DIA / LFQ compatibility

[prvst]

Hello, Is scp compatible with DIA or LFQ data? If that's the case, can you please provide me with an example of how to structure the quantitative input table and the sample input table, for the readSCP method?

Thank you

[lgatto]

Yes, and type of DIA/DDA or labelled/LFQ data can be analysed with QFeatures/scp. We have a collection of replication analyses in SCP.replication, that include LFQ experiments.

You have two options

• you either load a table with all precursor-level cells/acquisitions along the rows into you starting assay, or
• have a series 1-column assays for each cell/acquisition - in that case, the sample data in the readSCP() function corresponds to one cell/acquisition.

@cvanderaa can probably provide more details.

[prvst]

Thanks, Laurent.

I reviewed some examples, such as the Brunner data, which uses DIA data, but the example starts with QFeature objects already built. I'm still learning how to work with the scp and QFeatures package, I'm struggling a bit to figure it out how to get my input data organized when there are no channels.

[lgatto]

You can find the scripts that generated these QFeatures objects in the scpdata repo. If these don't help, let us know, and we'll provide further details.

@cvanderaa - we should probably update the readSCP() documentation or vignette with more details/examples.

[prvst]

Perfect, thank you!

[cvanderaa]

Hello,

I reopen this issue as I fully agree that we should clarify (maybe also improve) how LFQ and DIA data are loaded.

@prvst I will work on improving this and will keep you updated on the progress. I would love to have your feedback on the future improvements.

Meanwhile, if you have DIA data identified and quantified through DIA-NN, you can have a look at readSCPfromDIANN (although I could also improve the documentation).

Loading LFQ data is not much different from loading multiplexed data, but you have a single channel. In your annotation table (colData argument), you need to have one column that specifies which column in your identification/quantification table (featureData argument) contains the quantification. For LFQ, this means that this column will contain all the same column because there is only 1 channel. I hope that can help a bit meanwhile.

So, I will leave this issue open until I improved the documentation.

[lgatto]

Here's some update with regard to reading DIA-NN output to create QFeatures:

• readQFeatures() has been updated and streamlined
• readQFeaturesFromDIANN() can be used to import label-free and plexDIA/mTRAQ data produced by DIA-NN

I'm going to close the issue, but feel free to re-open (or open a new one) if you have questions or comments.