I can't follow all the cancer terms in this paper despite hearing lots about HER2 and some of these other things over the years. What I can follow is this is a big cohort multi-omics study that appears to have been done very very well.
It represents a tremendous amount of work, starting with 113 FFPE tissues from patients broken down by genetic representation of their tumors and the treatments they received, as well as how they responded to the treatments they received. I think it represents something like 30 individuals, given the pre- and post- treatment samples. On top of this cell lines were also used for both proteomics and metabolomics.
Super-SILAC was used for the proteomics from the laser microdissected (pretty sure that's how they did it?) samples as well as the cell lines (?) a little fuzzy on the design here without digging in much further and the metabolomics utilized heavy glucose and glutamine. The LCMS for the metabolomics is completely new to me, and I think it deserves exploration. Something called a zipHILIC was used with a low flowrate (100uL/min with AmBiC/ACN gradient and a 59 min gradient!)
The study keeps going. They use CRISPR and do some mouse work to support their findings and they even use a SeaHorse (not the mythological creature, the Agilent high throughput metabolism thingy).
This is a really inspiring amount of work with a great story about the value of proline metabolism in chemotherapeutic response.
690 RAW files can be downloaded at PRIDE here (PXD012000). I haven't found the metabolomics ones yet. This may just be the proteomics! And...it's somewhere in the range of a freaking TERAbyte of RAW data!!)
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