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.

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.

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.

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'.

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.

The requirement for Waters data conversion is really strict. Please check the following requirements again. Some of them are not listed in Reifycs website.
 64-bit machines
 Windows 8 or later OS
 Microsoft Visual C++ Redistributable Package for Visual Studio 2013 for 64-bit version (vcredist_x64) installed
 Be sure to use MassLynxRaw.dll for 64bit version, to be added to the ABFCvtSvrWtrRw sub-folder in the AbfConverter application folder.

Recently, SCIEX started to use new format WIFF2 which has already been used in 500R QTOF system. Although the direct conversion from WIFF2 to ABF is not possible yet, the format can be imported by using ProteoWizard MSconvert as follows.

The summary is:
1. Convert WIFF2 to mzML (centroid) using ProteoWizard.
2. Convert mzML to ABF using ABF converter.*
3. Process in MS-DIAL.
*Direct import of mzML is also ok in MS-DIAL where the minimum peak hight of peak detection parameter tab should be set to around 1–10.

Below is the detail.
1. Download ProteoWizard.
2. Run MSConvert from ProteoWizard folder.
3. Convert wiff2 files to mzml using setting bellow including also centroiding (this is important otherwise files in mzml profile files would be extremely large).

4. Run ABF converter.
5. Convert mzml files to ABF format.
6. Run MS-DIAL.
7. In 'Start up a project', Data type (MS1): Centoid data; Data type (MS/MS): Centoid data
8. In 'Analysis parameter data', Peak detection, Minimum peak height: use values between 5 and 10 (check the results using different values to get a reasonable number of features).

Note:
For SCIEX profile data we have found that Minimum peak height of 2,000–3,000 works well but for mzml centroid -> ABF data much lower values should be used.
This procedure works well for data acquired in (i) MS1 only mode and (ii) MS1 with data-dependent acquisition (DDA).
Unfortunately, the current work flow does not work for SWATH-MS data yet although it can be processed in MS_DIAL to get MS1 information in MS-DIAL.
After SCIEX releases the Software Developer Kit which is needed for modification of ABF converter, the flow will become easier and SWATH-MS data can be also imported.

Recently, several users using a specific language OS (Denmark, France, Italy, etc) for MS-DIAL had the trouble where none of identification result is obtained by text file or msp file.
The reason was that several Windows OS use 'comma (,)' as the default decimal separator while the 'dot (.)' separator is used in msp format files.
MS-DIAL is written by C#, i.e. .NET framework, and therefore, the behavior is highly dependent on the environment of Microsoft .NET frameworks installed in the user's PC.
If you face on the similar issue, i.e. no identification result from MS-DIAL, please check your PC condition.
Definetly, English OS should be the best OS for the use of MS-DIAL (in addtion to MRMPROBS, MS-FINDER, and others).

The fill % means the "gap-filled" sample % (but 1 means 100% in the output).
If you analyzed 10 samples, and if a metabolite is detected in eight samples of them, the fill % value becomes 0.8.

1. Download and install "netCDFmajor.minor.point-NC4-64.exe" or later version at the Unidata webpage.
2. Select an option 'Add to PATH'.
3. Now, you can import netCDF in MS-DIAL directly.