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Messages - spapaz

31
MS-DIAL / Re: Selecting peaks to export as .mgf
Yes, I agree, it would be wonderful to have the possibility to select some features from the Table Viewer and export only those spectra them in mfg so that we can focus on only some important features for identifications (for use in SIRIUS).

Thanks!

Stefano
32
MS-DIAL / Re: question about QuantMass
Thank you Hiroshi.
FYI, the spectra I posted above is from a GC-Orbitrap project.

Questions:
1) is it the same way how the algorithm work for the QuantMass, between a GC and an LC project?
2) how does the algorithm decide for the QuantMass, between preferences for the most abundant ion and higher m/z values?

Thanks

Stefano
33
MS-DIAL / Re: question about QuantMass
Hi,
Thanks. Yes I am aware that one can change each one of the QuantMass manually in the alignment result. I was wondering if there is a way to define how the QuantMass is picked. I assume(d) that it is the most abundant mass, but that does not seem to be always the case. 
34
MS-DIAL / Re: Can't start a new project
Hi Jean,
I had the same problem, it is either due to the dotnet (.NET) configuration in your system, or that you do not have English language set

Stefano
36
MS-DIAL / Re: crash MS-DIAL --> MRMPROBS
Hi Hiroshi,

I am using GC-MS data. Attached the export settings.

The "Save" function from focused spot creates an empty .TXT file with only the headings
(Compound name   Precursor mz   Product mz   RT min   TQ Ratio   RT begin   RT end   MS1 tolerance   MS2 tolerance   MS level   Class)

The "Copy" function does not seem to work either.

I guess I am doing something wrong.

Thanks!
37
MS-DIAL / crash MS-DIAL --> MRMPROBS
Hi Hiroshi,

I am experiencing a crash with MS-DIAL (v.4.12) when exporting the aligned focused (target) peak spot to MRMPROBS format file
(as described in Section 5-3-1, here: https://mtbinfo-team.github.io/mtbinfo.github.io/MRMPROBS/tutorial)

The program crashes and an empty txt file is created (only the headings are there). The function works fine instead if I do not select (tick the box) with the option "focused (target) peak spot" (which instead only produces a file with always the same reference peak spectra).

Thanks

Stefano
38
MS-DIAL / question about QuantMass
Hi Hiroshi,

I was wondering why in some deconvoluted features the QuantMass is not the major mass observed in the representative spectra, like in this case (attached). Is there a setting to change this?

Thanks

Stefano
39
MS-DIAL / Re: GNPS export function
Hi Hiroshi,

yes exactly what I meant. I created these kind of networks / pie-chart node visualization in Cytoscape before, but by using GNPS exported metadata.
I think one can use the metadata from the Peak-ID matrix as you suggest.  But if possible, it would be great to add a summary to this matrix, that would report for each ion/peak in which "Class" of samples it was found. Say, if you have 3 classes, a peak may be found e.g. in Classes 1,2 , another in Classes 1,3, and another in 2,3.
GNPS exported metadata gives you a similar summary list of which samples your peak was found , as  in the defined "Group" (e.g. G1, G2, G3..), see here at min 6:00 https://www.youtube.com/watch?v=ujYR0Hugb2M&t=374s

Thanks

Stefano
40
MS-DIAL / Re: GNPS export function
Hi Hiroshi,

would it be possible to add to export table, also a column with the list of sample (classes) where the ion was found?
That is how also GNPS creates the output table. In that way it is possible to make nodes in the newtork that are colored as "pie-charts", so split and colored by the sample class.

I did not try the mz-Tab export yet, maybe you already have this feature there, but it would be good to have also in the other export tables.

Thanks!

Stefano 
41
MS-DIAL / Re: Export alignment results to .MSP file with retention time, S/N, etc. information
Ah, OK, so now you modified the exporter so from the next version RT / RI are recognized? That would be awesome
Please add also a new "ID" in front of them, which helps the comparison. Thanks!

At the moment, one can fix it in python like this:

Before the new version is out, if someone is using python, I fix it like this:
(it will create a new file with the "Align ID)

data = open('spectra_test_MS-DIAL.msp', 'r')
data_new = open('spectra_test_MS-DIAL_new.msp', 'w')

counter=0
for line in data:
    stuffinline = line.split()
   
    if stuffinline != []:
        first_element = stuffinline[0]
        second_element = stuffinline[1]
        if first_element == "NAME:":
            counter+=1
            second_element_new = "Aligned ID #" + str(counter)+ " - " + second_element + "\n"
            line = first_element + second_element_new
   
    data_new.write(line)
42
MS-DIAL / Re: networks
Before the new version is out, if someone is using python, I fix it like this:
(it will create a new file with the "Align ID)

data = open('spectra_test_MS-DIAL.msp', 'r')
data_new = open('spectra_test_MS-DIAL_new.msp', 'w')

counter=0
for line in data:
    stuffinline = line.split()
   
    if stuffinline != []:
        first_element = stuffinline[0]
        second_element = stuffinline[1]
        if first_element == "NAME:":
            counter+=1
            second_element_new = "Aligned ID #" + str(counter)+ " - " + second_element + "\n"
            line = first_element + second_element_new
   
    data_new.write(line)
43
MS-DIAL / Re: networks
Hi Hiroshi,

that´s great!

If it is not a big issue, would it be possible for you to also already in the next version, that when using the function to export the spectra (in .msp) from the Alignment, we also get reported as the "Name", the aligned variables (e.g. in order, ID 1, ID 2..) corresponding to the order in the matrix tables? At the moment we only have either "Unknown" or the putative metabolite.
That would be super useful for when importing the msp into NIST!

Thanks

Stefano
44
MS-DIAL / networks
Hi Hiroshi,

I am currently experiencing a crash of MS-DIAL when trying to export the molecular network file (GC-MS data).   Could you look into that?

Interestingly, the network is processed and the visualization works fine using the menu --> Data Visualization, even in Chrome seems to work.

About the network visualization in the browser, it would be nice if possible, to add the options to:
- change the network layout (at the moment it is very dense)
- color by sample category

This I would do in Cytoscape, but at the moment I cannot export the file :)

Best,

Stefano