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91
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
92
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!
93
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
94
XCMS / Re: XCMSonline down?
Last post by 18751996731 -
the website is currently undergoing maintenance mode to enhance the browsing experience
95
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?
96
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
97
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

98
MS-DIAL / Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found
Last post by drchrispook -
Quote from: Hiroshi Tsugawa – on
candidate 3: out of memory issue.

For candidate 3, when UC Davis's Tobias Kind tried to analyze >2000 abf files at once, MS-DIAL required around 200 GB RAM when the joint alignner is executed.

In the peak picking process for each file, MS-DIAL stores the entire MS data on the PC memory.
It means, if you set the thread size as 1, and if your abf file size is around 1GB, the program requires < 2GB RAM for the processing.
On the other hand, in the alignment process, the peak picked data (stored in *.pai2 format file) for all analysis files will be stored on the PC memory.

Although the file size of PAI2 file is around 1M, it will be elevated if you import many files.


This is really important to know. I got this error trying to process 985 mzML DIA files of ~100MB each. My VM has 64GB of RAM and the PAI2 files generated are ~3.5MB each, so that seems like plenty for this analysis. I assume that MS-DIAL builds its alignment file by combining all these individual files so the data in memory will be double that amount, but that's still a fraction of what it's using. I've rerun the analysis with some repeat samples removed, so 680 files, and I've got the same error. I'm now seeking a temporary boost to the RAM on the VM to get this analysis done.

People in the Australian Biocommons community have told me that they don't use MS-DIAL because it couldn't handle large datasets. It might help broaden the user base for the documentation to make these limits explicit.
99
MS-DIAL / Re: No peak information
Last post by QizhiSu -
Hi MaiAmmar,

I am running GC-MS data, but I have a similar issue. MSDIAL crashes during the alignment step because of no peak information.
The weird thing is that not all files have this problem and when I run different times, different files have this problem.
100
MS-DIAL / Re: AIF data analysis
Last post by romanas chaleckis -
Hi, indeed the order of different scan types is vendor-specific. For example you can check the order in MZmine and if your scan type order is like in the attached screenshot then use your example 2 (ID0: SCAN, ID1: AIF). If you also set "DecTarget" 1 for the SCAN, then you will get deconvoluted in-source fragmentation.