Benchmark with a good dataset for absolute intensity quantification

[ypriverol]

We should reanalyze some good datasets for absolute intensity base quantification datasets where the expression/concentrations are known to benchmark the package and the algorithms behind.

@daichengxin @WangHong007 can you let me know a dataset that we can use to benchmark IBAQ methods.

[ypriverol]

Potential datasets:

• PXD014765, PXD012836: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8788469/. @WangHong007 They both need to be annotated.
• PXD011725: https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10.1002/pmic.202000093. @WangHong007 need to be annotated.

[WangHong007]

@ypriverol PXD014765 and PXD012836 link to the same thesis, and I've completed anontation of the former, please check it, especially the bio_replicate column. For the later, it's similar to the former and it included three organisms of yeast, but I found limited experimental design info in PRIDE record and no sign in the thesis. Should we guess it?

[ypriverol]

@daichengxin can you help here?

[daichengxin]

You can see the informations in Supplementary file. Combined mode of samples: standard (T2), high temperature (T3), osmotic shock (T4), low pH (T5), anaerobic (T6) and three (biological) replicates for each condition (A, B, C). Plus 6 bulk samples (Bulk, A-F)

[WangHong007]

@daichengxin Yes but this is experimental info of PXD014765, I don't know how to generate SDRF of PXD012836 since they both linked to the same thesis.

But I can infer that from the author's naming conventions