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1
MS-DIAL / Re: MS-DIAL and MS-FINDER library limits
Last post by drchrispook -
Hi Biswapriya,

thanks for your response. Good to know that there's no limits to this brilliant software! I've run the same tests as you and it seems to work fine. I've also imported a subset of the subset as query spectra into MS-FINDER as a sanity check and it does a pretty good job matching them up. Not perfect though, which is worrying. For example, searching a series of query spectra for PC(16:0, 18:2) across varying collision energies I get five spectral matches returned from the library for query CE of 14, none for CE16 and seven for CE20. Visually inspecting the CE16 spectra there is little difference between that and adjacent CE spectra, as you would expect. So I don't understand why I get no matches. It would be great to have a variety of matching algorithms, as are available in MS-DIAL (dot product, reverse dot product, unweighted dot product, presence peak score, total MS/MS similarity score). I can't see where to vary the match factor threshold in MS-FINDER either and I can't tell what the algorithm its using is.

Do you use your own scheme for .msp keys? I am thinking I will edit the libraries to remove fields that the software doesn't use, in case those are the problem.
Cheers,
 Chris
2
MS-DIAL / Multiple collision energies in MS/MS file
Last post by Otto -
Hi,
We are using 3 different collision energies in our msms methods and the data is used only for identification. Is there a way to read in a msms parameter file and see the different msms channels separately when using the ┬┤standard┬┤ metabolomics workflow?

Thanks!
3
MS-DIAL / Re: MS-DIAL and MS-FINDER library limits
Last post by biswapriya -
Hi Chris,

At least size is not a problem. I am using concatenated libraries in .msp formats that go well above 5-6 GB and no problems at all!
Most likely, its the "keys/ fields" with formatting issues.

For a test run, I always take  few known spectra from this 3GB library and create a small .msp file to see if it works with say 0% or 5% cosine similarity cut off to make sure at least the library is recognized!

Hope it helps.

Thanks,
Biswa
4
MS-DIAL / MS-DIAL and MS-FINDER library limits
Last post by drchrispook -
Hello,

I have converted the 2020 NIST HR-MSMS library to .msp format and tried using it in MS-DIAL and MS-FINDER. I had to amend some keys as the NIST ones didn't match that of the MS-DIAL libraries. Once I had done this small subsets of the entire NIST library worked. However the whole library (3Gb) doesn't provide any annotations in MS-DIAL or MS-FINDER. Is there a limit to the size of a .msp file these programs can use? Is there some way that I can test to see if MS-DIAL or MS-FINDER are loading the library correctly?

Thanks in advance.
Chris
5
MS-DIAL / MS-DIAL on Supercomputer Failed to Annotate Metabolite
Last post by Xinsong Du -
Greetings:

I was trying to use supercomputer to run MS-DIAL, it successfully produced a peak table, but no peak was annotated even though locations of libraries were provided in the parameter file (i.e., all rows of column "Metabolite name" are "Unknown"). Has any one used command-line version to annotate metabolites successfully? I will very much appreciate it if anyone can help me out.

Following is the content of the parameter file I used:

```
MS-DIAL ver. 4.48

#Project
MS1 Data type   Centroid
MS2 Data type   Centroid
Ion mode   Positive
Target   Metablomics
Mode   ddMSMS

#Data collection parameters
Retention time begin   0
Retention time end   100
Mass range begin   0
Mass range end   2000
MS2 mass range begin   0
MS2 mass range end   2000

#Centroid parameters
MS1 tolerance   0.01
MS2 tolerance   0.025

#Isotope recognition
Maximum charged number   2

#Data processing
Number of threads   10

#Peak detection parameters
Smoothing method   LinearWeightedMovingAverage
Smoothing level   3
Minimum peak width   5
Minimum peak height   1000

#Peak spotting parameters
Mass slice width   0.1
Exclusion mass list (mass & tolerance)

#Deconvolution parameters
Sigma window value   0.5
MS2Dec amplitude cut off   0
Exclude after precursor   True
Keep isotope until   0.5
Keep original precursor isotopes   False

#MSP file and MS/MS identification setting
MSP file   /blue/djlemas/xinsongdu/jupyter_notebook/projects/milkmetabolomics-humanbovine/data/design_files/MSMS-Pos-MassBank.msp
Retention time tolerance   100
Accurate mass tolerance (MS1)   0.01
Accurate mass tolerance (MS2)   0.05
Identification score cut off   70
Using retention time for scoring   False
Using retention time for filtering   False

#Text file and post identification (retention time and accurate mass based) setting
Text file   /blue/djlemas/xinsongdu/jupyter_notebook/projects/milkmetabolomics-humanbovine/pos_msdial.txt
Retention time tolerance   0.1
Accurate mass tolerance   0.01
Identification score cut off   85

#Advanced setting for identification
Relative abundance cut off   0
Top candidate report   False

#Adduct ion setting
[M+H]+

#Alignment parameters setting
Reference file   /blue/djlemas/xinsongdu/jupyter_notebook/data/metabolomics/Human_Bovine/mzML/demo/QE2_jdg_242_Lemas_1[NeatQC]p.mzML
Retention time tolerance   0.05
MS1 tolerance   0.015
Retention time factor   0.5
MS1 factor   0.5
Peak count filter   20
N% detected in at least one group   0
Remove feature based on peak height fold-change   True
Sample max / blank average   5
Sample average / blank average   5
Keep identified and annotated metabolites   True
Keep removable features and assign the tag for checking   True
Gap filling by compulsion   True

#Tracking of isotope labels
Tracking of isotopic labels   FALSE

#Ion mobility
Ion mobility data   FALSE

```
7
MS-DIAL / Re: How to export alignment result in mztab-M format
Last post by biswapriya -
Hi Vladimir,

The mzTab-M export will only work if you have (A)  'aligned' the data, and from the alignment option, and (B) when choosen with the corresponding text file export for either height/ areas, and not for mzTab-M exclusively etc. PLUS, importantly, either "Area" or "Height" has to be chosen besides the "mzTab-M" option, as it will export them in pairs,i.e., .text version of height/ area alongside the mzTab-M version of height/ area. So, at least 2 checks.

I do not face such issue with mzTab-M export at least in the current versions or 1-2 versions earlier.

If you have NOT normalized the data after alignment is done, then checking 'Normalized data' option will result in a crash/non-export etc. So prior to exporting data as :"Normalized data matrix" the data needs to be normalized while you are on the "aligned results" tab on your (left) hand side panel/bars.

Check out the 2 attached figs and see if those help too!

Thanks,
Biswa
9
MS-DIAL / Re: Importing Sciex Data for Building In-house Mass Spectral Library in MSDIAL
Last post by biswapriya -
Hi,

Taking a stab at it from my past experience. Here can be the helpful steps:


[a] Sciex's WIFF/WIFF2 files can be converted using ProteoWizard's MS convert
: http://proteowizard.sourceforge.net/tools.shtml where you can convert Sciex file into "mzML format that are centroided data". See attached pic on "MSconvert".

Once this individual mzML files with spectra for reference standards are available to you, you can run them on MSDIAL and export out individual spectra from each file as a NIST .msp format file, as shown in the attached pic: "Exporting Spectra"!

[c] Once you have exported all the reference MS/MS spectra as .MSP files you can simply add them up in a .text file or following instructions here: https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-8txhwpn

I followed the same workflow as above [a-c], but for a different instrument from Thermo and GC-MS : https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00774

Hope it helps!

Thanks,
Biswa
10
MS-DIAL / Re: Not able to see MS2
Last post by biswapriya -
Plus also,:

[A]  see here for a relevant response from Hiroshi san on converting data out from Shimadzu software: http://www.metabolomics-forum.com/index.php?topic=1605.0  (to make sure you got the .mzML out in "Centroid" mode!)

Whats "w/o MS2 NAME" here: http://www.metabolomics-forum.com/index.php?topic=1580.msg4749#msg4749

Exactly. See the FAQ site.
http://prime.psc.riken.jp/compms/msdial/faq.html
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'.


Hope these two points above help you!

Thanks,
Biswa










Thanks!