I am also adding an organized labâready protocol for Digital SizeâIndexed ImmunoSequencing (DSIâSeq) here.
This is written to let you prototype, optimize, and validate the method on benchtop equipment. The protocol implements the IPâlean singleâtag digital immunoPCR style readout inside each size bin, and it avoids proximity ligation or proximity extension chemistry. It supports two readouts:
NGS counting for high multiplex and practical bin indexing.
dPCR counting for small target panels or early debugging.
The workflow is plateâbased, since that is the fastest and most accessible path to working data.
0. Scope and outcome
Goal. Resolve proteins by apparent size into many narrow fractions, then quantify specific targets in each fraction by converting each captured protein into one DNA tag and counting tags. Output is a matrix of counts: targets by size bins, calibrated to kDa using a coârun ladder.
Typical first build. 48 bins across a 12 minute separation window, 12 to 24 targets by NGS readout, input 1 to 10 micrograms total protein per lane, results in one day after library prep.
1. Safety and handling
Acrylamide and SDS are irritants. Handle with gloves, lab coat, and eye protection. Dispose of acrylamide waste as hazardous.
UV photocleavage variants require eye and skin protection. Shield the UV source.
Nucleases can aerosolize. Open tubes slowly and decontaminate surfaces.
Segregate preâPCR and postâPCR spaces. Use UDG carryover control.
2. Materials and reagents
2.1 Buffers and solutions
Lysis buffer, PCR compatible50 mM HEPES pH 7.5, 150 mM NaCl, 1 percent NPâ40 or 0.5 percent Triton Xâ100, 10 percent glycerol, protease inhibitors, phosphatase inhibitors if needed.
Optional SDS denaturing load buffer for chip1x TGS or TBE, 0.1 to 0.5 percent SDS, 10 mM DTT, 10 percent glycerol. Heat 70 to 90 C for 5 minutes if full denaturation is required.
Replaceable sieving polymer for SDSâCECommercial SDSâCE polymer or 2.5 to 4.0 percent linear polyacrylamide in 1x TBE with 0.1 percent SDS.
Collection buffer per well20 mM HEPES pH 7.5, 150 mM NaCl, 0.05 percent Tweenâ20, 10 mM methylâbetaâcyclodextrin, 2 mg mLâ1 BSA. The cyclodextrin scavenges SDS on contact.
Bead capture bufferPBS, 0.05 percent Tweenâ20, 1 mg mLâ1 BSA.
Wash bufferPBS, 0.05 percent Tweenâ20.
Cleavage bufferDepends on linker. For disulfide linkers: PBS with 10 to 50 mM TCEP. For oânitrobenzyl photocleavage: PBS.
UDG mix for carryover controldNTPs with dUTP substitution, thermolabile UDG.
Benzonase mix25 to 50 U mLâ1 Benzonase with 2 mM MgCl2. Stop with 10 mM EDTA or heat inactivation per supplier.
2.2 Controls and standards
Protein ladder 10 to 250 kDa, prestained.
Spikeâin protein standards for at least two targets, quantified concentration.
Negative control lysate with phosphatase treatment for PTM assays.
2.3 Antibodies and DNA tags
Capture antibodies coupled to magnetic beadsUse Protein G beads with oriented coupling or covalent coupling kits. Aim for 1 to 5 micrograms antibody per mg beads. Prepare one capture bead type per target.
Detector binders that are monovalent with one DNA tag eachPrefer Fab fragments or nanobodies engineered with a single cysteine. Conjugate one DNA tag per binder by maleimideâthiol chemistry. Confirm 1:1 stoichiometry by intact mass.
DNA tag designLength 60 to 100 nt.Layout: 5â universal priming site A, 8 to 12 nt UMI, 12 to 16 nt target ID, 5â half of an Illumina adapter if using NGS, 3â blocking group if needed.The tag is attached to the detector via a generic, cleavable linker. No twoâprobe hybridization is used.
Perâbin index adapters for NGSShort doubleâstranded adapters with binâspecific index sequences and universal priming sites. These are ligated or appended in PCR to encode bin identity.
TaqMan probes for dPCROne probe per target tag. For dPCR you cannot multiplex many bins in one tube, so plan perâbin reactions only for 1 to 4 targets.
2.4 Equipment
Microchip or capillary SDS electrophoresis instrument with replaceable polymer.
Simple fraction collector setupA motorized XY stage for a 96âwell plate under the capillary outlet. Alternatively a commercial fraction collector with programmable step time.
Magnetic racks for 96âwell plates.
Thermocycler and a bench NGS library prep kit.
dPCR instrument if using the dPCR readout.
Plate shaker, microcentrifuge, fluorometer or qPCR for library QC.
Optional UV source for photocleavage, with shielding.
3. Panel design and conjugation
Choose targets. Begin with 12 to 24 proteins. Favor clones validated for Western or IP. Include one reference housekeeper.
Epitope check. Select capture and detector epitopes that do not compete. For oligomers or large complexes, expect a calibration factor as noted later.
Conjugate detectors.
Reduce Fab or nanobody to expose the engineered cysteine.
React with maleimideâtagged DNA at 1.5 to 2.0 molar excess.
Purify by size exclusion or affinity to remove free DNA.
Confirm 1:1 by intact mass or denaturing CE.
Bead coupling. Couple capture antibody to magnetic beads. Block with BSA. Store in PBS with 0.02 percent sodium azide at 4 C.
Document the perâtarget conversion factor Ï. If two detectors can bind one captured protein or the protein is oligomeric, measure Ï using purified protein and record it in the target sheet.
4. Sample preparation
Harvest cells or tissue. Keep cold.
Lyse in PCRâcompatible lysis buffer. For maximum size resolution across proteoforms you may choose an SDS denaturing load immediately before separation.
Clarify by spinning at 14,000 g for 10 minutes.
Protein quant by BCA.
Nuclease treatment for proteinâonly readout. Add Benzonase mix to lysate, incubate 15 minutes at room temperature. Stop with EDTA or heat inactivate. This ensures no endogenous DNA or RNA is counted.
Spikeâin controls. Add defined copies of two recombinant controls.
Add ladder for a dedicated ladder run. Prepare a separate tube with the prestained ladder in the same matrix for calibration runs.
5. Microchip SDS separation
You can run native or denaturing. For size indexing you will typically run SDS.
Prime the chip with replaceable sieving polymer per instrument instructions.
Equilibrate with 1x running buffer containing 0.1 percent SDS.
Load sample. If using SDS, mix lysate with SDS load buffer to 0.1 to 0.5 percent SDS and heat 70 to 90 C for 5 minutes.
Injection. Electrokinetic inject for 3 to 5 seconds at reduced field.
Separation. Field strength 200 to 300 V cmâ1, total separation window 10 to 15 minutes. Record the exact time zero when injection ends.
Run a separate ladder trace with the same separation program and collect fractions the same way as the sample run.
6. Plateâbased fractionation into size bins
Prepare a 96âwell plate. Dispense 10 to 15 microliters of collection buffer into the wells you will use.
Define bins. For a 12 minute separation choose 48 bins at 15 seconds per bin. That uses half a 96âwell plate.
Position the capillary outlet above the first well. Use a dropletâfriendly tip or align to touch the meniscus.
Collect. Start separation and move the plate on a schedule so that each bin collects exactly 15 seconds of eluent. A simple script on the stage controller is enough.
Finish. Seal the plate. The cyclodextrin in the collection buffer reduces free SDS below 0.02 percent in seconds and helps renaturation of linear epitopes.
Optional fraction concentration. If fractions are very dilute, you can add 1 mg of dry BioâBeads SMâ2 per well for 5 minutes to further scavenge SDS, then remove beads with a magnetic wand or by decanting. Validate that your targets are not lost.
7. Perâbin immunoassay with singleâtag detectors
This yields one DNA tag per captured protein complex in each bin. No proximity ligation or extension is used.
For each bin well:
Add capture beads
Add 10 to 20 microliters of bead suspension with the capture antibody for target i, or use a bead mix containing distinct bead codes if you run targets in parallel within a bin.
Incubate 30 minutes at room temperature with gentle shaking.
Magnet and wash
Pull beads down. Remove supernatant.
Wash 3 times with 100 microliters wash buffer.
Detector binding
Add the monovalent detector conjugate carrying a single DNA tag, at 1 to 5 nM in bead capture buffer.
Incubate 30 minutes.
Wash 3 times.
Release DNA tags
Add 20 microliters cleavage buffer.
For disulfide linkers, incubate with 10 to 50 mM TCEP for 10 minutes.
For photocleavage, illuminate with the specified UV for the vendorâs oânitrobenzyl linker. Keep temperature controlled.
Collect the supernatant which contains the released DNA tags.
UDG carryover control
If you use dUTP in tags, add thermolabile UDG and incubate per supplier before amplification to remove any carryover products. The released tags do not contain prior amplicons.
Pooling strategy
For NGS readout keep each bin separate through the next indexing step.
For dPCR readout proceed per bin per target. dPCR is best limited to 1 to 4 targets across a small number of bins during development.
Notes
If you prefer, perform steps 1 to 3 in bulk per bin with a mixed bead cocktail for all targets. This speeds handling. The detector step remains one DNA per bound protein because each detector is monovalent.
If an antigen accepts two detectors per captured protein, apply the perâtarget factor Ï during analysis.
8. Readout A. NGS library and sequencing
NGS is the practical route for many bins and many targets because you can encode bin identity by indexing.
Perâbin index addition
Set up a PCR using primers that add a unique bin index i5 or i7 to each bin. 10 to 14 cycles are typical since the tag pool can be low copy.
Use a common reverse primer so that only the index changes across bins.
Target identity in the tag
The target ID is already encoded in the tag sequence. You do not add any probe hybridization step between oligos on two antibodies. You simply amplify what you cleaved.
Pool and clean up
Pool equal volumes or equal mass from all bin PCRs for a sample.
Clean up with SPRI beads at 1.2x ratio.
QC and run
Measure library size and concentration. Expect 150 to 300 bp.
Sequence pairedâend or singleâend, 50 to 100 cycles is usually enough.
Depth target per sample 1 to 3 million reads for a 24 target by 48 bin design.
Demultiplex
Demultiplex by sample and by bin index.
Parse reads to tag IDs and UMIs. Collapse UMIs to unique molecules.
9. Readout B. dPCR per bin for 1 to 4 targets
Use this for early method checkout or when you only need a few targets.
Set up dPCR reactions
For each bin and each target, set up a reaction with the targetâspecific TaqMan probe.
Partition and run endpoint PCR.
Count
Record positive partitions k and total partitions N.
Compute lambda per bin as λ = âln(1 â k/N).
Molecules per bin equals λ times N.
Scale
Apply the perâtarget calibration factor Ï if relevant.
Continue to the size calibration step below.
10. Size calibration using the ladder
You will convert bin index to apparent kDa.
Collect a ladder run with identical fractionation
Run the prestained ladder alone with the same separation and fraction schedule used for the sample. Collect into a plate with the same 48 bins.
Quantify ladder protein abundance in each bin by simple absorbance at 595 nm if dye permits, or by a quick fluorometric protein assay across wells.
Identify peaks
Ladder proteins will appear as peaks across bins. Fit peak centers to their known molecular weights.
Fit the mapping
A robust model is: log10(MW) = a b·t c·t^2 where t is bin center time in minutes.
Fit a, b, c by least squares using the ladder peaks.
For each bin j in the sample, compute its center time and then its apparent kDa by inverting the relationship.
Uncertainty
Compute 95 percent confidence intervals on MW per bin from the residuals of the fit.
11. Data processing and outputs
Counts table
For NGS, produce a table of unique molecule counts per target per bin after UMI collapse.
For dPCR, produce molecules per bin from Poisson correction.
Normalize
Divide by the external spikeâin recovery to correct for runâtoârun variation.
Optionally normalize per bin by a total protein signal if measured.
Proteoform calling
For each target, smooth the binned profile with a small window.
Identify local maxima as proteoform peaks.
Report peak bin, apparent kDa, and integrated counts under each peak.
Final report
Matrix: targets Ă bins with counts.
Proteoform summary table with apparent kDa, counts, fraction of total per target.
QC panel with ladder fit, spikeâin recovery, background levels, replicate CVs.
12. Acceptance criteria and QC
Adopt these hard thresholds before you trust a run.
Reagentâonly background. After full library prep with no protein, fewer than 0.2 percent of reads assign to valid tag IDs or fewer than 0.2 positives per 20,000 partitions for dPCR.
Blank lysate after nuclease. With universal primers but no released tags, signal must be at background.
Spikeâin recovery. 0.8 to 1.2 across a 100âfold range.
Dilution linearity. Two dilutions at 2x load must yield 1.8 to 2.2x counts per bin.
Ladder fit residual. Standard error of log10(MW) fit less than 0.03.
Replicates. Technical replicate CV less than 10 percent in bins with at least 400 molecules.
13. Validation plan
Run in this sequence.
Separation and fractionation stub
Ladder only. Build the bin to kDa mapping and verify timing precision over three runs.
Singleâtarget endâtoâend
One target in a control lysate. Spike a dilution series of the purified protein. Validate linearity and the expected single peak at the known kDa.
Isoform resolution
Use a biology that creates a known cleavage, for example PARP1 cleavage in apoptosis. Confirm two peaks at expected apparent sizes.
PTM specificity
Use a phospho target with a modification specific detector. Compare stimulated vs phosphatase treated. The modified target should vanish in treated samples without a shift in the pan profile.
Multiplex crossâtalk
Build the panel in subpanels of 6 to 8 targets. Check background in noâantigen wells and confirm no offâtarget rises when subpanels are combined.
Reproducibility and lot stability
Ten technical replicates. Track perâbin perâtarget CV.
New detector lots get a check of the conversion factor Ï and a small ladder redo.
14. Troubleshooting
Weak or no signal in all binsCheck detector conjugation efficiency and cleavage step. Confirm 1:1 stoichiometry. Verify that the UDG step is not destroying tags.
High background in noâprotein controlsSuspect amplicon carryover or free DNA tag contamination. Increase physical separation of spaces, add UDG, and reâpurify detectors to remove free tag.
Flat size profile without peaksFraction timing off or excessive diffusion. Shorten bin width to 10 seconds or increase field strength. Confirm collection buffer is dispensed before the run.
Shifted ladder mapping between runsTemperature or polymer batch differences. Always run a ladder with each batch and refit a, b, c. Apply mapping per run.
Loss of antibody binding due to SDSIncrease cyclodextrin concentration in collection buffer to 20 mM. Add a short beadâbased buffer exchange before detector binding. Use clones validated for linear epitopes.
15. Options and upgrades
Droplet fractionationReplace the plate with a Tâjunction droplet maker that encapsulates the outlet stream at a fixed rate. A side stream can inject a droplet index oligo that is appended later by standard ligation. This increases bin count to 96 to 128 at the same run time.
Bin reduction mergeFor abundant targets, merge adjacent bins in software to increase counts per bin and improve precision.
Alternative SDS scavengersPotassium chloride can precipitate SDS as potassium dodecyl sulfate. Use with care due to protein precipitation. Validate recovery on spikeâins.
16. IP and compliance posture
One DNA tag per detector binder.
No proximity ligation or proximity extension between two nucleic acidâbearing probes.
No singleâmolecule enzyme arrays.
Bin identity is appended during library prep by standard indexing, or dPCR is run per bin per target without any probeâprobe interaction.
Include UDG carryover suppression and commodity linkers only.
Record these choices in your design history file from day one.
17. Starter T cell panel
Begin with 12 to 18 targets that are Western or IP validated and bind linear epitopes. For example: CD3ζ, ZAP70, LAT, SLP76, PLCG1, ERK1, ERK2, AKT, mTOR, 4EBP1, NFâÎșB p65, PARP1, and a reference such as betaâactin. Add phosphoâspecific detectors as a separate subpanel and always run a phosphatase control.
18. Example day plan
Day 1 morning
Conjugate 2 to 4 detectors and QC one by mass.
Couple 2 to 4 capture antibodies to beads and block.
Day 1 afternoon
Prepare lysates, nuclease treat, spike controls.
Run ladder and sample separations with fractionation to 48 bins.
Day 1 evening
Perform perâbin bead capture, detector binding, cleavage.
Start perâbin index PCR for NGS. Pool and clean up.
Day 2
Sequence.
Analyze counts, fit ladder, produce target by bin matrix, call proteoforms.
Review acceptance criteria.
19. Calculations you will use
dPCR occupancy. λ = âln(1 â k/N). Molecules per bin = λ·N.
Perâtarget correction. Molecules corrected = molecules measured divided by Ï.
Ladder mapping. Fit log10(MW) = a b·t c·t^2 on ladder peaks. Then MW(bin j) = 10^(a b·tj c·tj^2).
20. Buffer recipes
PBS, pH 7.4. 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4.
HEPES buffer, pH 7.5. 50 mM HEPES, 150 mM NaCl.
Bead capture buffer. PBS, 0.05 percent Tweenâ20, 1 mg mLâ1 BSA.
Wash buffer. PBS, 0.05 percent Tweenâ20.
Collection buffer. 20 mM HEPES pH 7.5, 150 mM NaCl, 0.05 percent Tweenâ20, 10 mM methylâbetaâcyclodextrin, 2 mg mLâ1 BSA.
Cleavage buffer example for disulfide. PBS with 25 mM TCEP, 10 minutes at room temperature.
21. Minimum documentation set
Run log with injection time, separation field, bin timing.
Ladder fit coefficients and residuals.
Detector lot QC with 1:1 stoichiometry evidence.
Perâtarget Ï values and dates.
Raw bin counts, UMI collapse stats, normalization factors, and final matrices.
Acceptance criteria outcomes and any deviations.
Final notes
Use NGS readout for full DSIâSeq because it solves bin indexing cleanly and scales to 24 or more targets. Keep dPCR for targeted troubleshooting or a very small panel.
The most common failure in early runs is residual SDS killing binding. Your collection buffer and bead wash are the leverage points.
Keep the chemistry proteinâonly by continuing to nuclease treat lysates and by ensuring the only DNA that can be amplified comes from the singleâtag detector after cleavage.