Given that Western blot display proteins enriched at their respective molecular mass location, the higher local density of A2M regions similar to CNDP1 may have lead this antibody to recognize A2M. We also demonstrate the possibility to combine mass spectrometric read-out with bead based assays, as proteins being captured by the immobilized antibodies can be identified as being CNDP1 specific by on bead trypsin digestion. Even though this was achieved on a single sample only, it supports this and previous studies in providing Bleomycin in vivo evidence for CNDP1 detection in plasma. In the mass spectrometric analysis, no peptides were assigned to A2M and strengthen the above observation of an A2M-free isoform
of CNDP1. To our current knowledge, this is one of the first studies that follows up on discoveries made with antibody arrays and it also represents a path on how to develop sandwich assays from such single binder assays. This may therefore be an important and noteworthy contribution to existing proteomic
studies in plasma, as it addresses the challenge of off-target binding through the use of several antibodies with distinct epitopes on one target protein. Further so, we anticipate that see more proteins detectable in plasma with single binder assays, such as PSA , should also be detectable using sandwich assays. Nevertheless, sandwich assays are still not a fist line tool to discover new candidates for Ribose-5-phosphate isomerase disease classification, thus argue for new sandwich assay technologies to be developed for a first line discovery. Until then, single binder assays may remain a first choice in affinity proteomics during screening, but preferably not during verification. Multiplexing offers the inclusion of several target assays into a single analysis. Rather than supplementing other target assays, we chose to determine one protein via parallel capture
reactions through the detection with one detection antibody. It might be argued for that using a single detection antibody could still not rule out that off-target interactions are being measured. But as shown here by the use of six capture antibodies that were generated in different species, targeting different epitopes, while being utilized in a multiplex fashion, correlating intensity profiles (median rho 0.93) were obtained to support the detection of CNDP1. In conclusion, our study shows the development and application of a multiplexed sandwich assay for a single target via the use of distinct epitopes of CNDP1. This confirmed decreasing levels of CNDP1 in plasma from patients suffering from prostate cancer and revealed that CNDP1 levels were particularly different in patients with diagnosed lymph node metastasis. This refined understanding of CNDP1 association may contribute to alternative detection of prostate cancer and lymph node status. We like to thank the entire staff of the Human Protein Atlas for their efforts.