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71
MS-DIAL / Re: SCIEX 5600 Qtof data (IDA mode) with MSDIAL
Last post by berrytf -
Ok. We have a 5600 QToF as well and I investigated what you're showing with my own data. A few things pop out.

First with respect to what you're seeing in Peakview you have the wrong data displayed(MS1 scan). If it is IDA data you need to pull up the IDA explorer and find the parent ion at the expected RT to pull out the relevant MS2 scans. Those would properly reflect what MS Dial is trying to find and display to you in the windows you showed containing only the parent ion.

I'm not sure if you're trying to process SWATH data or not. You mentioned IDA, but what's shown in the MS-Dial Parameters includes deconvolution settings that differ from the standard inputs including an MS2 cutoff. That might also be part of the problem, however if that's not the case then no worries.

Also why are you converting to mzML file format? That might also be part of the problem. You can use wiff files so long as you select 'profile' for both MS1 and MS2 settings up front.
72
MS-DIAL / Problem in converting NIST23 to MSDIAL compatible msp format
Last post by Sophiadj -
Hi everyone,
I'm having a problem in converting NIST23 MS/MS library to MSDIAL compatible msp format.
I tried different settings, but none of them worked. Error "No spectra fromC:NISTDEMO\MSSEARCH hr msms nist" have been converted" kept popping out.  Below are snapshots of the settings.  I wonder if I got the setting wrong.
Thanks in advance!
73
MS-DIAL / TIC normalization and Raw values?
Last post by Massspek -
Hey Scientists,

During Alignments for MS-DIAL you have the option to normalize to TIC.

I am wondering if there is a way to Export the TICs for the loaded chromatograms? Looking for a high throughput way to acquire tics instead of manually integrating all plots.

Thanks!
74
Other / LIPID MAPS .LBM
Last post by MatyashSupp -
Good day you'll

 Someone know how to compress lipid maps in .lbm for database uses at MS DIAL?

 Already tried to do it sometimes, but never works.

Ty
76
MS-DIAL / Matching QTOF and Orbitrap datasets (via setting up a custom database?)
Last post by mniku -
Apologies for perhaps a primitive question, but I’d like to ask advice about how to optimally proceed with the following task:

We have an Orbitrap dataset and an QTOF dataset, generated from partially overlapping sample sets, using ~same LC instrument.
We need to match the molecular features in these datasets (I mean, find what feature corresponds to a QTOF compound in the Orbitrap dataset).

I’m thinking this could be accomplished by setting up a custom metabolite database from one of the datasets, and use that to annotate the other dataset in MSDIAL.
If you agree, could you please point us to a tutorial about converting our dataset to a database for this purpose?
If you have better suggestions for a protocol, please let us know.

As a side note, the QTOF dataset has files for 10-20-40 kV. Apparently 10 kV would be best match for Orbitrap (because of the fragmentation power). But 20 kV and 40 kV would provide additional fragmentation info. Is it possible to somehow more or less merge these to utilize all available data for the matched compounds, after we have completed that?

With best regards,
Mikael Niku
77
MS-DIAL / Re: Which version is more stable?
Last post by James -
I have heard that version 4.24 works for some people with these issues, but it doesn't fix the problems for me.

I don't do lipidomics, but I've found the most reliable way for me to avoid crashes is to first run alignment steps without any identification, and then go back and run identification after saving the alignment file. For some reason it seems to crash less frequently this way for me.

James
80
MS-DIAL / Which version is more stable?
Last post by MatyashSupp -
Hello everyone

 Im having alot of trouble with the new versions of MS Dial, even with 32gb ram I cant use it without trouble. Suffering with stutters and alot of crashes.

 Im running lipidomics with a single database with .wiff files and Dial crashes everytime, or just freeze.

Anyone know some version more stable?