MS-DIAL project

Question: the condition of ABF file converter

To convert files of some MS vendors including Bruker, LECO, Shimadzu, Thermo, and Waters, the specific data access library needs to be installed on your PC.



Agilent: Almost all of Agilent’s raw data (.D) can readily be converted without any additional steps. However, the only exception is GCMS data sets obtained from ChemStation, which cannot be directly converted to ABF. Therefore, you have to convert your files into netCDF (AIA) in ChemStation. Then, convert your AIA files into ABF using our file converter.

Bruker: Go to https://www.bruker.com/service/support-upgrades/software-downloads/mass-spectrometry.html. You have to register first and obtain the installer. Finally, download and install the version compatible with your operating system environment (32-bit or 64-bit).

LECO: All of your data has to be converted to netCDF (AIA) first. Then, convert them into ABF using our file converter.

Shimadzu: In case that you had a direct conversion of raw data, please convert your data into the common data format (netCDF or mzML). For GC/MS, convert your data into netCDF using GCMS solution. For LC-ITTOF/MS, convert your data into mzML using ProteoWizard (http://proteowizard.sourceforge.net/index.shtml). Then, convert them into ABF.

Thermo: The following link explains how to install MSFileReader. http://fields.scripps.edu/rawconv/. For GC/MS data, you may have to convert your data into netCDF. Then, convert them into ABF using our converter. We validated the direct conversion of GC-QExactive raw data to ABF, but some GC/MS data (DSQ etc) had to be converted to netCDF first.

Waters: 1. Download MassLyncs Raw Data Reader Interface Library (http://www.waters.com/waters/supportList.htm?cid=511442&filter=documenttype|DWNL&locale=en_US). 2. Unzip the archive file `watersrawsdkredist.zip` and copy `MassLynxRaw.dll` (64-bit) to `ABFCvtSvrWtrRw` folder in the ABF converter. Note that 32–bit environments are not supported yet for file conversion.

NetCDF: When you get an error about the J# dependency problem, download and install the Microsoft Visual J# 2.0 library at https://www.microsoft.com/en-us/download/details.aspx?id=15468.

Question: error message in converting netCDF "Could not load file or assembly 'vjslib, Version=2.0.0.0, ..' or one of its dependencies"

The current ABF converter requires J# 2.0 DotNet framework to convert netCDF data. Therefore, please download the J#2.0 package from the below link, and install it.

Question: error message in converting netCDF "The type initializer for 'java.lang.System' threw an exception"

I got this error when I updated my Windows OS on Oct.4, 2016. I could fix this program after I reinstalled J#2.0 package.

Question: what is the 'w/o' tag of identification results?

1. This program first tries to find a metabolite candidate from a MSP file by means of MS/MS similarity, accurate mass, isotope ratio, and retention time. A metabolite getting 'highest score' in the metabolite candidates is annotated. Note that this score is the total score from retention time similarity, isotope ratio similarity, accurate mass similarity, and MS/MS similarity.

2. But if the 'highest score' is less than user-defined identification cut off, 'non-MS/MS based identification' is performed. That is, this program next tries to find a metabolite candidate by means of accurate mass, isotope ratio, and retention time. Then, a metabolite getting 'highest score' in candidates is annotated. Note that this score is the total score from retention time, isotope ratio, and accurate mass. This result will be shown as 'w/o MS2:***'.

3. If any compounds are not found from the above two criteria, the result will be 'unknown'.

Question: can we process Bruker's DIA QTOF data with MS-DIAL?

Yes. Note that for DIA (data independent MS/MS acquisition) Bruker QTOF data, the calibration segment needs to be at the end.
See page number 10 of MS-DIAL tutorial too.

RIKEN Center for Sustainable Resource Science (formerly Plant Science Center)
Practical and Useful Data Analysis Tools for Metabolomics Research