Re: [Psidev-qc-dev] Input on QC in MS Imaging for mzQC use case

[Alexandrov, T. <tal...@he...>]

Hi Wout,

Thanks for the invitation! As we quickly discussed off this thread, I’m introducing Chris Anderton and Kumar Sharma with whom we worked on developing QC criteria for MALDI-imaging in KPMP.


Chris and Kumar,

I think this can help multiply the impact of our QC work in KPMP.


All,

Shall we have a joint meeting in the week of Nov 4th (I’m traveling till then) to discuss it? Maybe we can meet at 5pm CET to cover CET, Central, and Pacific time zones?

Cheers,
Theo


From: Wout Bittremieux <wou...@ua...>
Date: Friday, October 25, 2024 at 4:01 PM
To: Alexandrov, Theodore <tal...@he...>
Cc: psi...@li... <psi...@li...>
Subject: Input on QC in MS Imaging for mzQC use case
Hi Theodore,

I hope the transition to UCSD is going well, though I understand from Bishoy at the NCEMS meeting a few weeks back that it's been a process. Navigating visa and administrative hurdles during an international move can be stressful—I'm all too familiar with that myself unfortunately.

I'm reaching out regarding a project within the Proteomics Standards Initiative (PSI) that we've been working on for some time now: developing the mzQC file format<https://urldefense.com/v3/__https:/hupo-psi.github.io/mzQC/__;!!LLK065n_VXAQ!i679mes717kblm6Ji4uTvOmPJysMJoIf78CWj_FsZZqu1HhnSdr20fycqqxMBLBiTis3BcF06CMEsIAsMxc3EW-b6sZbtfwIMoEzMQ$> to store QC data specifically for biological mass spectrometry. The mzQC format has successfully passed the formal PSI approval process, and we've recently published a technical note<https://urldefense.com/v3/__https:/doi.org/10.1021/jasms.4c00174__;!!LLK065n_VXAQ!i679mes717kblm6Ji4uTvOmPJysMJoIf78CWj_FsZZqu1HhnSdr20fycqqxMBLBiTis3BcF06CMEsIAsMxc3EW-b6sZbtfzCnHrv6A$> detailing software libraries for operating on mzQC data.

As the next step, we're working on a more comprehensive manuscript to formally introduce the mzQC format to the community. We plan to show its utility with a variety of use cases, including outlier detection and longitudinal QC applications. To further demonstrate mzQC's broad relevance across diverse MS applications, we think that including MS imaging as a use case would be very interesting. However, our team lacks experience in that area.

I wanted to see if you might share your insights on QC practices currently used in MS imaging, including commonly used methods and tools. Additionally, if you have or know of any datasets we could use, that would be extremely helpful. Naturally, we would be happy to include you and relevant team members as co-authors on the manuscript.

Thanks very much in advance, and I look forward to any input you can offer.

Best regards,
Wout