This post contains instructions for how to create a HMDB Metabolites CSV database for searching mass spectrometry spectra without using scripts such as Python or R scripts. Two options will be described with Option 1 not requiring any specialized software and the simplest approach. Options 2 uses freeware and is useful to convert sdf files. Some biofluid specific HMDB databases only appear to be available as sdf files so Options 2 may come in useful.
Option 1.
Navigate to the HMDB.ca website and from the top menu select “Metabolites” from the Browse dropdown
Choose your filters, apply the filter then select the Export button which should be below the filters on the right side (the entire database is approx 248K entries)
The export may take a few minutes. Try again if it does not work the first time. Once it completes the file will either automatically be downloaded to your browsers default download location or a Save As box will pop up depending on how you have things configured. Notice that the file does not have an extension. Rename the file as desired and add the .CSV extension on the end.
Open the file in Excel.
Modify as needed. For example, delete any columns you don't want, and change column headers so they recognizable by your mass spec software. For example, the Agilent MassHunter Qualitative software recognizes the following column headers:
Formula Retention Time, RT Mass Compound Name, Compound, Cpd, Name Description, Notes, Comments CasId, CAS KeggId, KEGG HmpId, HMP Structure
Load the sdf file. Delete any columns, then go to File > Save Special > Textfile… Alternatives to deleting the columns in Datawarrior is to import the file from within Excel by navigating to Data > From Text and selecting the desired columns using the Excel import wizard. Alternatively you can just edit the file directly in Excel. If an error is returned when searching the csv file, considered running the Excel CLEAN function on some of the columns.
Other biofluid specific databases available through the https://www.tmicwishartnode.ca/databases/ website are offered as sdf files and, since they are subsets of the main HMDB database, are much smaller. The same biofluid databases are offered through the HMDB.ca website but only as zipped XML files.
The Ion Table only shows the fold change for the max and min bars. Is it possible to get the fold change for other combinations? For example, if I have three bars (i.e. 3 groups) with one being the control and the other two being treatment 1 and treatment 2, I would like fold change/p-value for treatment 1/control and treatment 2/control.
I did try assigning them as QC's in the file property dialog after peak detection, alignment etc., and the MS2 samples bar did disappear but the fold changes did not change and I suspect the fold change calc uses the MS2 samples bar when it is the largest bar. BTW, I assume the fold change is the largest bar height divided by the lowest bar height (?).
Does MSDial support an iterative exclusion DDA Q-TOF workflow where a pooled sample is used to generate a series of MS2 data files by iterative exclusion DDA and each individual sample is analyzed by MS1 only. The DDA files are only used for identification and the MS1 files are used to look for fold changes.
Hovering over a bar gives a value in the top right corner of the bar chart. This does not correspond to the average of the values for the bar. Where does it come from? See attached screenshot for more info.
I have a lipidomics QC sample prepared by pooling equal amounts of each sample. The QC sample is injected up front and analyzed by data dependent MS/MS for lipid identification five times using a rolling exclusion list (QTOF). Then the samples, interspersed with periodic injections of the QC sample, are analyzed using MS1 only. Both the MS/MS and MS1 analysis data files are defined as a QC type in MS Dial. Is there a way to differentiate between the QC MS/MS data files and QC MS1 data files? The MS1 QC data is desired for data processing while the QC MS/MS data files are for ID only.
Is there a way to remove the QC/MSMS and blank from the aligned bar chart plots after processing for presentation purposes?
I have not used MS Finder yet, but can the QC MS/MS data files be used in MS Finder to ID lipids after MS Dial processing?
