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91
MS-DIAL / What's the difference between adduct under Identification tab and adduct tab?
Last post by JL -
Hi,

In the lipid database setting, there are two places that we could select adduct. One is under "Identification" tab,  where we choose lipid class and adduct type. Under "Adduct "tab, we could also choose adduct again. What's the difference between the adduct under "Identification" tab and "Adduct" tab?
Thanks!

JL
92
MS-DIAL / View Alignment Table
Last post by Ro_Nina -
Hello everyone,
I recently had some issues with MS-Dial crashing down a lot, so I reinstalled it. Now it workes a lot smoother, but somehow I can not open the alignment table viewer. It just shows the loading bar and nothing happens. I am working with MS-Dial version 4.9. Has anyone encountered the same issue?
Thanks for your help  :)
Ro_Nina
93
MS-DIAL / Re: Spectra extraction for database creation
Last post by Jude Leung -
Hi,

about the second question,  we have some questions. which collision energy (10 20 40ev) of the data import to MS dial? And now the software have been updated to version 5,  this version also uses only one of the MS/MS spectra assigned to a precursor peak? Are there any plans to consider providing new solutions, such as allowing collision energy selection, etc

Thanks
94
MS-DIAL / MS-DIAL v5.1.230807: LOWESS unavailable when trying to normalise
Last post by ThmsBrnt -
Hi,

I am currently experiencing an issue with MS-DIAL v5.1.230807. After processing my SWATH data, including peak detection, deconvolution, identification, and alignment, I have encountered a problem with the normalization step using LOWESS. The "Normalize" button appears to be greyed out and inaccessible.

I want to note that I have QCs available and that I have configured the settings for the overall data, including analytical order and sample type. Despite this, the "Normalize" button remains inactive.

Has anyone else encountered a similar issue and found a solution? Your insights would be greatly appreciated.

Thank you.

Thomas
95
MS-DIAL / MS Dial crash upon library upload
Last post by acbarne5 -
I have an external RT library that I am trying to upload to analyze my lipidomics data, and no matter what I do, MS Dial crashes when I upload it. I am uploading my files as mzML. Someone else gave me one of their libraries, and that will sometimes load, but mine will not ever load. I've tried both versions 4.70 and 5.1.230517, but nothing newer. My library is saved as a .txt. Any help is greatly appreciated!
96
MS-DIAL / MS2 spectra Precursor value in alignment result "Rep. vs. Ref" tab
Last post by JL -
Hi All,

One question about the MS2 spectra Precursor value in the alignment results "Rep. vs. Ref." tab, see the highlighted part with red rectangle in the picture. This value is  not consistent with the measurement value (>0.1 Da difference). How is this MS2 spectra Precursor value obtained in MS Dial? I am manually curating this lipid, and I think for [M+H]+ the measurement doesn't match with the library since the measurement value 648.4619 is not consistent with library value 648.6289 due to >0.1 Da difference. But then I found this piece of info "MS2 spectra Precursor: 648.62781" on this tab. If the MS2 (DDA) is performed at this value, then the measurement value would match really good with library. I guess my question is how to make a right judgement based on these information.

Could anyone help? Thanks!

JL
97
XCMS / Re: XCMSonline down?
Last post by 18751996731 -
the website is currently undergoing maintenance mode to enhance the browsing experience
98
XCMS / XCMSonline down?
Last post by srosolina -
I haven't been able to reach xcmsonline all day, including the contact form. Anyone else experiencing this or have an idea on when the server will be back up?
99
XCMS / Select specific samples from correspondance file
Last post by E_ -
Hi!
I wonder how to select specific samples after correspondance? For example remove all quality control samples?

# Example code from https://bioconductor.org/packages/devel/bioc/vignettes/xcms/inst/doc/xcms.html
## Perform the correspondence
pdp <- PeakDensityParam(sampleGroups = sampleData(xdata)$sample_group,
                        minFraction = 0.4, bw = 30)
xdata <- groupChromPeaks(xdata, param = pdp)

With filterFeatureDefinitions  its possible to filter features, but how to do it for samples?

Many thanks!
Best,
Elise
100
MS-DIAL / How does MS-Dial deal with saturated peak?
Last post by Pegah MF -
Hello all,

I am working on GC-QTOF-MS data using MS-DIAL v.4.9.
As there are many saturated peaks in my data, I was wondering if anybody knows how MS-Dial deals with those peaks?
I am not sure whether the peak area generated by MS-Dial can be reliably used for statistical purposes.

I have attached screenshots of an example of a saturated peak in QUAL and its representation in MS-Dial.

Thank you very much!

Pegah