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Topic: SCIEX 5600 Qtof data (IDA mode) with MSDIAL (Read 4257 times) previous topic - next topic

SCIEX 5600 Qtof data (IDA mode) with MSDIAL

Dear all,
I met a problem when I implemented MSDIAL to process data from SCIEX5600 acquired with data-dependent (IDA) under positive ESI mode. When I directly use PeakViwe to check how spectra look like, for 2 standards (chaconine and solannine), they all seem good with pretty good spectrum quality as showed in A1 and B1, however, after MSDIAL processing these 2 centroided mzML file, all fragments are gone (A2 and B2), I’ve no idea how to solve this problem.

I stored these 2 std mzML files here(
and, please download them and give it a shot. The expected spectrum should pretty like showed in A1 and B1, the parameters setting also attached here. The version I’ve used is MSDIAL 4.6.

Many thanks for your help!


Re: SCIEX 5600 Qtof data (IDA mode) with MSDIAL

Reply #1
Hello Mwang, I got the same Sciex but I'm doing Lipidomics instead. But I did some tests to understand how MS DIAL works and I have some issues when, first: MS DIAL just dissapear with the channels, with makes me question about the confidence of DIAL, and second: I could just use my datas in MS DIAL when it accepts the .wiff, it because when I use ABF, I lost many data infos.

 Did u already tried to use the recent versions of DIAL? Maybe it'll help.

Re: SCIEX 5600 Qtof data (IDA mode) with MSDIAL

Reply #2
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.

Re: SCIEX 5600 Qtof data (IDA mode) with MSDIAL

Reply #3
Here is the information I used to check what you were displaying. My data is directly from a wiff file though. Didn't bother with converting before churning it in MS Dial