Proteomics raw data and max quant result display

[mikkonie]

In GitLab by @mkuhring on Jun 19, 2018, 15:07

For proteomics, we need to display sample-wise raw data and the MaxQuant results.

Integration of proteomics raw data

There is a RawData sub folder in the iRODS file system. In this folder, all *.raw files live next to each other together with their MD5 sums. The file links of the assay table simply link to this folder with the "list files" and in the "link to Davrods" icons.

MaxQuant results

Assumptions:

• Each proteomics measurement result goes into at most one MaxQuant process node (data transformation) in the assay.
• Each MaxQuant node creates creates one material node in the assay.

In reality, there might be more than one MaxQuant run, but we do not represent this in the assay sheets.

On the file system, there will be one folder MaxQuantResults in the assay folder. This folder will contain one or more runs, each in its own sub folder. Users are responsible for naming these sub folders appropriately and this will have no mapping in the assay sheets.

The reason for this is that modeling different applications of MaxQuant, e.g., for trying different parameters or fixing mistakes made earlier is not possible at the current time with current resources. It might never be.

UI-wise, this can could be integrated

• a "display plugin" at the top of the sample sheet display similar to the germline BAM/VCF view at the moment (probably just one button for each the MaxQuantResults and the RawData)
• links in the assay table display

Currently, the visible components in the UI should be

• link out to DavRods HTTPS URL of MaxQuantResults/ for users to browse
• display contained files of MaxQuantResults such as they are displayed for samples currently

[mikkonie]

In GitLab by @mkuhring on Jun 20, 2018, 11:13

This should be configured based on the AssayInfo variables measurement_type and technology_type.

In this specific case:

measurement_type == "protein expression profiling"
technology_type == "mass spectrometry"

[mikkonie]

mentioned in commit 4db4c81f61e6627a79abb7e9b82317844f85f89c

[mikkonie]

mentioned in commit 4238bb0477e26770fddc68d774e0b20671066e15

[mikkonie]

mentioned in commit 49ac8c229b7c11742878431590ef8ebf8f89753d

[mikkonie]

mentioned in commit 62c42de21735ed7af72d99bc3f19552394b2edb1

[mikkonie]

mentioned in commit 58a49cbf68f8f50749f17bf962c6396a4868556a

[mikkonie]

mentioned in commit cc0e6e113261493bac3f485b251d18cf8a2383fe

[mikkonie]

mentioned in commit 550f5f5b1ba169de73660b096cd1bf781e4d7ca9

[mikkonie]

mentioned in commit 031c783c848b9acfeab42733b45ccd9f919ffa54

[mikkonie]

Done, unless some issues are detected.

[mikkonie]

closed