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22
MS-DIAL / new features on File Property Setting
Last post by Angrist -
Dear Developers
some suggestions in reference to the "File Property Setting":
1) have the possibility to select\deselect all files with only one flag.
2) select \ deselect files using only the group they belong to (QC, Control, Treated etc..).
these simple features would simplify a lot the work on wide samples avoiding stupid selection errors.

I would like if it was possible to have a clarification on column Y varaibile 0-1.

all the best
Andrea
23
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
Last post by 7clouds7 -
Thanks, Romanas!  Can you please guide me as to how to filter by scans instead of by seconds?  I have not done this before.  How would I get the # of scans at 0.25 minutes?  I have the acquisition rate which is 4 spectra/seconds, which means there are 60 spectra at 0.25 minutes.  Should I then filter from 80 scans - 2000 scans?  I chose 80 just to make sure I am out of the inconsistent range.  Thanks!
24
MS-DIAL / Tables
Last post by Angrist -
Dear Developers
In the "Show ion table" the functions "Annotated Compound Table" and "Spot Relation Table" are not clear to me. My difficulty is to understand exactly what they refer to and how to use them.
thanks for your time
Andrea
26
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
Last post by 7clouds7 -
HI Romanas,
  I tried using proteowizard and just only focusing on data from 50-500 seconds.  But unfortunately, I am still seeing the high %CV's. This is a bummer.  I have included the picture of the proteowizard parameters and also some of the amino acids that normally had low %CV's (phenylalanine and glutamic acid) using Masshunter but I am still seeing high variation in MSDial.  But when I did just regular MS1 without any deconvolution, I am getting really good %CV's. 
27
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
Last post by 7clouds7 -
Thanks, Romanas!  And so you recommend for us to use proteowizard to convert our files and not use ABF converter?

Also, we usually do not acquire anything from 0-0.2.  It just goes to waste.  And so, just to be clear, currently, there is no remedy yet for this.  I am glad we found the culprit but too bad there is no remedy yet.  What is the process for requesting this for MSDial?  Thanks and keep safe.
28
MS-DIAL / Re: MS-Dial is giving very noisy data in comparison to Masshunter Qual (Help!)
Last post by romanas chaleckis -
probably the having multiple time segments in the method causes the issue. For the future try acquiring all data in one segment, or stop acquiring data in the 0-0.2min segment. Anyway, are you sure your flow-through peak with salts comes around 0-0.2min?

for the current files, if you want to use the MS2Dec and CorrDec in MS-DIAL, I am afraid you will have to check and crop (subset function in ProteoWizard MSconvert) the files one by one to make sure they match MS-DIALs experiment settings file. However, if you just want MS1 then proceed with simply filtering MS1 - no deconvoluted MS2 spectra in such case.
30
MS-DIAL / Re: Error in grouping Br and Cl isotopes
Last post by lisa.d -
Hi Hiroshi,

In looking at our data set after adjusting the centroiding parameter, we found a concerning issue with one of a few features that we'd tentatively identified previously. With the centroiding parameter at 0.005 Da or lower, we identified dichlorophen, which was a very large feature in a number of samples. The three chlorine isotopes show up as separate alignment spots, as shown in the attached image of the alignment spots. The M+0 peak is at m/z 266.9979 (Figure 1).

Using the centroiding parameter of 0.01 Da, the dichlorophen alignment spot disappears from the final alignment and the nearest spot is at m/z  266.9205 and appears to be a satellite peak (a Fourier transform artifact, Figure 2).

Looking at a sample to determine how it disappeared, shows that the M+0 has been classified as the M+2 of a peak 2 orders of magnitude smaller than the dichlorophen peak that happens to be close enough to the mass difference for a C13 isotope peak (Figure 3). Because of this issue, we are not going to be using data processed with a centroid parameter of 0.01.

Cheers,
Lisa