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MS-DIAL / Re: MSFINDER problems
Last post by Sukis -
Many thanks for your answer.
1. I have downloaded the latest version, only selected local databases were for structures search, but the "resources" still contains databases not selected. Is it designed for purposes that all embedded databases are used for formula search and scoring regardless of any selection? I am wondering if it is possible to use only selected databases for formula as well as structure scoring. or maybe it is better to offer us the option, because for research field other than metabolomics, the embedded databases are not that related and other user-defined databases are preferred.

2. The latest version still have the crash problem, that is when i select "always use pubchem". version 3.30 works fine.
MS-DIAL / Re: Improving the speed of opening Compound Search for GC-MS data
Last post by Hiroshi Tsugawa -

I understand. The reason for requiring too much time in compound search is due to the lack of retention time or retention index in the NIST original library. MS-DIAL will use the retention information for searching spectra in GC-MS project as it has been done in LC-MS by the precursor m/z. However, most of users will not use retention time information or use very large value like "100000" as the retention time tolerance for annotation. That's why, the compound search function is very slow...

In my case, I predicted retention times (for my lab) and retention indexes (for Alkanes and FAMES) for all NIST and Wiley queries. The confidence interval is less than 100 for kovats RI. Therefore, I can quickly open the compound search window even thought such a huge library is imported.

Please ask me privately, and I can help the msp file preparation.


MS-DIAL / Re: Exporting CorrDec spectra
Last post by Ipputa Tada -
Dear Taylan

Sorry for my late reply.

MS-DIAL v.4.20 cannot export all CorrDec spectra at once in "SWATH-MS or conventional All-ions method" project. Sorry for the inconvenience, we will fix this issue in the next version.

By your steps, MS2Dec spectra will be exported. We will also make a function to select the target spectra type (MS2Dec, CorrDec, or raw).
Best regards,
MS-DIAL / Re: Few MS Annotations
Last post by Hiroshi Tsugawa -
Hi, if you use LTQ-Orbitrap, in the start up project window of msdial, please set
1. data type for MS1 as "profile"
2. data type for MS/MS as "centroid".
According to my understanding, the orbitrap detector and LTQ detector are used for MS1 and MS/MS scanning, respectively, in LTQ-Orbitrap.

MS-DIAL / Re: coefficient of variation
Last post by Hiroshi Tsugawa -
Thanks Stefano,

the CV value is simply calculated by the original, i.e. non-transformed values although the Y-scale is finally visualized by log-transformed value. I will prepare both CV values into the figure at next update.


MS-DIAL / Re: MSFINDER problems
Last post by Hiroshi Tsugawa -

sorry for the delay.
(1) I'm sorry but actually, I uploaded MS-FINDER 3.4 again two days after I uploaded it because of an issue. So if you downloaded it on time (i.e. May 1st), please re-download it, then try it again.

(2) If it does not work yet, please send me your query file. By the latest version, I cannot reproduce your issue, that is, even though I ticked 'only use when there is no query in local db', it works well in my dataset.

MS-DIAL / Re: MSFINDER problems
Last post by Sukis -
Thanks for your answer. I have tried many times. It seems to happen only when I check "only use when there is no query in local DBs" or "always use it" in the pubchem online setting.
MS-DIAL / coefficient of variation
Last post by spapaz -
Hi Hiroshi,

regarding the coefficient of variation (CV%) shown by the MS-DIAL normalization report.
I have been manually calculating  the QCs across samples and QCs, for some internal standards,
but I do not manage to reproduce exactly the same values.

in MS-DIAL, are the CV% calculated based on the log transformed values? (as the report shows the log scale)

I tried both with and without log transforming. When I use the log values, I use the following formula:
= SQRT (10^(LN(10)*STDEV^2)-1)
as discussed here:  10.15406/mojpb.2017.06.00200

I attach the CV% calculated on the log values (for QCs and Samples), and the corresponding ones from MS-DIAL (in red)
(Note: they are not expressed as %, but as fraction, i.e. CV 0.15 = 15%)

Thank you!


MS-DIAL / Re: MSFINDER problems
Last post by spapaz -
I also experienced some crashes of the latest MSFINDER-3.40, usually right after performing structure search.  It is difficult to say what is the problem as often, after it crashed once, I try to re-run it (with the same settings) and I do not experience the crash again.

MS-DIAL / Few MS Annotations
Last post by Matthew Keller -
Hello all,

I'm trying to process a DDA lipidomics sample set I have and after running identification, I'm getting a lot a MS1 annotations (without MS2), but very few assignments that use the MS2s (164 vs 8). Looking at the data by hand, the MS2 look to be of at least moderate quality, so I'm not sure why there would be so few MS2 annotations.
Has this happened to anyone else? Do you know what parameters might need to be adjusted? I'm using an LTQ-Orbitrap in case that's relevant.