DOI: 10.5061/dryad.9zw3r22df
title: Identification and evaluation of serum protein biomarkers which differentiate psoriatic from rheumatoid arthritis

description: Objectives To identify serum protein biomarkers which might separate early
 inflammatory arthritis (EIA) patients with psoriatic arthritis (PsA) from
 those with rheumatoid arthritis (RA) and may be used to support
 appropriate early intervention. Methods The serum proteome of patients
 with PsA and RA was interrogated using liquid chromatography mass
 spectrometry (LC-MS/MS) (n=64 patients), a multiplexed antibody assay
 (Luminex) for 48 proteins (n=64 patients) and an aptamer-based assay
 (SOMAscan) targeting 1,129 proteins (n=36 patients). Multiple reaction
 monitoring assays were developed to evaluate the performance of putative
 markers in the discovery cohort (n=60) as well as an independent cohort of
 PsA and RA patients (n=167). Results Multivariate analysis of the protein
 discovery data revealed that it was possible to discriminate PsA from RA
 patients with an area under the curve (AUC) of 0.94 for nLCMS/MS, 0.69 for
 Luminex based measurements; 0.73 for SOMAscan analysis. Random forest
 models confirmed that a subset of protein measured by MRM could
 differentiate PsA and RA patients with an AUC of 0.79 and 0.85 during
 separate evaluation and verification studies. Conclusion We report a serum
 protein biomarker panel which can separate EIA patients with PsA from
 those with RA. We suggest that the routine use of such a panel in EIA
 patients will improve clinical decision making. With continued evaluation
 and refinement on additional and larger patient cohorts including those
 with other arthropathies we suggest the panel identified here will
 contribute toward improved clinical decision making.
description: <b>Supplementary
 tables associated with the paper entitled: Identification and Evaluation
 of Serum Protein Biomarkers Which Differentiate Psoriatic from Rheumatoid
 Arthritis</b> <b>Suppl Table 1</b>.
 Lists 66 proteins were significantly differentially expressed between PsA
 and RA patients<b>.</b> This table reports a list of 66
 proteins that were found to discriminate between patients with PsA (n=30)
 from those with RA (n=30) during nLC-MS/MS analysis of individual patient
 serum samples (FDR 0.01, p &lt; 0.01). <b>Supp Table 2</b>: Lists top 50
 ‘nLC-MS/MS’ proteins that discriminate PsA patients from those
 with<b> </b>RA.<b> </b>Multivariate analysis (RF
 model) of nLC-MS/MS data revealed a list of serum proteins that could be
 used to discriminate between patients with PsA and RA (AUC 0.94). The top
 50 most discriminatory proteins are reported here. Proteins are listed
 based on their contribution to the AUC (from high to low). <b>Supp Table 3.</b>
 Lists 175 proteins found to be significantly differentially expressed
 between individuals with psoriatic (PsA) and rheumatoid arthritis (RA).
 Proteins were identified using an aptamer based assay which supported the
 analysis of 36 patients with PsA (n=18) and RA (n=18).
 <b>Supp Table 4.</b> List the top most discrimantory
 proteins identied during two round of MRM analysis. Proteins are listed
 alphabetically were rerpresented by proteotypic peptides when measured by
 MRM <b>(A)</b> Of the 34 listed, 25 were measured in both MRM
 phase I and phase II assays. <b>(B)</b> Of those 25 proteins,
 8 proteins were top contributers to the AUC in generated during phase I
 (AUC 0.79) and phase II (AUC 0.85). <b>(C)</b> Of the 8
 protiens in (B), 6 were significantly urpegualted in RA (un-pairded T
 test, see <b>Suppl Fig 4</b>). *Coagulation factor X1 and
 thrombospndin did not reach statstical signficance during phase I analysis
  (<b>Suppl Fig 4)</b> Of the 34 proteins listed in
 <b>(D),</b> 9 proteins providing AUC 0.85 were exclusively
 present in the MRM phase II assay.  <strong>Suppl Table
 5.</strong> Lists functional roles of discriminatory proteins
 included in MRM analysis. Table was generated based of results from STRING
 software.