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Prepare mqpar.xml

How to prepare mqpar.xml for a pipeline?

LAMPrEY can use a custom mqpar.xml, but the file must follow a few rules so the server can turn it into a reusable single-run template.

Note

If you do not upload a custom file, the application uses the bundled mqpar_2.4.12.0.xml template built to work with MaxQuant v2.4.12.0 automatically. This file contains the default paramteres frm Maxquant to process TMT-11 data. You can use it as a reference for the required structure and placeholders when preparing your own mqpar.xml file. The bundled template is a good starting point if you are using the recommended MaxQuant version and do not need custom search settings.

  1. Open MaxQuant locally.
  2. Configure the search with one representative .raw file.
  3. Set the FASTA file and all other search parameters as desired.
  4. Export mqpar.xml.
  5. Check that the file contains only one raw-file entry and one experiment entry.
  6. Upload it when creating the pipeline in LAMPrEY.

Core requirement

Create the mqpar.xml in MaxQuant with exactly one representative .raw file loaded.

LAMPrEY rewrites that single-run template at runtime for each uploaded file. The code path expects one raw-file entry only.

Required placeholders

The uploaded template must be convertible into this pattern:

<fastaFiles>
  <FastaFileInfo>
    <fastaFilePath>__FASTA__</fastaFilePath>
  </FastaFileInfo>
</fastaFiles>
...
<filePaths>
  <string>__RAW__</string>
</filePaths>
...
<experiments>
  <string>__LABEL__</string>
</experiments>

What each placeholder means:

  • __FASTA__: LAMPrEY replaces FASTA with the pipeline FASTA file path
  • __RAW__: LAMPrEY replaces RAW with the current uploaded raw file path
  • __LABEL__: LAMPrEY replaces LABEL with the run label used for the sample

When you upload a normal single-run mqpar.xml, LAMPrEY converts the FASTA entry, the raw-file entry, and the experiment entry into these placeholders automatically.

Important constraints

1. Use a single RAW file

Do not export an mqpar.xml with multiple raw-file entries.

LAMPrEY's template conversion checks the file and expects exactly one <string>...raw</string> entry in <filePaths>.

2. Do not hard-code the production FASTA path

The FASTA path must be replaceable by the pipeline FASTA file. In the bundled example, this is:

<fastaFilePath>__FASTA__</fastaFilePath>

3. Keep the file-path section simple

The bundled example uses:

<filePaths>
  <string>__RAW__</string>
</filePaths>

That is the expected single-file pattern for a LAMPrEY pipeline template.

4. Keep experiment labels template-friendly

The bundled example uses:

<experiments>
  <string>__LABEL__</string>
</experiments>

LAMPrEY converts the single experiment entry into __LABEL__, then replaces that value per run so the generated MaxQuant run uses the correct label.

Example from mqpar_2.4.12.0.xml

The bundled example at app/seed/defaults/config/mqpar_2.4.12.0.xml already shows the required structure:

  • <fastaFilePath>__FASTA__</fastaFilePath>
  • <string>__RAW__</string> inside <filePaths>
  • <string>__LABEL__</string> inside <experiments>
  • a single fraction entry
  • a single parameter-group index

These sections are what make the file usable as a reusable pipeline template instead of a one-off local MaxQuant run file.