FTICR/DMS data access

[kaizadp]

21-Oct-2020 RED, SJF, KFP

1. Access DMS : https://dms2.pnl.gov

• DMS > Datasets > Report

• understanding the data/sample name:

  • example: Fansler_51618_Blank_MeOH_Alder_Inf_05Oct2020_300SA_IATp1_1_01_55835 Alder = autosampler name 300SA =300 scans IAT = ion accumulation time SRFAII = Suwannee River FA standard

  • Rating column: use only the "Released" files

  • at the bottom -- download in other formats > Excel. This will download a "report" that is identical to the DMS page, with all the sample information.

2. Open in Excel

• Filter > Rating > check only the "Released" rows

• exclude all the standards/blanks, etc. (Filter > Dataset > search term "DOC" because all our files have DOC in the name)

• highlight and copy the ID cells

• go to MAGE

3. Mage

• paste in Datasets by ID

• click Get Datasets. This goes through all the entries in DMS and pulls the matching IDs

• go to Get Files from Datasets > File Name Filter> type in "*.baf"

• Click/select Subdirectories, Include Files, File Search. Click Find Files For All Entities

• a bunch of files will appear in Files. We need the analysis.baf files

• Copy Files to Local Folder

• Destination Directory: set the directory

• Apply prefix to file name: keep checked (ticked). Enter "Dataset" in the bar

• Click Copy All

• This will start copying/saving files (almost-raw files) to the selected directory

4. DA_rename

• this script will create a new folder for each file, and then move the file into the folder
• setwd (AAAAAAAAArgh)

5. Data Analysis: peak picking program

• make sure Data Analysis is downloaded/installed, with the key

5a.

• open for-loop.txt
• change the the input directory
• this will run DA on every sample within the directory

5b.

• save and extract DA_Scripting.zip in the C directory. Save in the Users/<<username>> if you can't save in C.
  • if you save somewhere else, modify the second part of the for-loop.txt script
• the three VBSC files are the most important

5c. Data Analysis

• keep everything default
• find the folder that was created from the for-loop, and drag into DA
• Method > Parameters> Mass List > Instrument type = "Fourier transform" | S/N = 7 | Relative intensity = 0.01 % | Absolute intensity threshold = 100 | use Centroid uncheck | filter exclusion masses uncheck > Save As = save method name
• Method > Default > choose the correct method to set as default
• to guarantee/confirm that the default method was set, close and reopen DA. do this just the first time, when you change the method

5d. Command Prompt

• open CMD
• hold down ctrl+shift+enter -- this tells Windows we're opening in Admin mode
• copy the for-loop code into cmd -- don't use ctrl+v. just right-click to paste
• run it -- a new window will pop up and then close for each file

5e. move xml

• move_xml.R script
• take the xml files, copy them (not delete), pastes them to a new folder and renames
• drag and drop into Formularity

[kaizadp]

Do not subtract blanks from the samples. Blanks can't be calibrated.

remove common contaminants

https://www.nature.com/articles/ngeo2940?WT.ec_id=NGEO-201706&spMailingID=54185184&spUserID=ODkwMTM2NjM4NgS2&spJobID=1180115076&spReportId=MTE4MDExNTA3NgS2

S-containing detergents could be an issue. filter those out if working with S in the data.