Mass tolerance for precursor ions in database search |Numeric value with unit |10 ppm, 20 ppm
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|comment[fragment mass tolerance] |OPTIONAL |Mass tolerance for fragment ions in database search |Numeric value with unit |0.02 Da, 20 ppm
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|comment[precursor min mz] |OPTIONAL |MS method-defined minimum precursor m/z setting used to acquire the data |PRIDE (PRIDE:0000476) |350, 400
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|comment[precursor max mz] |OPTIONAL |MS method-defined maximum precursor m/z setting used to acquire the data |PRIDE (PRIDE:0000477) |1600, 2000
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|comment[precursor min charge] |OPTIONAL |MS method-defined minimum precursor charge state setting used to acquire the data |PRIDE (PRIDE:0000472) |1, 2
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|comment[precursor max charge] |OPTIONAL |MS method-defined maximum precursor charge state setting used to acquire the data |PRIDE (PRIDE:0000473) |4, 6
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|comment[min retention time] |OPTIONAL |LC method-defined minimum retention time setting used to acquire the data |PRIDE (PRIDE:0000474) |0, 5
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|comment[max retention time] |OPTIONAL |LC method-defined maximum retention time setting used to acquire the data |PRIDE (PRIDE:0000475) |120, 90
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|comment[min ion mobility] |OPTIONAL |MS method-defined minimum ion mobility setting used to acquire the data |PRIDE (PRIDE:0000841) |0.6, 0.7
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|comment[max ion mobility] |OPTIONAL |MS method-defined maximum ion mobility setting used to acquire the data |PRIDE (PRIDE:0000842) |1.4, 1.6
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|===
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endif::[]
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[[diaPASEF-example]]
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== diaPASEF Example
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For ion mobility-enhanced DIA (diaPASEF), additional columns may be relevant:
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For ion mobility-enhanced DIA (diaPASEF), the following columns capture the ion mobility acquisition window:
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|===
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|Column Name |Description |Example Values
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|Column Name |Description |PRIDE CV |Example Values
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|comment[ion mobility]
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|Ion mobility separation used
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|TIMS, FAIMS, not applicable
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|comment[min ion mobility]
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|MS method-defined minimum ion mobility setting used to acquire the data
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|PRIDE:0000841
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|0.6
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|comment[1/K0 range]
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|Ion mobility range
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|0.6-1.6 1/K0
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|comment[max ion mobility]
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|MS method-defined maximum ion mobility setting used to acquire the data
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|PRIDE:0000842
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|1.6
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|===
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[[best-practices]]

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