Total Alkalinity and Proteomics.

Yesterday I met with Micah at DNR in Olympia and got my badge to access the lab to measure TA and got acclimated to the process. I wrote a walkthrough for the process which an be found here.

Aside from writing the walkthrough this morning, I helped Laura get Pecan working for DIA proteomic analysis. Interesting program, that Pecan. It requires, among other things, a text file that spells out the different .mzML files that need processed. It appears to the append the path for the text file to the .mzML files which creates some odd situations.

For example: If your text file has ~/Documents/Proteomics/Converted/Sample1.mzML in it, and the text file is located in ~/Documents/Proteomics/ the Pecan looks in ~/Documents/Proteomics/~Documents/Proteomics/Converted/ for the sample file. That doesn’t work.

We eventually got it to work by copying all of the .mzML files in to the same directory as the text file and having the text file just consist of a list of file names, with no associated directory.

Next hurdle, Pecan estimates it needs 92gb of RAM to run. Emu only has 48 gb, so we’ll have to see if that’s enough to appease Pecan.

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