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Messages - FalcoB

1
MS-DIAL / "MS1 factor" and "RT factor"
Hi,

my question refers to the MS-Dial parameters "MS1 factor" and "RT factor". As I understand right, the parameters determine the weighting of mass and retention time (deviations) used for calculating the total score of an feature annotated by the post-identification process.

However, are those parameter also relevant when using an MSP-file for feature annotation,
i.e. do the values for "MS1 factor" and "RT factor" also have impact on the total score calculation of an MSP-file annotated feature?

Can anyone comment on this?
Thanks!

Best regards
FalcoB
5
MS-DIAL / Re: Spectral Similarities of in-house measured reference compounds quite low
Hi,

Regarding your first paragraph:
It´s the case that "whether if you analyse a file from which the exact library spectra was extracted you should get a dot product of 1.00 (you should)".

Regarding your second paragraph:
In fact, we measure DDA. Four build-up of our in-house MSMS database we are currently using MS-Dial following the instructions described here: http://www.metabolomics-forum.com/index.php?topic=1627.msg4889#msg4889

We do it step-wise, i.e. processing approx. 10 standards in parallel
step 1: converting the raw data files (wiff->abf) of the standard runs by ABF converter
step 2: processing abf files by MS-Dial
step 3: extracting the appropriate MS2 spectrum from MS-Dial GUI (as a single MSP-file)

Note: Per standard only one single MS2-spectrum (presumably that one with the highest absolute intensity, but I am not sure) is displayed in the MS-Dial GUI when selecting the corresponding ion of the reference compound. That means, we have no option to choose between different MS2 spectra for the same peak. The raw data of this MS2 spectrum we export to single MSP-File.

step 4: We then copy the data from the single MSP-files in our database-MSP-file (we copy the original MS2-data without making any changes in the mz/intensity matrix).

step 5: We re-process the standard runs in MS-Dial, however, in this case using the updated database-MSP-file (including the before added reference compound data) for automated identification.

Usually, when you have a look at the MS/MS spectra alignment figure, both spectra look identical. Nevertheless, sometimes (regularly) we get score values (dpc, rdpc) < 1000 (the lowest ever observed value was 750 I think). And we do not know why.
7
MS-DIAL / Adduct-based filtering of featurelist
Hello at all,
I´m interested in reducing the number of features of my raw feature list. The steps I´am currently doing are the following:
- MS-Dial data processing: using parameters "peakcount filter" & "N% detected"
- MS-Dial data processing: elimination of blank features (by applying a specific limit value for sample average/blank average ratio)
- manually after data processing: elimination of features by QC-specific filters (using specific limit values for missing rate and CV value)

By performing these steps, I can reduce the number of features from ca. 10.000 (or more) to about let´s say 4000-5000. But there are still redundant features, i.e. adducts!

So my question: Is there a simple way to (semi-)automatically delete all the adducts from the feature list in MS-Dial? How would be a reasonable way to do this?
As I remember right, in XCMS "peak grouping" at least facilitates eliminaton of adducts. In MS-Dial, somehow similar information is given in the column "post curation result" within the aligned feature list, but based on these data you are not able to delete all adducts from the list in a reasonable time.

Unfortunately I´m not experienced in programming. So, I would prefer using a tool that does not require deep knowledge in programming. However, can someone recommend any tool?

One additional question. Just to be sure, the isotopes are excluded automatically from the aligned feature list in MS-Dial?

MS-Dial version: 4.90

Best regards
FalcoB
8
MS-DIAL / Formula for calculating spectral similarity and total score
Hi all,

We are interested in how exactly the spectral similarity and the total score is calculated in MSDial. In particular, It would be nice to have the exact calculation path (step-by-step including the values used) for the examples in the FAQ document
(MSDIAL FAQMat-vs2/ page 20 and 21; Link: prime.psc.riken.jp/compms/msdial/download/mathematics/MS-DIAL%20FAQ-vs2.pdf)
It is also unclear to us how the two formulas shown for "dot product" and "reverse dot product" on pages 20 and 21 are related. Do they calculate the same values?

Thank you very much for your help!
With kind regards
FalcoB
9
MS-DIAL / Spectral Similarities of in-house measured reference compounds quite low
Hi all,
We have performed MSMS matching in a measurement file for certain reference substances, from which the reference MSMS is taken. It would be expected that the spectral similarities would result in 1000, since identical spectra are compared with each other. However, we obtain results that differ significantly from this (see appendix: results for dpc/rdpc: 750 or 880). How can this be?

The detailed procedure was as follows:
1) Export of the respective MS2 spectra from the ABF files of single standard runs (as single txt-files)
2) MS2 spectral data from exported txt-files are merged in in-house spectral library (MSP file)
3.) In order to control, if MSP-file based annotation is working in MS-Dial, this updated MSP-file is regularly used to annotate the reference standards in the standard runs

Thank you very much for your help!
With kind regards
FalcoB
10
MS-DIAL / Re: PCA function
Hi,

I want to add something for the community.

Before you are able to select the PCA option, you have have to make a selection in the normalization menu, but you can also choose "none" here (i.e. no normalization is performed).

Best regards
FalcoB
11
MS-DIAL / Re: Options for Noise Cleaning of MS2 spectra for Build an Inhouse Spectral Library?
Hi Triston,

thanks for sharing the workflow.
You mentioned "deconvolution of spectra". I suppose you analyzed your samples by DIA, right? We are using instead DDA. We are choosing one vial per compound. For each vial we have five injections by applying five different collision energies.

Is the workflow you mentioned only applicable for DDA, too?

When I look at the intensities of my fragments MS2 spectra I regularily observe the same low value for several fragments, i.e. pure noise. From my opinion, it would be nice, to have the ability to set a cut-off with respect to absolute intensity in MS2 Dial during data processing.

Best regards
FalcoB
12
MS-DIAL / Options for Noise Cleaning of MS2 spectra for Build an Inhouse Spectral Library?
Hi,

we are going to built an MSMS-library in MS-Dial (MSP-file containing MSMS spectra of reference compounds analyzed on our MS device).

Is there a possibilty to do a noise cleanup of acquired MS2 spectra during data processing? Here, I only found one parameter "Relative Abundance Cut-Off" (Identification Reiter). From my point of view this parameter only determines the way the spectral matching is done but this is not a cleaning of MS2 spectra itself. So, the only way would be to curate each single MS2 spectrum manually?

Thanks for your support.

Regards Falco
13
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