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

[Wout B. <wou...@ua...>]

Hi Theo,

Great to hear that there are robust QC initiatives for MS imaging ongoing. We'd be more than happy to include Chris and Kumar as co-authors on the manuscript as well, based on the use case to be developed. This is already going to be a paper with a decent number of authors because many people contributed to mzQC over the years. 🙂

Sounds good to have a meeting to discuss this in some more detail, where I can then highlight mzQC. Do you mind making the initial connection with Chris and Kumar?

Thanks,
Wout
________________________________
From: Alexandrov, Theodore <tal...@he...>
Sent: Friday, October 25, 2024 16:22
To: Wout Bittremieux <wou...@ua...>
Cc: psi...@li... <psi...@li...>
Subject: Re: Input on QC in MS Imaging for mzQC use case


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Hi Wout,



Yes, lab transition is never simple and we hit more roadblocks than I imagined, but we are blessed with a large part of our EMBL moving to UCSD. And great that you connected with Bishoy and thanks for the kind words.



Great to hear about the mzQC initiative – it’s great and very forward-looking.



I suggest to include into this discussion Chris Anderton from PNNL and Kumar Sharma from UT San Antonio. Together with Chris and Kumar, we participate for 5+ years in the NIH-funded Kidney Precision Medicine Project (KPMP), by performing MALDI-imaging-based spatial metabolomics and lipidomics on clinically-relevant samples from kidney, and a big part of our work was to develop QC criteria. Those criteria were reviewed by the KPMP project and NIH.



So, we can consider the QC criteria developed in KPMP as an example of QC criteria for MALDI-imaging for both metabolites and lipids.



If that’s OK, maybe we all can have a meeting to better understand what specifically you have in mind, what you call “QC criteria”, how our work and criteria can be formulated as an example.



I have not Cc’ed Chris and Kumar, because if we go down this route, this would include the number of authors in your manuscript (from our team it would be only me, but Chris and Kumar would need to be included and maybe +2 people from their team, up to you and them to decide), and I’d like to make sure that you are ok with this for an example section.



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