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21
MS-DIAL / Total ion current boxplots
Last post by ncrohrbaugh -
Hello,

I am a beginner to MS-Dial, which I am using for untargeted metabolomics, and I have a question about its capabilities. In my work with XCMS, I have found that comparing total ion current between defined classes or between samples is a useful way to compare groups and identify potentially problems in MS runs.

Is there a way to see this in MS-Dial? The box plots I have seen in MS-Dial seem to only compare one identified feature at a time, and do not allow for comparison of the signal from all features identified between different groups. If anyone knows how to compare different groups on a broader scale, please let me know!
22
MS-DIAL / MS_DIAL_FAMES Dictionary
Last post by Jurica -
I trying make preprocessing GC/MS data in MSDIAL. I have problem when I use FAMES dictionary, if I use ALKANE dictionary everything it's OK.
That is, it throws me an error: The aligned EIC file (alignmentResult_2024_1_19_14_18_44.EIC.aef) cannot be found. Please excute peak alignment for the use of aligned EIC viewer.

I first time using MSDIAL, and I hope someone can help me.

23
MS-DIAL / Re: MS-DIAL beginner
Last post by ilaria. -
Hello Biswa,
thanks for your reply!
About the point 2, I am trying to normalize with LOWESS or LOWESS+internal standard but the "Normalize" button is not clickable. I set QC in correspondence of the QC run in the table where you specify the type of the data. Do you know why?
Regarding point 3, with the term "validated" I meant the assignment of the true positives compounds. Thank for the suggestion to how find them in the final table!
24
Job opportunities / Experimental Officer in Metabolomics – University of Birmingham,
Last post by e.voros -
We are recruiting an Experimental Officer in Metabolomics to join our team at the University of Birmingham. Phenome Centre Birmingham (PCB) has an international reputation specialising in toxicological and biomedical metabolomics.  We have an exciting opportunity for an enthusiastic and committed chemist or biochemist who has experience in LC-MS metabolomics. This fixed-term position is ideally suited for someone who gained experience in applying high-throughput analytical methods, including advanced robotic sample preparation and state-of-the art hybrid LC-MS metabolomics assays that combine untargeted analyses with targeted measurements of metabolic biomarkers.

Closing date for applications: 13th of February 2024

If you are interested in applying for the post please find further details on the University of Birmingham’s job site.
25
MS-DIAL / Re: MS Dial v5 keeps crashing + Mass normalization
Last post by biswapriya -
Hello,

1. MS Dial (v5) is still unstable and I would not recommend using it as many things can cause it to crash. Better use stabled 4.9 versions as I see.you have started using!: )

2. In the 4.9 version, just use the "sample mass scaled to 1" and add to the "injection volume (1 uL) column" by adding different values scaled to whatever numbers they are. Should factor in as well.

Hope this helps.
Biswa
26
MS-DIAL / Re: MS-DIAL beginner
Last post by biswapriya -
Hello,

1. No- cannot use Metlin unless you buy it (expensive!) and use locally- so possible if you spend USD 5K. Use MSDIAL libraries and also, you can add more LC-MS/MS libraries from MoNA (https://mona.fiehnlab.ucdavis.edu/downloads) and GNPS (https://gnps.ucsd.edu/ProteoSAFe/libraries.jsp). For combining libraries, you can use a simple method like https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-eq2ly33rqgx9/v1 but for your LC-MS/MS use case use ESI-MS or LC-MS or MS/MS libraries only. Add and combine as many as possible and does not matter Pos or Neg mode as they all help and do not mess up with matching.

2. Export "Area" or "Height" and both works fine for me. If normalized(if you ran multiple pooled QCs)  then hit normalize using LOWESS and QC or using internal standards and then export the "normalized data file" from Alignment Results.

3. Not possible. Export everything and then "filter out your validated". What is your definition of validated? If MS/MS matched with library without RT match, then fine too and can be filtered from the final area/ height file export as "MS/MS pos match" and a "cosine/ dot product" similarity score of say >70 or 0.7.

Hope this helps.

Thanks,
Biswa
27
MS-DIAL / Error with uploading experiment file_data processing with SWATH-MS method type
Last post by Zareen S Khan -
Hello Community,

Season's Greetings! Merry Christmas and Happy New Year!

I have started to use MS-DIAL recently. I face the following error message, ''Invalid analyst experiment information'' while trying to upload the experiment file (.txt) with the experiment information of my DIA method. I am trying to upload the following experimental details saved in a notepad.
Experiment       MS Type  Min m/z   Max m/z
0        SCAN      200       380
1        SWATH    200       210
2        SWATH    210       220
3        SWATH    220       230
4        SWATH    230       240
5        SWATH    240       250
6        SWATH    250       260
7        SWATH    260       270
8        SWATH    270       280
9        SWATH    280       290
10       SWATH    290       300
11       SWATH    300       310
12       SWATH    310       320
13       SWATH    320       330
14       SWATH    330       340
15       SWATH    340       350
16       SWATH    350       360
17       SWATH    360       370
18       SWATH    370       380

I am not sure what is going wrong. Is there any body who experienced something similar or can give any insights to resolve this?
I would be very grateful. Thank you in advance!

Happy Holidays!
Zareen
28
MS-DIAL / .NET format version needed to run
Last post by mw_uwchem -
Hi, does anyone know the .NET format needed to run the latest version of MS Dial? It keeps reading the .NET v4.0 and says its incompatible, despite me downloading the latest version.
29
MS-DIAL / MS-DIAL beginner
Last post by ilaria. -
Hello everyone,
I'm just approaching to use MS-DIAL. I would like to ask some questions about it.

1) Is it possible to introduce METLIN library in the MS-DIAL searching? If not, do you recommend to use just the libraries downloadable from MS-DIAL website for the human metabolome?
2) Which file should I export for the metabolites quantification and which table column should I consider as a normalized value to quantify metabolites?
3) Is it possible to export only the validated metabolites after the post-processing analysis to discard the false positives?

Thank you to everyone who will reply  :)
Ilaria
30
MS-DIAL / MS Dial v5 keeps crashing + Mass normalization
Last post by mw_uwchem -
Hi all,

#1 I'm wondering if there is a solution to the newest version of MS Dial (v5) crashing? Soon after I press "Run", the software closes with no warning or error message. Also- I've updated to the newest pre-released version AND tried another user's solution to add msp files for IDs after running the initial search. When I try this, everything works fine but then the program crashes again once the msp files are uploaded. :( Is this an issue with too large of libraries or too many samples?

#2 I've started using v4.9 and am wondering if there is a scalar to normalize by sample mass? I originally was using the newest version's analytical factor column.

Thanks,
Mallory