Are the values in the filtered proteomic data for subchallenge 2 (Filtered data: https://www.synapse.org/#!Synapse:syn10139526) protein abundance log-ratios to the reference sample of 40 tumors?
Created by Ioannis Zervantonakis zervantonakis . In case of the test data will the reference samples be the same as in the train data? Hi Ioannis,
For ovarian cancer data, please don't make such assumption as the mixing strategy is different. Thank you for the very quick response!
So the filtered data are indeed log2-ratios of each sample relative to the pool (reference sample mix)? Hence they are not absolute measurements, but relative measurements.
I was referring to the breast cancer dataset (Mertins P, Nature 2016: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5102256/) .
Please see Extended Data Figure 1a and also legend: "Each iTRAQ MS/MS spectrum measures a peptide from 4 samples (3 individual patients and the reference sample mix of 40 patients)" Hi Ioannis,
The filtered data are log2-ratios, while I don't think the pool is a mix of 40 samples. Could you please specify the source of this number?
Thank you for the response. Can you please confirm that we the values we are provided in the filtered data are iTRAQ log2-ratios ?
From CDAP Protein Report Description (https://cptac-data-portal.georgetown.edu/cptac/documents/CDAP_ProteinReports_description_20160503.pdf)
I am able to find the following information
Page 7: iTRAQ quantification
"We report the log2 of the ratio of each (non-POOL) reporter ion with respect to the POOL reporter ion and associate it with the appropriate
peptide and sample. "
Page 15: iTRAQ protein quantification report:
"[Sample] Log Ratio
Average log-ratio of sample reporter-ion to common reference of peptide ions associated with
the gene in acquisitions from a specific biological sample.3"
My interpretation of this is that the protein abundances are relative values, based on the POOL reporter ion (40 samples). Hi Ioannis,
No, they are not abundance based on 40 tumors. Please refer to CPTAC common data analysis pipeline for detailed description. ([CPTAC CDAP](https://cptac-data-portal.georgetown.edu/cptac/aboutData/show?scope=dataLevels))