Laura’s Notebook: Demultiplexing & converting from .raw to .mzml

Let’s revisit the DNR geoduck mass spec data!

After the initial DNR geoduck data processing (MSConvert, Pecan, Skyline), we’ve learned that there are a few changes that need to be made. Specifically:

  • When converting .raw files (from Lumos MSMS) to .mzml, I need to demultiplex the data. What is demultiplexing you ask? More on that later.
  • When running Pecan, do all my sample files first (including my blanks). Then, go back and run the “cleaning” blank files after.
  • Need to use Genome Sciences server, Hyak, or some other powerful machine to run Pecan, since our computers don’t have enough memory

Demultiplexing .raw files and converting to .mzML

NOTE: all the programs needed for processing Lumos data files require Windows. For this workflow I’m using the Roberts Lab’s Woodpecker machine

Step 1: Download .raw files from Owl to local folder on Windows computer.
Step 2: Extract the files from the .zip folder didn’t work, as only a few files extracted correctly and the rest resulted in 0kb files. I thus downloaded WinZip program to computer and unzipped.
Step 3: Open command window. One Windows search for: cmd.exe
Step 4: Change working directory to the folder containin .raw files: cd C:\Users\srlab\Documents\geo **Step 5:** Use the following script outlined in the [DIA data Analyses]( instructions, with a couple directory edits. This first run only includes 1 file, so I can see if I get any errors: C:\Users\srlab\Documents\oystertest\20170412_pwiz_testBuild_addMinWindowSize\msconvert.exe –zlib –64 –mzML –filter “peakPicking true 1-2” –filter “demultiplex optimization=overlap_only” 2017_January_23_envtstress_geoduck1.raw`
Step 6: No errors! To run more files in tandem, open up more terminal windows, navigate to the directory housing the .raw files, and enter the same script (with different file names). I have 4 windows running at the same time, on geoduck1-geoduck4.


Step 7: Wait! Started on Friday 3/14 @ 2pm. Let’s see when they finish.

from The Shell Game


Grace’s Notebook: April 14, 2017

  1. SRA Data: Sean showed me the process of downloading SRA data directly into my folder in Scaphapoda using command line. Link to Sean’s explanation of the process here.
  2. Histology Images: I took some pictures of Laura’s oly histology slides. There’s a folder here that includes two papers that I found which have oly histology images of gonads, and a folder of the images I have taken so far, labeled as the slides are labeled.
  3. Proteomics paper refs: I was sent a newer revision of the Timmins-Schiffman et al. proteomics paper with a request to update the references. I used paper pile originally, so in an attempt to not waste too much time, I uploaded the word doc to my google drive. Then I right-clicked on the file in order to open it using google docs. All of the comments, images, and tables from word was present in the google doc. The only thing that wasn’t transferred was the line numbers. I updated the references using paper pile, then downloaded as a word doc to send back to Emma.