Adrian Brown

Member Resolved


May 12, 2022
Sequential processing of multiple data-files in ProteinPilot

I would like to use ProteinPilot 5.0.2 to process data-sets containing 16 wiff files acquired from fractionated peptides on a TripleTOF 6600. A Precision T7910 workstation struggles to process four files in parallel and I would like to be able to queue sequential processing of individual files overnight. I currently use the ‘LC ‘ tab to load and process individual data-files but this leads to parallel processing. Is it possible to generate 16 .group files sequentially?


  1. Jenny Albanese

    Thanks for your question!

    So if I understand right, you want the 16 fractions processed independently but in the fastest time possible right?
    The software will utilize available memory and processor speed across multiple files as best as it can but yes it will be limited by the hardware of the computer. The other key thing is to ensure that you have a ProteinPilot license that will invoke all the processor cores, do you have a 16-core license on your computer? We do recommend using a 16-core computer with a 16-core license to get the best processing performance (the T7910 is a 16-core computer so that is good).

    The other option would be to move your processing into the cloud. We have ProteinPilot App running OneOmics suite in the cloud now, so there you can queue up as many searches in parallel that you want! It is also much easier to queue up a large batch of files to process individually in the cloud as well. You can have a look at these CloudTalks to learn more about where we are with cloud processing.
    • ProteinPilot app for data processing
    • Visualize your Protein ID results
    • OneOmics suite overview

  2. Adrian Brown

    Thank you for the response. I have a 1-16 core upgrade license that should have been activated during spectrometer installation. The T7910 has always struggled to process in parallel 4 IDA wiff (scan) files of ~1GB acquired with microflowLC. I wanted to be able to queue the processing of 16 such files so they could be left to run sequentially overnight.

    I didn’t mention that the T7910 has recently been upgraded to Windows 10 for network security reasons. Are there known issues running ProteinPilot 5.02 in Windows 10, or fixes that can be applied? Processing 3 wiff files of about 1GB is currently taking >4 hours with intermittent freezing of the computer and the 32GB RAM cyclically maxed out.

    Processing in the cloud is an attractive option and I will look into it further.

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