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Proteomics

Sample preparation is the #1 bottleneck in high-throughput proteomics. It's also the #1 source of error.

Your mass spec can process hundreds of samples a day. Your sample prep can't match that pace. PIXUL changes that. 96 samples in parallel, in 10–30 minutes, with LC-MS/MS-validated protein identification equivalent to probe sonication.

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PIXUL multi-sample sonicator processing a 96-well plate for high-throughput proteomics sample preparation
The Challenge

Current approaches to proteomics sample prep

Each method has its place. Each breaks at scale.

Visualization showing that 75% of proteomics error originates from sample processing, with 72% from extraction alone

75% of proteomics error originates from sample processing. 72% from extraction alone.

Probe sonicators

The lab default. One sample at a time, operator-dependent results, localized thermal spikes that degrade proteins, and cross-contamination risk between samples.

Where it breaks: throughput, reproducibility

Bead beaters

Handle tissue disruption at scale, but introduce bead contamination into LC-MS/MS samples. Heat generation degrades proteins. Variable extraction quality between wells.

Where it breaks: contamination, consistency

Focused ultrasonicators

Deliver precision but at ~$400 per proprietary plate and sequential processing that takes 7+ hours for 96 samples. Vendor lock-in compounds the operating cost.

Where it breaks: cost, throughput at scale

Chemical lysis

Simple and inexpensive but incomplete, with particularly poor recovery of membrane-bound and nuclear proteins. Published data confirms sonication significantly improves detection of these protein classes.

Where it breaks: proteome coverage

Full liquid handling automation

Solves throughput but costs $150K–$300K and requires dedicated lab space, specialized operators, and extensive validation.

Where it breaks: cost, footprint, complexity

What if your sample prep matched your mass spec throughput?

The ideal solution would process 96 samples in parallel, deliver reproducible protein extraction validated by LC-MS/MS, handle any sample type from FFPE to fresh cells, and use standard consumables at $2 per plate.

Researcher working with PIXUL Multi-Sample Sonicator in a proteomics laboratory
The Solution

PIXUL: High-throughput sonicator for proteomics sample preparation

PIXUL processes 96 samples in parallel, in 10–30 minutes, in a standard $2 plate. Combined with S-Trap or SP3 digestion, it is the fastest path from cells to peptides, with the reproducibility your data demands.

Built by researchers at the University of Washington. Licensed and supported by Active Motif.

1

Your mass spec is fast. Your sample prep should be too.

PIXUL processes 96 samples in parallel, so your sample preparation finally matches your instrument throughput. Load samples in a standard microplate, set conditions on the touchscreen, and walk away. Combined with S-Trap or SP3 digestion, it is the fastest cells-to-peptides workflow available.

~1/3 of PIXUL installations are proteomics labs, from word-of-mouth alone, zero active marketing.
2

Sample prep causes 75% of proteomics error. PIXUL cuts it at the source.

Published research shows that sample processing causes 75% of total error in proteomics, with 72% from extraction alone. PIXUL's arrayed 2 MHz transducers deliver uniform cavitation in every well, independently and simultaneously. No positional effects. No operator variation.

LC-MS/MS: 7,265–8,380 protein IDs (PIXUL) vs 7,803–8,124 (probe). Equivalent depth, 96x throughput.
3

From FFPE archives to fresh cell lines, all in the same plate.

Load your FFPE, frozen, and cell samples on the same 96-well plate, assign up to 12 different sonication conditions by column, and process them all simultaneously. Combined with HYPERsol and S-Trap, PIXUL unlocks your tissue archives for high-throughput proteomics.

MultiomicsTracks96 (2024): 8-dimensional omics datasets from matched frozen and FFPE mouse organs.
LC-MS/MS Validated

Protein identification: PIXUL vs. probe sonication

Head-to-head LC-MS/MS validation from PIXUL-prepared mouse liver tissues shows equivalent protein identification depth with maintained quality control metrics.

PIXUL (96 samples simultaneously)
7,265–8,380
protein identifications
96 samples in 10–30 min
Probe sonication (1 sample at a time)
7,803–8,124
protein identifications
1 sample at a time, manual

Equivalent depth. 96x the throughput.

Missed Cleavages

Within normal range

N-Terminal Acetylation

Within normal range

Oxidized Methionine

Within normal range

Source: Active Motif LC-MS/MS technical documentation. Mouse liver tissue samples.

From Cells to Peptides

Proteomics workflow with PIXUL

Standard plate format at every step. No proprietary consumables. No sample transfers between vessels.

PIXUL proteomics workflow diagram: Cells or tissue loaded into 96-well plate, PIXUL sonication, S-Trap or SP3 digestion, LC-MS/MS analysis

Standard workflow

FFPE workflow

FFPE tissue proteomics with PIXUL: archival specimens processed alongside fresh samples on the same 96-well plate
Technical Specifications

PIXUL for proteomics

Compact, walk-away operation with no proprietary consumables.

Throughput 1–96 samples per run
Run Time 10–30 minutes
Plate Format Standard 96-well round-bottom
Frequency 2 MHz megasonication
Conditions per Plate Up to 12
Dimensions 45 × 59 × 34 cm
Weight 23 kg
Setup Time 15 minutes
Consumable Cost ~$2/plate (standard)
PIXUL Multi-Sample Sonicator instrument, compact benchtop design with built-in chilling and touchscreen interface
Proven in Proteomics Labs

The data speaks for itself

Approximately one-third of PIXUL installations are proteomics labs, driven entirely by word-of-mouth with zero active marketing. Pharmaceutical companies are repeat purchasers.

~1/3

Proteomics installs

Of all PIXUL installations, from word-of-mouth alone

7,265–8,380

Protein IDs (PIXUL)

LC-MS/MS validated, equivalent to probe sonication

42+

Publications

Peer-reviewed validation across all applications

$2

Per plate

Standard consumables vs. ~$400 proprietary

Since the first time that I sonicated my samples and I got the expected results all in ~30 min, I don't want to look back at those days when I had to hold my tube and be seated for hours sonicating all my samples one by one.

PIXUL User , Proteomics researcher

Dr. Alexander Schmidt Webinar: PIXUL in Proteomics Workflows

Independent validation from Dr. Alexander Schmidt's laboratory, confirming PIXUL's performance in high-throughput proteomics sample preparation. The webinar covers integration with established LC-MS/MS pipelines and real-world throughput data from an active proteomics core facility.

Pharmaceutical companies are among the repeat purchasers of PIXUL, deploying multiple units across proteomics core facilities.

Downstream Integration

Works with your existing pipeline

PIXUL integrates directly with the proteomics workflows you already use. No protocol changes required.

S-Trap

ProtiFi partnership validated

Si-Trap

Compatible digestion workflow

SP3

Bead-based sample processing

HYPERsol

FFPE proteomics protocol

Ready to accelerate your proteomics workflow?

See how PIXUL fits into your LC-MS/MS pipeline. Test with your own samples on your own mass spec platform.

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Frequently Asked Questions

Proteomics questions, answered

Is PIXUL validated for mass spec workflows?
Yes. LC-MS/MS validation data from PIXUL-prepared mouse liver tissues shows 7,265–8,380 protein identifications, equivalent to 7,803–8,124 from traditional probe sonication. Quality control metrics including missed cleavages, protein N-terminal acetylation, and oxidized methionine levels were all within normal range. PIXUL integrates directly with S-Trap and SP3 digestion workflows for LC-MS/MS sample preparation.
Does PIXUL work with FFPE tissues?
Yes. The MultiomicsTracks96 publication (2024) demonstrated 8-dimensional omics datasets from matched frozen and FFPE mouse organs using PIXUL. Combined with the HYPERsol protocol and S-Trap digestion, PIXUL processes FFPE tissues, frozen biopsies, and cultured cells on the same 96-well plate with up to 12 optimized sonication conditions per run. Same-plate processing eliminates transfer steps where irreplaceable clinical specimens can be lost.
How does PIXUL compare to focused ultrasonicators for proteomics?
PIXUL processes all 96 samples simultaneously in 10–30 minutes, while focused ultrasonicators process wells sequentially, taking over 7 hours for a 96-well plate. PIXUL uses standard plates at approximately $2 each versus ~$400 for proprietary consumables. For a lab running 3 plates per week, that is $312 per year on PIXUL versus $62,400 on proprietary consumables. LC-MS/MS data shows equivalent protein identification depth between the two approaches.
Will PIXUL work with my existing lysis buffer?
PIXUL is compatible with standard proteomics lysis buffers and integrates directly with S-Trap, Si-Trap, SP3, and HYPERsol downstream workflows. Researchers use their existing protocols and buffers with PIXUL, adding the instrument to their established sample preparation pipeline without changing their downstream chemistry. The ProtiFi S-Trap partnership has validated PIXUL as the most efficient plate-based protein extraction system available.
What about protein degradation from sonication?
LC-MS/MS quality control data from PIXUL-prepared samples shows maintained quality metrics: missed cleavages, protein N-terminal acetylation, and oxidized methionine levels were all within normal range. PIXUL's built-in chilling and temperature control maintains sample integrity during processing, and the 2 MHz megasonication frequency delivers controlled, uniform cavitation without the localized thermal spikes associated with probe sonication.