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proteomics.md

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Proteomics

Annotation

The parameters file should be named proteomics_annotation.params.

The annotations file has 7 columns. 3 of them contain gene related information. The required order is probesetID, uniprotID, species, gpl_id, chromosome, start, end.

Constraints:

  • The only mandatory columns are probesetID and uniprotID.
  • All gene region columns (chromosome, start and end) are required if at least one is provided. That is, either all or none of the gene information columns must be included.

Note: The proteomics platform upload relies on the proteomics dictionary to seek uniprot names for the given uniprot identifiers. Currently proteomics dictionary could be uploaded by means of transmart-data. If there is no such protein information in the dictionary or the dictionary is not loaded at all the pipeline would fill in uniprot names with uniprot ids and warn user about this action.

Example file:

probesetID uniprotID species gpl_id chromosome start end
5060 Q9UBS8 Homo Sapiens PROT_ANNOT 5 141348450 141369856
2739 P62805 Homo Sapiens PROT_ANNOT 6 26021906 26022278
2260 P35573 Homo Sapiens PROT_ANNOT 1 100316044 100389579
611 E9PC15 Homo Sapiens PROT_ANNOT 7 141251077 141354209
2959 Q09161 Homo Sapiens PROT_ANNOT 9 100395704 100436029
1860 P11021 Homo Sapiens PROT_ANNOT 9 127997126 128003666
2243 P34932 Homo Sapiens PROT_ANNOT 5 132387661 132440709
4041 Q8WX92 Homo Sapiens PROT_ANNOT 9 140149758 140168000

Refer to the general annotations documentation for general information about annotation loading jobs, including their parameters.

Subject-Sample Mapping

Here is a subject-sample mapping example file:

trial_name site_id subject_id sample_cd platform sample_type tissue_type time_point cat_cd src_cd
CLUC CACO2 LFQ.intensity.CACO2_1 PROT_ANNOT LFQ-1 Colon Week1 Molecular profiling+High-throughput molecular profiling+Expression (protein)+LC-MS-MS+Protein level+SAMPLETYPE+MZ ratios STD
CLUC CACO2 LFQ.intensity.CACO2_2 PROT_ANNOT LFQ-2 Colon Week1 Molecular profiling+High-throughput molecular profiling+Expression (protein)+LC-MS-MS+Protein level+SAMPLETYPE+MZ ratios STD
CLUC COLO205 LFQ.intensity.COLO205_1 PROT_ANNOT LFQ-1 Colon Week1 Molecular profiling+High-throughput molecular profiling+Expression (protein)+LC-MS-MS+Protein level+SAMPLETYPE+MZ ratios STD
CLUC COLO205 LFQ.intensity.COLO205_2 PROT_ANNOT LFQ-2 Colon Week1 Molecular profiling+High-throughput molecular profiling+Expression (protein)+LC-MS-MS+Protein level+SAMPLETYPE+MZ ratios STD

Data

The parameters file should be named proteomics.params. For the content of this file see the HD data parameters and the study-specific parameters.

Example data file:

ID_REF LFQ.intensity.CACO2_1 LFQ.intensity.CACO2_2 LFQ.intensity.COLO205_1 LFQ.intensity.COLO205_2
1860 9089400000 8792800000 8949100000 7252500000
2243 4997100000 5527800000 4280900000 4196200000
2739 2160700000 2090600000 30589000000 4188200000
2959 395180000 468840000 349410000 494790000
2260 101860000 84585000 93405000 101120000
4041 52779000 62863000 53180000 72288000
611 37153000 30627000 87144000 42039000
5060 0 26186000 0 0

Format expectations:

  • The first column has to be named ID_REF and contain a row identifier. The row identifier has to match the probesetID from the related platform.
  • The rest of the columns have to be intensities. There must not be other columns in the file.
  • The header names for the intensities columns have to match the sample_cd values of the subject sample mapping file.

Read more on how HD data are processed.