Sample Multiplexing

Consistency across batches, sites, and timepoints – powered by CyTOF barcoding

  • Combine more than 100 barcoded samples in a single tube
  • Minimize technical variability with unified staining
  • Proven method with over 500 publications using CyTOF™ barcoding
 

Sample Multiplexing

Consistency across batches, sites, and timepoints – powered by CyTOF™ barcoding

  • Combine more than 100 barcoded samples in a single tube
  • Minimize technical variability with unified staining
  • Proven method with over 500 publications using CyTOF™ barcoding

Overview

Cell barcoding is a powerful method for multiplexing samples with mass cytometry (CyTOF technology). By staining and acquiring samples in a single tube, barcoding significantly reduces workflow burdens, acquisition times and technical variability, while conserving precious clinical material. In this method, samples are tagged with unique identifiers to enable single-tube staining, reduce staining variability and boost acquisition throughput.  

Scalable workflows. Reliable results.

Whether multiplexing fewer than 10 samples or more than 100, barcoding scales experiments and improves data consistency.

download CyTOF Barcoding flyer

Learn more about CyTOF barcoding

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Workflow

Individual samples are barcoded with unique metal isotopes for combined staining and acquisition, followed by debarcoding seamlessly integrated within CyTOF Software.

Barcoding workflow diagram

Now available: support for custom debarcoding with CyTOF Software

Learn more

Improved sample-to-sample staining consistency

Barcoding minimizes sample-to-sample technical variation when multiplexed samples are stained and acquired together.

See application note

CD4 T Cells and B cells plot chart

Data from replicates of the same sample are compared between non-barcoded (No BC) and barcoded (BC) samples.


Applications

CyTOF technology demonstrates barcoding for diverse cell types across a variety of research areas.

A Phase 2 metastatic breast cancer clinical trial

  • Unique mass-tag cell barcoding with doublet-filtering scheme
  • Paired PBMC samples collected before and after treatment were barcoded, reducing batch effects

Mo, H. et al. Nature Medicine (2024)

126-plex barcoding of organoid samples

  • Thiol-reactive tellurium maleimide (TeMal) with cisplatin (Pt) barcoding
  • Triplicates from 390 colonic organoid cultures were barcoded in situ

Qin, X. et al. Cell (2023)

A study of neuroinflammation in an EAE 
mouse model

  • Cell-ID palladium (Pd)-based barcoding
  • Barcoded samples of mouse spinal cord mononuclear cells were combined in a single tube for a staining and storage

Peruzzotti-Jametti, L. et al. Nature (2024)

A trial on exercise effects in adults 
with prediabetes

  • Anti-CD45 Pd-based barcodes
  • Paired whole blood sammples were barcoded and stained together, reducing intra-patient technical sample variability

Baker, C.J. et al. Journal of Diabetes and its Complications (2024)

CyTOF XT PRO

No CyTOF? No problem!

Our Standard BioTools™ Service Lab can help. Simply ship your samples and get results within 72 hours of sample receipt.

Methods

CyTOF barcoding reagents – choose the right barcoding method that fits your needs

Novel advancements in barcoding reagents and methods enable researchers who use CyTOF systems to select the ideal barcoding reagent and scheme tailored to their sample type, quantity and cell profiling needs for surface or intracellular targets.

Palladium-based
barcoding

  • Universal, cell-agnostic
  • Up to 20 samples
  • Compatible with downstream staining workflows
mockup of app note

Read application note

Live-cell
barcoding

  • CD45+ leukocytes
  • 35-plus samples
  • No fix/perm step required. Fix-sensitive epitopes are preserved.
mockup of application note

Read application note 

Custom
barcoding

  • Live or fixed cells
  • Multiplex over 100 samples in a single CyTOF experiment
  • Largest-scale cell barcoding in the industry
mockup of application note

Read application note

View recent publications by each barcoding method here.

BARCODING PRODUCTS

CyTOF Software (v9.2.1)

Automated support for a seamless barcoding and analysis workflow

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Debarcoder application optimizes analysis pipeline of multiplexed samples

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Integrated support for custom debarcoding of any isotope combination

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Increased number of barcoding schemes

Learn more

CyTOF XT PRO Screenshot

Product documents


Recent CyTOF barcoding in the literature

Cell-ID 20-Plex Pd Barcoding Kit:

CD45 live-cell barcoding:

Custom barcoding:

For Research Use Only. Not for use in diagnostic procedures. Patent and License Information: www.standardbio.com/legal/notices. Trademarks: www.standardbio.com/legal/trademarks. Any other trademarks are the sole property of their respective owners. ©2025 Standard BioTools Inc. All rights reserved.