Translate, convert SDRF to configuration pipelines
Project description
sdrf-pipelines
Convert to OpenMS: Usage
python parse_sdrf.py convert-openms -s sdrf.tsv
Description:
- experiment settings (search engine settings etc.)
- experimental design
The experimental settings file contains one row for every raw file. Columns contain relevevant parameters like precursor mass tolerance, modifications etc. These settings can usually be derived from the sdrf file.
URI | Filename | FixedModifications | VariableModifications | Label | PrecursorMassTolerance | PrecursorMassToleranceUnit | FragmentMassTolerance | FragmentMassToleranceUnit | DissociationMethod | Enzyme |
---|---|---|---|---|---|---|---|---|---|---|
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/XX/PXD324343/A0218_1A_R_FR01.raw | A0218_1A_R_FR01.raw | Acetyl (Protein N-term) | Gln->pyro-glu (Q),Oxidation (M) | label free sample | 10 | ppm | 10 | ppm | HCD | Trypsin |
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/XX/PXD324343/A0218_1A_R_FR02.raw | A0218_1A_R_FR02.raw | Acetyl (Protein N-term) | Gln->pyro-glu (Q),Oxidation (M) | label free sample | 10 | ppm | 10 | ppm | HCD | Trypsin |
The experimental design file contains information how to unambiguously map a single quantitative value. Most entries can be derived from the sdrf file. However, definition of conditions might need manual changes.
- Fraction_Group identifier that indicates which fractions belong together. In the case of label-free data, the fraction group identifier has the same cardinality as the sample identifier.
- The Fraction identifier indicates which fraction was measured in this file. In the case of unfractionated data the fraction identifier is 1 for all samples.
- The Label identifier. 1 for label-free, 1 and 2 for SILAC light/heavy, e.g. 1-10 for TMT10Plex
- The Spectra_Filepath (e.g., path = "/data/SILAC_file.mzML")
- MSstats_Condition the condition identifier as used by MSstats
- MSstats_BioReplicate an identifier to indicate replication. (MSstats requires that there are no duplicate entries. E.g., if MSstats_Condition, Fraction_Group group and Fraction number are the same - as in the case of biological or technical replication, one uses the MSstats_BioReplicate to make entries non-unique)
Fraction_Group | Fraction | Spectra_Filepath | Label | MSstats_Condition | MSstats_BioReplicate |
---|---|---|---|---|---|
1 | 1 | A0218_1A_R_FR01.raw | 1 | 1 | 1 |
1 | 2 | A0218_1A_R_FR02.raw | 1 | 1 | 1 |
. | . | ... | . | . | . |
1 | 15 | A0218_2A_FR15.raw | 1 | 1 | 1 |
2 | 1 | A0218_2A_FR01.raw | 1 | 2 | 2 |
. | . | ... | . | . | . |
. | . | ... | . | . | . |
10 | 15 | A0218_10A_FR15.raw | 1 | 10 | 10 |
For details, please see the MSstats documentation
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