arthritis-research.com

Table 1
Proteomics technologies for autoantibody profiling: selected published studies
System	Assay format	Detection	Antigens tested in citation(s)	Estimated capacity per array	Comments	Reference

Antigen microarrays	Robotic attachment of antigens in ordered arrays on membranes and derivatized microscope slides	Secondary antibody; chemiluminescence	18	5000+	Demonstrate sensitive and specific detection of autoantibodies in serum on planar arrays	[16]
Protein microarrays	Robotic attachment of antigens in ordered arrays on derivatized microscope slides	Direct labeling of samples with fluorescent markers for comparative analysis	115	10,000+	Comparative analysis requires fluorescent labeling of individual samples; 50% of antigens detected	[7]
Antigen microarrays	Robotic attachment of antigens on derivatized microscope slides	Secondary antibody; fluorescence; comparative analysis with direct fluoresecent labeling of samples	196	10,000+	Detection of autoantibodies characteristic of eight autoimmune rheumatic diseases, including autoantibodies against proteins, peptides, nucleic acids, and macromolecular complexes	[17]
Bead microarrays (LabMAP™; cytometric bead array)	Antigens conjugated to sets of spectrally resolvable fluorescent beads	Fluorescence; analysis of individual beads using a flow cytometer	16	64 per well; 5000+ per 96-well plate	Fluid-phase; commercial development by Luminex, and Becton–Dickinson	[35]
Nanobarcodes™ particle technology	Attachment of antigens to addressable multimetal microrods encoded with submicrometer metal stripes	Light microscopy; fluorescence; mass spectrometry	2	80,000 using three distinct metals	Fluid-phase; Commercial development by SurroMed	[8]
Arrayed proteins from cDNA expression libraries	Expression and purification of polypeptides encoded in a cDNA expression library in microtiter plates, followed by robotic attachment to PVDF filters	Chemiluminescence	4800	10,000+	Performing autoantigen discovery; bacterial expression of autoantigens does not confer post-translational modifications	[13,14]
Protein in situ array	Protein array generated in situ using PCR and a cell-free transcription/ translation expression system	Colorimetric	15	96 per plate	Probably less robust than other systems	[36]
Photolithography-generated peptide arrays	In situ synthesis of peptides by photolithography	Fluorescence		10,000+	Linear peptide epitopes only; not under active development	[4]
Microarrays of cells expressing defined cDNAs	Robotic printing of cDNA in expression vectors on slides followed by incubation with adherent mammalian cells	Fluorescence	192	10,000+	Mammalian expression system confers certain post-translational modifications	[9]
Protein arrays of living transformants; modified yeast two-hybrid screen	Robotic delivery of yeast transformants expressing yeast open reading frames fused to an activating domain	Colorimetric	6000	Performed in 384-well microtiter plates	Arrays of yeast expressing fusion proteins	[10]
'Line immunoassay'	Electrophoresis of antigens and transfer to nitrocellulose membranes (western blot of purified antigens)	Chemiluminescense	15	< 50	Not high-throughput; commercial development by Innogenetics	[12]
'Universal protein array'	Dot-blots of purified antigens on nitrocellulose membranes	Secondary antibody; radioactivity	48	< 200	Requires large quantities of purified antigen and serum samples	[11]
'Lab-on-a-chip', microfluidics	Microchannels etched in solid supports; electrokinetic, electro-osmotic, electrophoretic, or pressure-driven flow	Fluorescence; UV light absorption	Limited	N/A	Fluid-phase assay; low-affinity binding detectable; kinetics can be calculated; commercial development by Caliper, Aclara, and Fluidigm	[37]
Peptides on pins (Multipin™)	In situ synthesis of peptides on polyethylene pins	Colorimeteric	96	96 per plate	Linear epitopes only; strip and re-use peptides on pins for subsequent experiments	[1,2]

N/A, not applicable; PCR, polymerase chain reaction; PVDF, polyvinylidene difluoride. For manufacturer details, please see text.
Hueber et al. Arthritis Res 2002 4:290 doi:10.1186/ar426

Table 1