Skip to main content
Topic: MS-DIAL Alignment export result (Read 309 times) previous topic - next topic

MS-DIAL Alignment export result

Dear MS-DIAL developers,
I start working with the software and took “Mouse tissues.(3.6GB)” as training project using “MSMS-Public-Neg-VS15” as MSP reference library.
At the end of data processing I exported the results into alignment results table (attached).
There are a lot of columns in the obtained table, part of them more clear part of them – less.
I would like to understand the meaning of each column.  Unfortunately I didn’t find related information in tutorials.
Where such an explanation could be found? 
Thank you.

Re: MS-DIAL Alignment export result

Reply #1
Is this the .mgf or .msp aligned export results? Looks like .mgf to me.

Re: MS-DIAL Alignment export result

Reply #2
It is .txt file opened with Excel.

Re: MS-DIAL Alignment export result

Reply #3

Most columns in the .text output file are 'self-explanatory' and for the annotation confidence level codes in the later columns refer:
Post-curation results are from: an exercise that relies on for peak redundancy
MS/MS asssigned: if there were spectral or MS/MS level matches or not between the dataset and spectral library used
Reference RT/ M/z refer to : if matches with the spectral library are true or not, and if matched what value of m/z


Re: MS-DIAL Alignment export result

Reply #5
Dear all,

below is the email communication.


see below? BTW, the sample data that you are trying to use is the data from our lipidomics experiment. Therefore, you should select "lipidomics" as the project information if you wanna see the full annotation performance of MS-DIAL program for the data.

1.       Why this metabolite is reported three times under different retention times (9.615min, 5.715min and 5.974min)?
-> When you do not use the retention time information, this situation will occur. That is, only using the MS/MS spectrum for annotation is not enough to distinguish isomers which have similar/same spectral patterns.

2.       Different area values are reported varying from 60 to 4199934. How I can interpret it?
->  Very small values like 80~500 can be interpreted as "noise level's peak". The peak was not be detected in the normal peak picking algorithm, but the peak information was inserted by the gap-filling algorithm.

3.       Reference RT is “null”. What does it mean?  In comparison for Naringenin (row 240) Relative RT value is 5.958min, while its Average RT is 1.379min. Shouldn’t it be very close?
-> The retention time information is not included in the reference msp file. Maybe, you did not use the retention time information for annotation (check the identification tab's parameter setting. You will see the check box like use retention time for filtering metabolites etc.)

4.       Fill%, which is equal to 0.091, 0.864 and 0.136 respectively. What is the meaning?

5.       Column P (RT matched) “TRUE” for all three cases. How it can be, taking into consideration the fact that RTs are very different?
The MSP file does not contain the suitable retention time information of metabolites for the "mouse tissue" data. Therefore, the retention time information of the msp file cannot be used for annotation actually.

6.       Manually modified for quantification “FALSE” – What does it mean?
In msdial, you can modify the peak picking result. If you modify, the case is changed to true.

7.       Total score with the value of about 85. What does it mean?
Max score will become 100. 85 would be a good score as the annotation criteria.

8.       Dot product and Reverse dot product. What is it?
See 20 page of

9.       Fragment presence % with value of 50 – What does it mean?
See 20-21 pages of