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Towards a proteomic plasma biomarker panel for diagnosing vasculitis remission

ABSTRACT: Active anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) requires intensive immunosuppressive therapy, but continued treatment after remission is achieved can cause serious harm. Reliable biomarkers to confirm remission are lacking, forcing clinicians to prolong cost-intensive and toxic therapy unnecessarily. Routine markers, such as C-reactive protein and anti-neutrophil cytoplasmic antibodies, lack sensitivity and specificity for the remission status, failing to guide treatment de-escalation safely. After adjusting for patient characteristics and clinical variables, we explored the plasma proteome to identify reliable biomarkers of disease remission in patients with AAV. We applied a two-tiered proteomics strategy combining global discovery with targeted validation to identify a protein signature of remission. The resulting 7-protein panel was successfully implemented in a targeted mass spectrometry-based assay, with diagnostic performance confirmed in an independent patient cohort. The panel consistently outperformed routine markers. Our findings suggest that this panel may serve as a starting point for developing a clinical tool to support decision-making, with the potential to reduce treatment-related burden, mitigate toxicity, and lower healthcare costs. Moreover, our confounder-controlled proteomics approach provides a scalable blueprint for biomarker discovery in complex inflammatory diseases.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

DISEASE(S): Autoimmune Vasculitis

SUBMITTER: Marieluise Kirchner

LAB HEAD: Philipp Mertins

PROVIDER: PXD079232 | Pride | 2026-06-05

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20220626_100209_Plasma_PR3_MPO_HC_Report_proteinGroups.tsv	Tabular
	20220626_101910_Jerke_Plasma_PR3_MPO_HC_qvalue_new_library.sne	Other
	Leia_20211223_SN_HS_AAT_plasmaLib_F01.raw	Raw
	Leia_20211223_SN_HS_AAT_plasmaLib_F02.raw	Raw
	Leia_20211223_SN_HS_AAT_plasmaLib_F03.raw	Raw

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Project description:There is an urgent need for robust and high-throughput methods for SARS-CoV-2 detection in suspected pa-tient samples to facilitate disease management, surveillance, and control. Although nucleic acid detection methods such as RT-PCR are the gold standard, during the current pandemic the deployment of RT-PCR tests has been extremely slow, and key reagents such as PCR primers, and RNA extraction kits are at critical shortages. Rapid point-of-care viral antigen detec-tion methods have been previously employed for the diagnosis of respiratory viruses such as influenza and respiratory syn-cytial viruses. Therefore, the direct detection of SARS-CoV-2 viral antigens in patient samples could also be used for diagno-sis of active infection and alternative methodologies for specific and sensitive viral protein detection should be explored. Targeted mass spectrometry techniques have enabled the identification and quantitation of a defined subset of pro-teins/peptides at single amino acid resolution with attomole level sensitivity and high reproducibility. Herein we report a tar-geted mass spectrometry assay for the detection of SARS- CoV-2 spike protein and nucleoprotein in a relevant biologi-cal matrix. Recombinant full-length spike protein and nucleoprotein were digested and prototypic peptides were selected for parallel reaction monitoring (PRM) quantitation using a high resolution Orbitrap instrument. A spectral library, which con-tained 7 proteotypic peptides (4 from spike protein and 3 from nucleoprotein) and the top 3 to 4 transitionsMS2 spectra, was generated and evaluated. From the original spectral library, we selected 2 best performing peptides for the final PRM assay. The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in-vitro de-rived mucus. The PRM assay provided a limit of detection (LOD) of ~200 attomoles and a limit of quantitation (LOQ) of ~ 390 attomoles. Extrapolating from the test samples, the projected titer of virus particles necessary for detection of SARS-CoV-2 spike and nucleoprotein detection was approximately 2E5 viral particles/mL, making it an attractive alternative to RT-PCR assays. Potentially mass spectrometry-based methods for viral antigen detection may deliver higher throughput and could serve as a complementary diagnostic tool to RT-PCR. Furthermore, this assay could be used to evaluate the pres-ence of SARS-CoV-2 in archived or recently collected biological fluids, in-vitro derived research materials, and wastewater samples

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Towards a proteomic plasma biomarker panel for diagnosing vasculitis remission

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