sdrf-pipelines 0.0.3

Translate, convert SDRF to configuration pipelines

sdrf-pipelines

The SDRF pipelines provide a set of tools to validate and convert SDRF files to different workflow configuration files such as MSstats and OpenMS.

Installation

pip install sdrf-pipelines

Validate the SDRF

How to use it:

Then, you can use the tool by executing the following command:

parse_sdrf validate-sdrf --sdrf_file {here_the_path_to_sdrf_file}

Convert to OpenMS: Usage

parse_sdrf 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