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Messages - FalcoB

1
MS-DIAL / Smoothing method - recommendaton?
Hi,

I have a question concerning smoothing method. Currently, we are using the Savitzky-Golay filter, since we also used it when processing our data with XCMS/R, and here this is working properly.

Is there a recommendation, what method performs best in MS-Dial: Savitzky-Golay or linear weighting method (as regularily mentioned on the MS-Dial website) or another method?
Do you have to expect great differences, e.g. with respect to the occurrence of peak splitting (i.e. features are splitted into two or more separate features, though they belong to the same peak/analyte).

Thanks for your time and support.

Best regards
FalcoB
4
MS-DIAL / Export of normalization results aborted - why?
Hi,

I would like to report some issues with respect to the export of normalization results.

Following data processing with MS-Dial (4.80) I performed LOWESS normalization. For the data set measured in negative polarity everything works fine, and I was able to export the normalization PDF without problems. And the plots in the PDF were okay. For the positive data set I used the same procedure but finally a problem occurred during plotting/export. The process needs a lot of time. At the end it crashed, and MS-Dial was closed immediately. I repeated this several times but without success.

I wonder what the problem might be, because for negative dataset it worked. The size of both datasets and the respective file sequences were equal. The only difference was the number of ´Ref. matched´ features (pos: 2867 vs. neg: 839).
The PC I used for data processing was also quite powerful (iCore i9, 12 cores, 128 RAM, Win10, 64 bit, engl.), and the utilized working memory was approx. 20% as the process aborted.

As we planned to use the normalization function for future studies, it would be nice, if some someone could help me with this issue.

Thanks for your support!

Best regards
FalcoB
5
MS-DIAL / Normalization plots of additional/individual features?
Dear all,

I have a question regarding the normalization plots, that can be exported from MS-Dial, in order to assess normalization procedure (at the moment, I used LOWESS).

As I understood right, these plots are generated only for ´Ref. matched´ features and TOP100 (Int.) of ´Unknowns´. But, in my opinion it would be interesting also to have plots of TOP500 (´Unknowns´) and of selected (statistical significant) features.

Is there currently a way to get access to additional/individual normalization plots in MS-Dial?

Best regards
Falco
6
MS-DIAL / Re: PCA function
Hey,

It seems to be that one can only select/use the PCA function, if you had done a normalization before.

Is that true?

Regards
FalcoB
7
MS-DIAL / PCA function
Dear all,

MS-Dial version: 4.80
I have a question regarding the PCA function. We have processed our LC/MS data set, but following data processing we can not select the PCA function (greyed out). This was independent whether we check the gap filling function. We also have filled in the class IDs prior to processing (in total, we have 8 groups: 1 x Blank group, 1 x QC group, and 6 x Sample groups)

Why this is the case, and what I have to do for being able to use the PCA function?

Really thanks for your support.

Best regards
FalcoB

8
MS-DIAL / Order of processing steps / Re-processing from identification
Hi,

two additional questions for my understanding:
1) Data processing in MS-DIAL is done the following way, isn´t it?
a. peak detection
b. identification (annotation of the peaks in all samples if possible)
c. alignment (und selection of top annoation hit by means of the highest total score)

2.)
if you re-process your data starting from "identification" (e.g. by using another MSP-File) which of the following statements is true?
a. The identification step and the subsequent alignment step is re-processed (but not the peak detection step).
or
b. Only the annotation hit in der respective aligned feature list is modified (no separate alignment step is performed)?

Really thanks a lot for your support.
FalcoB
9
MS-DIAL / Re: Smoothing parameter
Maybe to be more precise with my question.

Would you for example suggest the following: if you have 20 or more data points per peak -> use smoothing level 4, whereas if you have less than 10 data points better use smoothing level 2 (or similar)? Just as an idea.

Of course, you have to proof this by your own data.

Thanks
FalcoB
11
MS-DIAL / Issues with parameter export/import function
Hello,
I checked the parameter export and import function (version: 4.80) und would like to report some currently occurring errors.

Parameter export: Following parameter settings were not correctly exported (via “Export > Alignment result”) in the txt-File:
- The setting for "Consider Cl and Br elements" is missing regardless of whether you checked this field or not.
- With respect to the blank filter option, independently what your settings were, you always get the following output (default setting):
"Sample max / blank average   5
Sample average / blank average 5"
- Regarding the annotation filter criteria: In the text file, you have a setting for "Keep identified and annotated metabolites", whereas in the GUI you can make selections for "Keep ´reference matched´ metabolite features" and "Keep ´suggested (w/o MS2)´ metabolite features".

Parameter import: Following parameter settings were not correctly loaded (via “Load parameter”) in the GUI:
- in the peak detection tab: the smoothing method is often not correctly imported, e.g. although I selected “Savitzky-Golay filter” the “linear weighting method” (default settings) was imported.
- in the alignment tab: Instead of my individual settings the default settings of MS1 and RT factor were imported. The “Reference file” is not correct after parameter import (I suggest, here always the first file of the analysis file list is selected).
- with respect to the blank filter option you have the same issue as mentioned above probably because the parameter export was not sufficient.

Maybe this bugs can be eliminated in one of the next updates.

Thanks
FalcoB
12
MS-DIAL / Alignment: MS1/RT factor, N% detected in at least one group
Hello,

I have some question with respect to specific alignment parameters.

1.) My first question refers to the parameters "MS1 factor" and "RT factor". As I understood right, the parameters determine the weighting of mass and retention time (deviations) used for calculating the total score of a feature matching the post-identification process. Up to now, my inetention was that the total sum of both parameters should be 1, e.g. 0.5 for MS1 and 0.5 for RT. However, I recognized that you can process your data also with parameter values whose sum is bigger than 1.
So, I am not sure how this weighting finally works?

2.) The second question concerns the “N% detected in at least one group” parameter. Does “one group” also includes the QC and the blank group, respectively?
If the value is smaller than the given parameter setting (valid for all sample groups, but not for QC/blank group), what will be the consequence? Is such a feature completely eliminated from the alignment output or is it only eliminated from the sample groups but not from the QC or blank group (and thus it would remain in the feature list)?

Thanks,
FalcoB

13
MS-DIAL / MS1 tolerance in peak detection vs. alignment / BPC mass slice width
Hi,

I was wondering how to deal with the different setting options for the MS1 tolerance (in Da) for peak detection vs. alignment. Is it generally recommended to have a "looser" setting for peak detection and a correspondingly "stricter" setting for alignment, or should both parameters be set very similarly or even identically?

Moreover, I have a question regarding the function of the BPC mass slice parameter. Does it determines whether data points are within the same slice and then assigned to the same peak?
We work with a high-resolution MS (QTOF). Values like 0.1 Da or 0.05 Da as recommended by MS-Dial seem quite generous at first glance. But I may not have fully understood the meaning of this parameter.

Thanks for your input.
FalcoB
14
MS-DIAL / Smoothing parameter
Hi,
I have a question about the smoothing parameters.
According to an older MS-Dial version the recommendation was 1-3, However, for the current version (4.80) it is 2-4. Does this recommendation apply regardless of the selected smoothing method?
Could it be simplified that for peaks with >10DP smoothing level 3 to 4 should be the better setting, and only for peaks with <10DP a smoothing level of 2 would be preferable?

Thanks.

Best regards
FalcoB