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.
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.