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. 2024 Jun 17;62(12):2507-2518.
doi: 10.1515/cclm-2024-0306. Print 2024 Nov 26.

An automated workflow based on data independent acquisition for practical and high-throughput personalized assay development and minimal residual disease monitoring in multiple myeloma patients

Charissa Wijnands  1 , Gad Armony  2 , Somayya Noori  3 , Jolein Gloerich  2 , Vincent Bonifay  4 , Hélène Caillon  5 , Theo M Luider  3 , Sven Brehmer  6 , Lennard Pfennig  6 , Tharan Srikumar  7 , Dennis Trede  6 , Gary Kruppa  8 , Thomas Dejoie  5 , Martijn M van Duijn  3 , Alain J van Gool  2 , Joannes F M Jacobs  1 , Hans J C T Wessels  2
Affiliations
Free article

An automated workflow based on data independent acquisition for practical and high-throughput personalized assay development and minimal residual disease monitoring in multiple myeloma patients

Charissa Wijnands et al. Clin Chem Lab Med. .
Free article

Abstract

Objectives: Minimal residual disease (MRD) status in multiple myeloma (MM) is an important prognostic biomarker. Personalized blood-based targeted mass spectrometry detecting M-proteins (MS-MRD) was shown to provide a sensitive and minimally invasive alternative to MRD-assessment in bone marrow. However, MS-MRD still comprises of manual steps that hamper upscaling of MS-MRD testing. Here, we introduce a proof-of-concept for a novel workflow using data independent acquisition-parallel accumulation and serial fragmentation (dia-PASEF) and automated data processing.

Methods: Using automated data processing of dia-PASEF measurements, we developed a workflow that identified unique targets from MM patient sera and personalized protein sequence databases. We generated patient-specific libraries linked to dia-PASEF methods and subsequently quantitated and reported M-protein concentrations in MM patient follow-up samples. Assay performance of parallel reaction monitoring (prm)-PASEF and dia-PASEF workflows were compared and we tested mixing patient intake sera for multiplexed target selection.

Results: No significant differences were observed in lowest detectable concentration, linearity, and slope coefficient when comparing prm-PASEF and dia-PASEF measurements of serial dilutions of patient sera. To improve assay development times, we tested multiplexing patient intake sera for target selection which resulted in the selection of identical clonotypic peptides for both simplex and multiplex dia-PASEF. Furthermore, assay development times improved up to 25× when measuring multiplexed samples for peptide selection compared to simplex.

Conclusions: Dia-PASEF technology combined with automated data processing and multiplexed target selection facilitated the development of a faster MS-MRD workflow which benefits upscaling and is an important step towards the clinical implementation of MS-MRD.

Keywords: M-protein; data independent acquisition; mass spectrometry; multiple myeloma; quantitative biomarker.

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References

    1. van de Donk, N, Pawlyn, C, Yong, KL. Multiple myeloma. Lancet 2021;397:410–27. https://doi.org/10.1016/s0140-6736(21)00135-5 . - DOI
    1. Dimopoulos, M, Kyle, R, Fermand, JP, Rajkumar, SV, San Miguel, J, Chanan-Khan, A, et al.. Consensus recommendations for standard investigative workup: report of the international myeloma workshop consensus panel 3. Blood 2011;117:4701–5. https://doi.org/10.1182/blood-2010-10-299529 . - DOI
    1. Mills, JR, Kohlhagen, MC, Dasari, S, Vanderboom, PM, Kyle, RA, Katzmann, JA, et al.. Comprehensive assessment of M-proteins using nanobody enrichment coupled to MALDI-TOF mass spectrometry. Clin Chem 2016;62:1334–44. https://doi.org/10.1373/clinchem.2015.253740 . - DOI
    1. Puig, N, Contreras, MT, Agullo, C, Martinez-Lopez, J, Oriol, A, Blanchard, MJ, et al.. Mass spectrometry vs immunofixation for treatment monitoring in multiple myeloma. Blood Adv 2022;6:3234–9. https://doi.org/10.1182/bloodadvances.2021006762 . - DOI
    1. Kumar, S, Paiva, B, Anderson, KC, Durie, B, Landgren, O, Moreau, P, et al.. International Myeloma Working Group consensus criteria for response and minimal residual disease assessment in multiple myeloma. Lancet Oncol 2016;17:328–46. https://doi.org/10.1016/s1470-2045(16)30206-6 . - DOI

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