The GC column is, of course, the same in both instruments.
This is a "misstatement of fact" by the Majority, on which some significant conclusions are based.
We see that the columns were NOT the same, based on parts of USADA 124, 153 for the A sample, and USADA 303 and 329 for the B sample:
These are completely different columns, with different "polarities". Polarities are known to causes significant location changes in peaks, including changing the order of peaks. It isn't known as fact whether these columns change the order of the 5bA and 5aA peaks in the setup used by LNDD.
For the record, Agilent used to be part of HP, and now also owns the rights to the DB-17. So both are made by the same company, but are of completely different specification.
Mr. Idiot writes:
[T]his all comes from Arnie Baker through email. I do have explicit permission to make it public. The down and dirty version of it is this - most of it is right there in the original LDP:
USADA 0124 says that the column used in the GCMS was an "Agilent 19091s-433." If you dig in the Agilent website, it is clear that an Agilent 19091s-433 is an "HP-5ms" column.
USADA 0153 says that the column used in the GC/C/IRMS was a "DB-17ms." Again at the Agilent website you can find the DB-17ms and learn that it is a different column with different characteristics than the HP-5ms.
Just as one example, the HP-5ms is "non-polar," and the DB-17ms is "mid-polar."
Baker has shown that the LNDD SOP required that the DB-17ms be used for both GC/MS and GC/C/IRMS, but for some (undocumented) reason they used the HP-5ms for the GC/MS. The evidence of that is a little more complicated, so I'll wait on explaining it.
The information Baker has given me also shows specific examples of how substances elute at different times and in different orders on these two columns, and even has an example of a steroid doing so (although not specifically 5aA or 5bA). That's part of the stuff that is graphics heavy and TbV will have to do something with it.
Obviously one of the first things you learn about the connection between GC/MS and GC/C/IRMS is that the chromatographic conditions have to be the same. Now we realize that not only were the temperature conditions different, the columns were different too.
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UPDATE: more in Different Columns - Details.