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71
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.
72
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.

73
MS-DIAL / Unsure if MS Dial is working or frozen
Last post by berrytf -
We have used MS Dial a decent bit. Typically we collect small molecule metabolomics data on a UHPLC-Sciex 5600 QToF set up. Typically we're collecting IDA data in 10 minute runs. Most experiments involve collection of the following data types:

  • Pooled Samples MS2
  • Pooled Sample MS1
  • Individual Sample MS1
  • Blank

We do not convert the data to a common centroided format before ingesting it into MS-Dial. We churn the data on a dedicated Dell work station that has a 6 core/6 hyperthreaded Xeon CPU, 32 GB of DDR4 RAM, and a mechanical HD. For small projects(5 - 30 samples) its fine, but for larger projects (>30 samples) we run into issues. Specifically the issues arise after the individual samples are processed and during the 'peak filling, identification, and alignment' stage. Add gap filling in there too.

The program bogs down the PC to the point where it's unresponsive or slugging. MS Dial's progress bar during that period often freezes at a low %. Sometimes the project completes and other times it does not. It could take half a day or multiple days to complete.

I've pulled up task manager and other monitoring software during the processing to see what's happening. During the initial sample processing the CPU use is most intensive, but since it can multi-threaded in parallel it's quick. During the aforementioned 'peak filling, identification, and alignment' stage the CPU usage drops to almost nothing where as the RAM and the Disk activity shoot up to 90-100%.

I have a few questions
  • Are there tips on improving the speed at which larger projects can be computed?
  • Would a faster writing data component, like a soild state drive, improve the speed of that step?
  • How can we tell if the 'peak filling, identification, and alignment' is actually progressing or the program has stalled out as unresponsive?

I'd be happy to provide any information on our process, computer system, or software if it would help us tackle the problem. We like a MS-Dial a lot, but the slow down and questionable completion of the data processing has us questioning using it further.
75
MS-DIAL / Re: SCIEX 5600 Qtof data (IDA mode) with MSDIAL
Last post by berrytf -
Ok. We have a 5600 QToF as well and I investigated what you're showing with my own data. A few things pop out.

First with respect to what you're seeing in Peakview you have the wrong data displayed(MS1 scan). If it is IDA data you need to pull up the IDA explorer and find the parent ion at the expected RT to pull out the relevant MS2 scans. Those would properly reflect what MS Dial is trying to find and display to you in the windows you showed containing only the parent ion.

I'm not sure if you're trying to process SWATH data or not. You mentioned IDA, but what's shown in the MS-Dial Parameters includes deconvolution settings that differ from the standard inputs including an MS2 cutoff. That might also be part of the problem, however if that's not the case then no worries.

Also why are you converting to mzML file format? That might also be part of the problem. You can use wiff files so long as you select 'profile' for both MS1 and MS2 settings up front.
76
MS-DIAL / Problem in converting NIST23 to MSDIAL compatible msp format
Last post by Sophiadj -
Hi everyone,
I'm having a problem in converting NIST23 MS/MS library to MSDIAL compatible msp format.
I tried different settings, but none of them worked. Error "No spectra fromC:NISTDEMO\MSSEARCH hr msms nist" have been converted" kept popping out.  Below are snapshots of the settings.  I wonder if I got the setting wrong.
Thanks in advance!
77
MS-DIAL / TIC normalization and Raw values?
Last post by Massspek -
Hey Scientists,

During Alignments for MS-DIAL you have the option to normalize to TIC.

I am wondering if there is a way to Export the TICs for the loaded chromatograms? Looking for a high throughput way to acquire tics instead of manually integrating all plots.

Thanks!
78
Other / LIPID MAPS .LBM
Last post by MatyashSupp -
Good day you'll

 Someone know how to compress lipid maps in .lbm for database uses at MS DIAL?

 Already tried to do it sometimes, but never works.

Ty
80
MS-DIAL / Matching QTOF and Orbitrap datasets (via setting up a custom database?)
Last post by mniku -
Apologies for perhaps a primitive question, but I’d like to ask advice about how to optimally proceed with the following task:

We have an Orbitrap dataset and an QTOF dataset, generated from partially overlapping sample sets, using ~same LC instrument.
We need to match the molecular features in these datasets (I mean, find what feature corresponds to a QTOF compound in the Orbitrap dataset).

I’m thinking this could be accomplished by setting up a custom metabolite database from one of the datasets, and use that to annotate the other dataset in MSDIAL.
If you agree, could you please point us to a tutorial about converting our dataset to a database for this purpose?
If you have better suggestions for a protocol, please let us know.

As a side note, the QTOF dataset has files for 10-20-40 kV. Apparently 10 kV would be best match for Orbitrap (because of the fragmentation power). But 20 kV and 40 kV would provide additional fragmentation info. Is it possible to somehow more or less merge these to utilize all available data for the matched compounds, after we have completed that?

With best regards,
Mikael Niku