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61
MS-DIAL / EI similarity and Dot. Product difference?
Last post by Hzamora14 -
Hello!

Does anybody know what is the difference between EI similarity score and Dot Product similarity score for GC-MS?

They both are in the Compoud Detail section or in the Compoud Serch Window. I know how the dot product works, but I don't understand how IE similarity differs from the dot product.

Thank you for your help!

Kind regards,

Hans
62
MS-DIAL / peak splitting: I want less peaks.
Last post by ethidium -
Hello,

I'd like to ask for help. I hope there is an easy answer.
My lipidomics abf files are quite big by themself (1+ Gb from QToF MSe), and the alignment is also very rich (13K features). Many of them come from peaks being split or picked as separate entities. In example attached below, there are four peaks. In some cases they have equal areas in some samples and in another subset of samples values can be very low or very high. Inspecting raw data on MassLynx show that they are in fact a single analyte.
http://www.metabolomics-forum.com/index.php?action=dlattach;sa=tmpattach;attach=post_tmp_16020_eaa3aec5bf9a284059c7925ca1df2a57;topic=0

Is there a setting a can play with to make sure the alignment will produce one instead of many features? I have tried changing smoothing, but without much success. Min. height = 1000.
Please help,
- Mariusz
63
MS-DIAL / Only Max/Min Fold Change?
Last post by !ndium -
The Ion Table only shows the fold change for the max and min bars. Is it possible to get the fold change for other combinations? For example, if I have three bars (i.e. 3 groups) with one being the control and the other two being treatment 1 and treatment 2, I would like fold change/p-value for treatment 1/control and treatment 2/control.
65
MS-DIAL / Re: Can MS2 of Pools just be used for identification?
Last post by !ndium -
I did try assigning them as QC's in the file property dialog after peak detection, alignment etc., and the MS2 samples bar did disappear but the fold changes did not change and I suspect the fold change calc uses the MS2 samples bar when it is the largest bar. BTW, I assume the fold change is the largest bar height divided by the lowest bar height (?).
66
MS-DIAL / Re: Can MS2 of Pools just be used for identification?
Last post by berrytf -
I'm pretty sure you can. MS2's as QCs. Remove the 'include' check next to them. Set the unknowns to groups you want to compare. Run the data.

You may have to play around a bit with it. You can do that by going back to 'file property setting' & changing things as needed.
67
MS-DIAL / Can MS2 of Pools just be used for identification?
Last post by !ndium -
Does MSDial support an iterative exclusion DDA Q-TOF workflow where a pooled sample is used to generate a series of MS2 data files  by iterative exclusion DDA and each individual sample is analyzed by MS1 only. The DDA files are only used for identification and the MS1 files are used to look for fold changes.
68
MS-DIAL / Re: Unsure if MS Dial is working or frozen
Last post by berrytf -
An update to our problem.

We were using a 10 minute reversed phase LC method of which most of the analytes of interest come out within the first 5-7 minutes. In addition were were trying to analyze 100+ human fecal samples along with a pooled QC sample. The samples contained a wild variety of additional material that often showed up during the high %B hold after 7 minutes or so. If you overlaid the samples you'd see that some had very little signal in that region while others had massive bulky TICs. Regardless cutting the RT window down to 5 minutes, removing that contaminated zone, allowed the alignment to continue as expected.

Anyhow it was not clear at first why the program wasn't moving forward at the time, but we figured it out.
69
Job opportunities / Research Associate, Lipid-based Drug Delivery
Last post by bellasmith -
We are looking for a motivated and enthusiastic research associate candidate. A Research Associate position is available at Creative Biolabs, a biotechnology company based in Long Island, New York State.

He/She will be a team member in the production of recombinant proteins and play a critical role in the discovery/development of novel molecular reagents.
He/she will be expected to participate in experimental design, conduct experiments, optimize throughput, maintain detailed records, and generate standard operating procedures.
Design and conduct experiments with limited supervision from scientists.
Evaluate data, make observations, troubleshoot, and keep detailed records in laboratory notebooks.
Communicate results and observations to colleagues in team meetings.
Other duties are assigned.
70
MS-DIAL / Re: Peak integration in MS-Dial
Last post by berrytf -
I've run into this issue as well. While I don't have an exact answer on how to solve it I can say I found 2 resources that explain what's happening.

https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial.html#section-9-4
"...The value of ‘-2’ in “Peak ID” column means that the peak is not detected by peak picking process. (but calculated by gap-filling method). In the case of gap-filled peak, the colors of the “Peak Int.” and “Peak Area” columns become light blue. In normal, the colors (red) reflect the level of peak intensity or peak area. You cannot refine the peak and alignment yet, but that function will be developed."

How Peak ID, alignment, and gapfilling work are explained in their math FAQ document which can be found here:

http://prime.psc.riken.jp/compms/msdial/download/mathematics/MS-DIAL%20FAQ-vs2.pdf

I wish their documentation were a bit better or a bit more up to date. Sometimes the examples are from an older version where the GUI choices or display is different from the version you're using.

So for what you've shown us for 'file ID' 0 -1, 4 - 7, 18, 19, and 21 are all examples of where gap filling by compulsion has happened. No peak was detected there, but because it's in your QCs it was forced into those samples (see last 2 pages of math FAQ).

I believe all the answers lie under the 'alignment' tab. I think you could have it exclude those by using a peak count filter(it says %, but I think it reflects an intensity value) or n% detected in one group, however in those cases it shouldn't even appear as an aligned feature rather than forcing signal into those blank samples. Alternatively you might be able to get them excluded by using blank subtraction. I'm thinking gap filling might be the problem here.

If I'm being honest all the stuff I've tried prior to exporting the aligned peak results has not had the desired results. For our data sets we have so many samples & ref matched IDs that it is incredibly laborious to manually investigate and possibly alter every sample over every data point.

Please let us know if you find a solution.