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| Introduction to quantms.io | ||
| ====================================== | ||
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| The ``.qms`` folder will contain multiple metadata files that will be | ||
| used to describe the project, the samples, the data acquisition and the | ||
| data processing. Each of these files will be described in the following | ||
| sections: | ||
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| - `METADATA.md <METADATA.md>`__: A json file for metadata about the | ||
| analyzed project | ||
| - `AE <AE.rst>`__ or `DE <DE.rst>`__: A csv file based on the | ||
| MSstats (TODO link) format for either absolute expression or | ||
| differential expression. | ||
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| Some general rules for all the files: | ||
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| - The files are tab-delimited, json or parquet files | ||
| - Parquet files are compressed and can be read with pandas. | ||
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| Common data structures and formats | ||
| ---------------------------------- | ||
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| We have some concepts that are common for some outputs and would be good | ||
| to define and explain them here: | ||
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| Peptidoform | ||
| ~~~~~~~~~~~ | ||
|
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| - **Peptidoform**: A peptidoform is a peptide sequence with | ||
| modifications. For example, the peptide sequence ``PEPTIDM`` with a | ||
| modification of ``Oxidation`` would be ``PEPTIDM[Oxidation]``. The | ||
| peptidoform show be written using the `Proforma | ||
| specification <https://github.com/HUPO-PSI/ProForma>`__. This concept | ||
| is used in the following outputs: | ||
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| - `PSM <PSM.rst>`__ | ||
| - `FEATURES <FEATURES.rst>`__ | ||
| - `PEPTIDE <PEPTIDE.rst>`__ | ||
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| Modifications | ||
| ~~~~~~~~~~~~~ | ||
|
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||
| - **Modifications**: A modification is a chemical change in the peptide | ||
| sequence. Modifications can be annotated as part of the Proforma | ||
| notation inside the peptide or as a separate column. When annotating | ||
| the modification as a separate column, the format should be as close | ||
| as possible to the `mzTab format | ||
| notation <https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/1_0-Proteomics-Release>`__. | ||
| The modifications will encode the following information on each | ||
| peptide or psm: | ||
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| - Modification name or accession: For example, ``Oxidation`` or | ||
| ``UNIMOD:35``. Modifications SHOULD be reported using UNIMOD. If a | ||
| modification is not defined in UNIMOD, a CHEMMOD definition must | ||
| be used like ``CHEMMOD:-18.0913``, where the number is the mass | ||
| shift in Daltons. | ||
| - Position: The position of the modification in the peptide | ||
| sequence. Terminal modifications in proteins and peptides MUST be | ||
| reported with the position set to 0 (N-terminal) or the amino acid | ||
| length +1 (C-terminal) respectively. For example, ``1`` or | ||
| ``1,2,3``. | ||
| - Localization Probability: The probability of the modification | ||
| being in the reported position. | ||
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| Those three properties can be combined in one string as: | ||
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| :: | ||
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| {position}({Probabilistic Score:0.9})|{position2}|..-{modification accession or name} | ||
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| For example: | ||
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| :: | ||
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| 1(Probabilistic Score:0.8)|2(Probabilistic Score:0.9)|3-UNIMOD:35`. | ||
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| This concept is used in the following outputs: | ||
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| - `PSM <PSM.rst>`__ | ||
| - `FEATURES <FEATURES.rst>`__ | ||
| - `PEPTIDE <PEPTIDE.rst>`__ |
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| quantms.io tools | ||
| ================================= | ||
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| psm converter tool | ||
| ------------------------- | ||
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| Use cases | ||
| ~~~~~~~~~ | ||
|
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| Note:: Make sure before generating the psm feature file that you generate the project.json | ||
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| :: | ||
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| python psm_command.py convert-psm-file | ||
| --mztab_file PXD014414.sdrf_openms_design_openms.mzTab | ||
| --output_folder result | ||
|
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| - Non-PRIDE project(Don’t not need to run the ``project_command.py``) | ||
|
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| :: | ||
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| python feature_command.py convert-psm-file | ||
| --mztab_file PXD014414.sdrf_openms_design_openms.mzTab | ||
| --generate_project False | ||
| --output_folder result | ||
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| Optional parameter | ||
| ~~~~~~~~~~~~~~~~~~ | ||
|
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| - –-output_prefix_file The prefix of the result file. | ||
| - –-verbose Output debug information. | ||
|
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| Compare psm.parquet | ||
| ------------------- | ||
|
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| Use case | ||
| ~~~~~~~~ | ||
|
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| :: | ||
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| python feature_command.py compare-set-of-psms | ||
| --parquets PXD014414-comet.parquet PXD014414-sage.parquet PXD014414-msgf.parquet | ||
| --tags comet sage msgf |