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Topics - spapaz

1
MS-DIAL / suspect bug in MS-DIAL - GNPS Export
To MS-DIAL users
FYI, TL;DR  - be careful if you use the GNPS export options (the normal Alignment export seems fine).
---
I am experiencing issues with GNPS Export function (in v.4.9 and 4.92).
It used to be that the Spectra (mgf) and Feature Table between normal export and GNPS export were almost the same,
except for that GNPS files had the exclusion of the very first feature (alignment “0”) and the removing of all the stats form the quant table.
However, now the generated mgf spectra are very different in sizes, and also the list of features in the tables is different.
Note: this seems to be an issue if you export while using the option “filter for ion abundances”.
It looks like the GNPS table is actually the features that are excluded from the normal MS-DIAL table.
There seem to be a bug that makes these two in conflict.
When tested  the export without the blank filter option, the two matrices correspond.
---
I already notified Hiroshi&MS-DIAL team
 
Stefano
2
MS-DIAL / Blank subtraction & Normalization
Dear MS-DIAL developers

I was curious if it could be possible to include a "blank subtraction" function - i.e. in addition to a blank filter, one step (option) to subtract the average area of the blanks to each corresponding feature in the sample.

Regarding normalization, it would be awesome if the QC/LOESS and IS normalization could be used on the peak Area (currently only possible on peak Height)

 It would be nice to have these features in both the GC and LC tools

Thanks!

Best,

Stefano
3
MS-DIAL / Exclusion mass list - GC projects
Hello,

in the LC projects it´s possible to specify unwanted m/z ions, from a user defined exclusion list.
Would it be possible to add the same option also for GC projects? 

In this way we could get rid of some background ions and column bleed siloxanes from (e.g. m/z 73, 207..),
which sometimes appear to interfere with deconvolution.
 
Thank you!

Stefano
4
MS-DIAL / coefficient of variation
Hi Hiroshi,

regarding the coefficient of variation (CV%) shown by the MS-DIAL normalization report.
I have been manually calculating  the QCs across samples and QCs, for some internal standards,
but I do not manage to reproduce exactly the same values.

in MS-DIAL, are the CV% calculated based on the log transformed values? (as the report shows the log scale)

I tried both with and without log transforming. When I use the log values, I use the following formula:
= SQRT (10^(LN(10)*STDEV^2)-1)
as discussed here:  10.15406/mojpb.2017.06.00200

I attach the CV% calculated on the log values (for QCs and Samples), and the corresponding ones from MS-DIAL (in red)
(Note: they are not expressed as %, but as fraction, i.e. CV 0.15 = 15%)

Thank you!

Stefano






5
MS-DIAL / Isotopes
Hi Hiroshi,

it seems that isotopic patterns are recognized (visible in the Peak Spot), but are not exported in the msp and mgf files.
Is it possible to include them?

Thanks

Stefano
6
MS-DIAL / mass slice width - Orbitrap
Hi Hiroshi

depending on the processing settings, sometimes we observe the same compound splitting into 2-3 different features, and we think the mass slice width (in Peak detection) may be one of the parameters driving this effect (in addition to the alignment tolerance across samples).

How can we properly to choose a slice width that fits our data, i.e. neither a too wide nor too narrow?
For high-res Orbitrap a width of 0.05 Da is suggested. As an example, attached is an internal standard run on our LC Orbitrap (acquired at 140.000 resolution, profile). 

From my understanding of Tsugawa et al 2015 (Peak spotting) https://www.ncbi.nlm.nih.gov/pubmed/25938372 and the math presentation describing the MS-DIAL peak detection algorithm (default 0.1 Da), it seems MS-DIAL would correct the merging of BPCs across different m/z widths, somewhat similarly to XCMS? Below, from Smith et al 2006 (Peak detection) https://pubs.acs.org/doi/10.1021/ac051437y

"An important detail is the relationship between spectral peak width and slice width.

- if the peak width is larger than slice width: the signal from a single peak may bleed across multiple slices. Low-res MS produce peak widths greater than the XMCS default 0.1 m/z slice. The MEND peak detection algorithm uses a scoring function to assess whether a chromatographic peak is also at the maximum of a spectral peak, preemptively removing such bleed. Instead of eliminating spurious extra peaks during detection, our algorithm uses a post-processing step that descends through the peak list by intensity, eliminating any peaks in the vicinity (0.7 m/z) of higher intensity peaks.

- if the peak width is smaller than the slice width: high-res TOF or Fourier transform MS often exhibit such behavior. In that case, depending on the scan-to-scan precision of the instrument, the signal from an analyte may oscillate between adjacent slices over chromatographic time, making an otherwise smooth peak shape appear jagged. Based on operator knowledge of the mass spectrometer characteristics, we optionally combine the maximum signal intensity from adjacent slices into overlapping EIBPCs (i.e., 100.0/100.1, 100.1/100.2, etc.), That initial step produces both smooth and jagged chromatographic profiles, which are then used for filtration and peak detection. During the vicinity elimination postprocessing step, peaks detected from smooth profiles (integrated from the full signal) are selected over peaks detected from jagged profiles (integrated from an incomplete signal)
."

Thanks!

Stefano

 
7
MS-DIAL / normalization
Hi Hiroshi,

Question about normalization (performed with LOESS + IS).
In my Alignment results I have a total of 3300 features. When I export the results of normalization (performed with LOESS + IS),  however, in the pdf report I only see 365 features (one feature per page). 

- Why not all 3300 features are reported in the pdf? Are the features missing also normalized like the rest?

The exported Normalized txt table instead contains all 3300. Comparing values of features (found in the pdf report and not) between the Height and the Normalized txt tables, I would say all features have been normalized.

In addition, could you consider for future versions:

-In the pdf report, would be possible to order the features by their ID number?
-Would it be possible to normalize also the area (not only the peak height)?

Thank you!

Stefano


 
8
MS-DIAL / Suggestion for "New Project" --> simplify creation of Sample List
Hi Hiroshi,

when creating a new project, in the "New Project Window", would it be possible to make it easier to define the type of samples?
i.e. the Class IDs and especially sample Type (currently scroll down menu, with options Sample, Standard, QC, Blank)
It is very tedious to have to set manually one by one, when we have hundred of samples. 

I would imagine two better options:
1) a "Fill down" option (similar to the one available for setting the alkane series dictionary path)
2) even better, the option to import the sample list from a user defined CSV file (strictly following the MS-DIAL format requirements)

If similar short-cuts are already available and I am missing them, please let me know :)
I did not find them in the pop-up tips, nor mentioned here: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#section-2-2

Thank you again for your work and incredible support!

Stefano
9
MS-DIAL / molecular networking
Hello Hiroshi,

I have some questions regarding the generation of molecular networks within MS-DIAL, as -->Export --> Molecular spectrum networking export:

1) does the similarity cut-off represent the edge cosine score (exactly as in GNPS)?
2) is it possible to set a minimum of matched peaks in the spectra? e.g. 4-5 peaks, and exclude consensus spectra with less than a threshold?
3) could you add more explanations relevant to these settings and different cut-offs (in their respective fields, as "pop-up" tips in the menu, but also if possible in the MS-DIAL tutorial page)?

Thank you so much

Stefano
10
MS-DIAL / Delete features
Hi Hiroshi,

would it be possible with the next version, to add the possibility to delete a feature directly from the Alignment Table (e.g. right click--> delete) ? That would be great while doing manual inspection of the features

Thanks!

Stefano
11
MS-DIAL / Manual curation of Alignment
Hi Hiroshi,

I am not sure if I do this steps correctly. I am following the instructions.
The second middle panel looks good with the peaks aligned, but the third panel  -"manually curated chomatograms"  - does not Update, and looks exactly the same as the top panel before manual curation.  See attachment

I see that in the bottom panel, it changes the color of the integrated chromatogram area.  Is it correct that the position of the chromatogram in this panel remains as in the first top panel (and not as in the middle one) ?

Thanks

Stefano

 
12
MS-DIAL / crash MS-DIAL --> MRMPROBS
Hi Hiroshi,

I am experiencing a crash with MS-DIAL (v.4.12) when exporting the aligned focused (target) peak spot to MRMPROBS format file
(as described in Section 5-3-1, here: https://mtbinfo-team.github.io/mtbinfo.github.io/MRMPROBS/tutorial)

The program crashes and an empty txt file is created (only the headings are there). The function works fine instead if I do not select (tick the box) with the option "focused (target) peak spot" (which instead only produces a file with always the same reference peak spectra).

Thanks

Stefano
13
MS-DIAL / question about QuantMass
Hi Hiroshi,

I was wondering why in some deconvoluted features the QuantMass is not the major mass observed in the representative spectra, like in this case (attached). Is there a setting to change this?

Thanks

Stefano
14
MS-DIAL / networks
Hi Hiroshi,

I am currently experiencing a crash of MS-DIAL when trying to export the molecular network file (GC-MS data).   Could you look into that?

Interestingly, the network is processed and the visualization works fine using the menu --> Data Visualization, even in Chrome seems to work.

About the network visualization in the browser, it would be nice if possible, to add the options to:
- change the network layout (at the moment it is very dense)
- color by sample category

This I would do in Cytoscape, but at the moment I cannot export the file :)

Best,

Stefano
15
MS-DIAL / retention index (dictionary)
Dear Hiroshi and MS-DIAL developers,

for GC-MS processing using RI, would it be possible to change so that the user has to define only once the reference ABF alkane file (and the txt dictionary) instead of doing it for every single ABF sample? Alternatively, if it is possible to have a "fill-down" function, or to copy and then past the path through all the sample rows at once.

Thank you!

Stefano