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Messages - spapaz

2
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.
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I already notified Hiroshi&MS-DIAL team
 
Stefano
3
MS-DIAL / Re: Smoothing parameter
For what I understood, the "smoothing level" is the number of data points that will be considered in function (e.g. moving average).
E.g. Smoothing level 3 = 3 data points. It would be nice if someone can confirm that´s the case in MS-DIAL.
Also, because for my basic understanding of the smoothing function, the number of data points should always be kept odd (e.g. 3, 5..) in order to maintain signal symmetry.

Can someone comment ?

Stefano
4
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
5
MS-DIAL / Re: MS-DIAL 4.70 and MS-FINDER 3.52 were released.
Dear Hiroshi

thank you for this update.

I was wondering if, with this new version, direct import works for both SCIEX .WIFF and .WIFF2 formats,
or if the WIFF2 still needs conversion to ABF (and in this case, do we need to first convert it to centroid mzML)?

And, is this information from the FAQ still up do date:
"Unfortunately, the current work flow does not work for SWATH-MS data yet although it can be processed in MS_DIAL to get MS1 information in MS-DIAL. After SCIEX releases the Software Developer Kit which is needed for modification of ABF converter, the flow will become easier and SWATH-MS data can be also imported".
http://prime.psc.riken.jp/compms/msdial/faq.html

Also, thank you for the FAQ page which is very useful. Given how fast you introduce new versions, could you perhaps indicate the date on the page? 

Thank you again

Stefano


7
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
8
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






9
MS-DIAL / Re: MSFINDER problems
Hi,
I also experienced some crashes of the latest MSFINDER-3.40, usually right after performing structure search.  It is difficult to say what is the problem as often, after it crashed once, I try to re-run it (with the same settings) and I do not experience the crash again.

Stefano
10
MS-DIAL / Re: mass slice width - Orbitrap
Hi Hiroshi,
whenever you find the time, this kind of pre-view function would be awesome! 

I will see if I can share some demo files later. We saw this problem  of feature splitting both with GC and LC

Thank you!

Stefano
11
MS-DIAL / Re: Isotopes
Hi Hiroshi,

Thanks. It would be great to export the aligned feature IDs as mgf, containing both MS1 and MS2 levels.
This in order to import it into Sirius, which recognize isotope patterns at the MS1 level

But as I understand it is currently not possible in MS-DIAL? I know it is possible in mzMine or OpenMS.
Of course the other option is to process the raw files in Sirius, but it would be great if MS-DIAL could also interface with Sirius

Thanks!

Stefano


12
MS-DIAL / Re: Isotopes
Thank you Hiroshi.
And instead, from the option menu: "Export" -->Peak List result,
would that work too to include isotopes? It seems is possible to define the isotope region (default 5 Da).
The export format make any difference if the exported file will include or not the isotope patterns?
E.g. mgf, mat, txt, msp...

Thanks

Stefano
13
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
14
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

 
15
MS-DIAL / Re: Could MS-DIAL handle with the data of large retention time drift？
Hi Bingpeng,

In MS-DIAL you can set to execute the "retention time correction" option (in Peak detection tab, check the box at the bottom).  A window will pop-up, before processing your data, allowing you to define a list of compounds/ IS (Rt and m/z) that you can use to correct your batch.  It works good for me. Personally, I did not try it with big shifts (minutes), but you can test how it performs and give feed-back here :)