Collection
Featured protocols, application notes, and publications demonstrating PIXUL for high-throughput proteomics sample preparation — from FFPE tissue to LC-MS-ready peptides.
37 resources
Brochure How a shared proteomics core facility preps its whole sample range, tough samples included, in one walk-away run instead of one sample at a time. This two-page reference covers the three-step acoustic workflow, the all-in-one advantage over probe and focused-ultrasonication sample prep, and a head-to-head showing equivalent peptide and protein recovery against a probe sonicator at 96-sample scale.
Guide A practical decision guide for choosing the cell-disruption and protein-extraction instrument at the front of a proteomics core facility's workflow. Walks the six criteria that matter (versatility, reliability and self-sufficiency, hard-sample confidence, throughput without babysitting, consistency, and easy-to-obtain standard plates) and includes a scoring worksheet to evaluate any candidate.
Infographic An at-a-glance comparison showing plate-based acoustic lysis delivers LC-MS proteomics results on par with probe sonication — a full 96-well plate processed in one run, high and consistent protein yield, and uniform lysate across every well. The same plate feeds the mass spec, Western blot, and high-throughput ELISA workflows your lab already runs.
Guide A methods guide for core-facility and translational proteomics scientists: how plate-based acoustic lysis disrupts cells and extracts protein across a full 96-well plate in one run, so the prep step stops deciding how many samples you can study. Covers lysis, protein extraction, and getting clean lysate into your LC-MS workflow.
Blog The samples that worry operators — yeast, bacteria, tough tissue — aren't a different-instrument problem. With PIXUL, they're mostly a question of how much disruption energy and time the wall in front of you needs. Worked protocols for bacteria (minutes, with an enzymatic assist for screening by gel — not deep LC-MS proteomics), yeast (30–60 minutes in SDS-based buffer, no beads), and tough tissue (in between, sometimes with a pre-step), with an honest concession that for a genuinely extreme matrix a dedicated mechanical method may still be the right tool.
Blog Bringing up a new sample-prep instrument usually means weeks of method development. With PIXUL — a 96-well sonicator — the honest answer is closer to: transfer the protocol, then choose a run time. A new user inherits a settled method instead of building one, tunes a single variable (disruption time) to their sample, and the protocol transfers cleanly across people and institutions — with the install handled over a call.
Blog Most of a proteomics pipeline is already standardized — reduction and alkylation, digestion, peptide clean-up, the LC gradient, the mass spec and its search. The step that's least settled, and most manual, sits right at the front: getting clean, solubilized protein out of whatever sample came in. PIXUL drops into that slot, disrupting cells and solubilizing protein from up to 96 wells of a standard plate in one hands-off run — so the disruption step changes while the rest of the pipeline (clean-up, digestion, peptide loading, LC-MS/MS) stays the workflow you already run.
Blog The case that wins funding isn't the lowest price. It's how much of the facility's range a single capital line absorbs — and how little it costs to keep running once it's in. The committee-defense argument that holds up: one versatile, self-maintained instrument that absorbs the facility's range and replaces several future single-purpose purchases — on open standard consumables the core controls.
Blog Both use the same acoustic disruption — the real question is what happens when you go from one sample at a time to a full plate. A side-by-side comparison of probe sonication and a plate-based high-throughput sonicator on format, operator involvement, consistency, cross-contamination, protein yield, exposure, and best fit.
Blog Acquisition is automated and prep is plate-based — but if cell disruption still runs one sample at a time, that's the step capping how many cohorts a proteomics core can take on. The bottleneck isn't the mass spec; it's the front end.
Blog The math facing a modern proteomics core is simple and unforgiving: more groups, more sample types, more requests against a budget that's flat. The economic and structural lens on why consolidating onto a versatile sample-prep front end is how a flat-budget core keeps saying yes.
Blog The constraint on a shared core isn't the mass spec. It's whether the front end can handle everything the mass spec is asked to measure. Five evaluation criteria a spec sheet misses, the emerging answer (high-throughput multi-sample sonication), and where the published evidence already points.
Blog If the disruption step varies from well to well or run to run, that variance rides through to the data — and you can't tell it apart from the biology. Plate-wide, run-to-run consistency is what lets a proteomics core validate a method once and reuse it: the same result in well 1 and well 96, documented rather than assumed, so a difference between samples is a difference in the samples — not an artifact of how each was lysed.
Blog A shared core can't put a dozen labs on hold while it waits for a field engineer. The disruption step every sample passes through has to be something the core can install and keep running day to day on its own. Self-sufficiency — install over a call, fluid and filters changed at the bench in minutes — is what keeps the day-to-day in the core's hands rather than on a service schedule, while a service contract sits in reserve for the rare, genuinely complex fault.
Blog The real constraint on a shared proteomics core isn't capability. It's how often you're forced to say no. Flat budgets and rising multi-omics demand have made the old 'a new instrument for every sample type' model untenable; versatility at sample prep is now the highest-leverage thing a core can buy.
Blog Most instruments handle a lot of one thing. A shared core needs the opposite — a little of everything, all the time. Real versatility in a proteomics front end isn't 96-well capacity; it's column-level programming that lets cells, bacteria, tough tissue, and FFPE run side by side, each with its own disruption time and energy, on a single plate in one run.
Blog You're not really choosing a sample-prep instrument. You're choosing whether your facility can say yes to the next question a PI walks in with. The five jobs your front end has to do for a shared core — absorbing the range, staying up in-house, freeing your operators, producing defensible data, and fitting one budget line.
Blog PIXUL runs on the same standard open-format plates your liquid handler already uses — so a stockout, a price change, or a long lead time on one supplier's part can't stall the whole core. A proprietary consumable turns the front end into a single point of supply failure; a standard open-format plate, available from several vendors and reusable on partial runs, keeps that supply uncaptive. The value isn't unlimited choice — it's that the plate you standardize on is a standard one you can actually get.
Blog It's the right question for a backbone instrument — and the honest answer isn't a promise. It's in what the instrument actually needs to keep running, and how widely it already does. A dependable backbone instrument is one that rarely needs an outside visit to keep running — PIXUL is designed so the core's own team installs it over a call and maintains it in-house, with operator-replaceable fluid and filters, a sealed low-maintenance system, and few parts that ever need a service engineer. And it's proven across an established installed base of proteomics cores worldwide.
Blog Both disrupt samples gently and in parallel. The real question is how far they scale — and how much control you keep when the samples aren't all the same. A side-by-side comparison of water-bath ultrasonication and a high-throughput multi-sample sonicator (PIXUL) on throughput, per-column protocol control, mixed-sample-type capability, output format, and run-to-run consistency at scale.
Blog The spec sheet is for you. The real test of a front-end instrument is whether the person who runs it every day will want to — so here's their day, not the datasheet. The operator's-day view: a half-day at the probe replaced by one hands-off plate run, in-house maintenance in minutes instead of a service ticket, a result they can trust across all 96 wells, and the samples they used to dread now working — because the operator's verdict after a week of real runs is the adoption signal a core lead should care about most.
Brochure How proteomics, epigenetics, and genomics labs eliminate the sample-prep bottleneck with 96-sample parallel ultrasonication and standard microplates. Two-page reference covering the 3-step workflow, five core value propositions, and a head-to-head proteomics validation showing equivalent peptide/protein ID against probe sonication at 96-sample throughput.
App Note How proteomics core facilities validated PIXUL as equivalent to VCX130 probe sonication while moving from 1-sample-at-a-time to 96 samples in parallel. VIB Proteomics Core tested PIXUL across four bottom-up LC-MS/MS QC parameters on HEK293T cells and fresh mouse liver tissue — including a finding that just 5 minutes of PIXUL sonication is sufficient for complete tissue lysis.
Publication SWATH-MS proteomic profiling of six tissues from Ndufs4 knock-out mice — a model of Leigh syndrome — identified over 3,000 proteins per tissue and 75-189 differentially abundant proteins (DAPs) per organ. The olfactory bulb and heart showed the greatest tissue-specific proteome alterations, while only NDUFS4 and NDUFA12 were shared DAPs across all six tissues. PIXUL multi-sample sonication was used to homogenise and lyse all six tissue types in a single 96-well plate prior to SWATH-MS analysis.
Publication Dual AAV delivery of two engineered laminin-linking proteins — mag and αLNNd — restored muscle and nerve function in a severe LAMA2-related muscular dystrophy mouse model. PIXUL-prepared muscle lysates were analyzed by DIA LC-MS/MS on an Orbitrap Eclipse to quantify linker protein expression and confirm dose-dependent rescue alongside histological, transcriptomic, and functional readouts.
Publication A proteomic survey of bull spermatozoa recovered from the testis, caput, and cauda epididymis identified 9,593 proteins and quantified 2,305–2,554 per population, mapping the protein turnover that drives post-testicular maturation. PIXUL sonication enabled consistent multi-replicate lysis of purified sperm, revealing 264 conserved mammalian sperm proteins and candidate fertility markers (Cylicin-1/2, ACRV1, IZUMO3, ENO1, VDAC2) across the epididymal transit.
Publication CRISPR/Cas9 Rictor knockout HEI-OC1 auditory cells reveal that mTORC2 disruption abolishes PKCα Thr638/641 phosphorylation, reduces the F/G-actin ratio, and reshapes the cytoskeletal proteome. DIA proteomics on an Orbitrap Exploris 480 — with PIXUL-based lysis — quantified 7,022 proteins per sample and identified 1,135 significantly deregulated proteins, including hair-cell targets CFL1, WDR1, Shroom2, and Map1b.
Publication A programmable mRNA-therapeutic platform delivers Epigenomic Controllers via lipid nanoparticles to durably modulate single or multiplexed gene expression in vivo. PIXUL-sonicated whole-cell lysates fed Jess Automated Western quantification of newly-translated controller protein — detectable within 6 hours, cleared by 96 hours — while downstream target-protein effects (97% CXCL8 knockdown by ELISA; 6-month Pcsk9 suppression in mouse serum) confirmed dose-responsive protein-level efficacy with a narrow off-target footprint.
Publication A multi-omic resource on translation dynamics in HepG2 and Huh7 human liver cancer cells, combining ribosome profiling, run-off ribo-seq with harringtonine and cycloheximide, pSILAC proteomics, RNA-seq, and polysome profiling. PIXUL sonication is used in the pSILAC sample preparation to lyse cells in SDS/TEAB/TCEP/CHX buffer before SP3 digestion and LC-MS/MS, yielding ~3,589 quantified proteins alongside ribosome footprints on 20,725 genes.
Publication Achter and colleagues benchmark a PIXUL-based, 96-well FFPE proteomics workflow on human cardiac tissue, quantifying ~4,000 proteins per single-shot sample and ~5,700 proteins with deep TMT fractionation. Formalin fixation contributed only 1.1% of proteome-wide variance versus 28.9% for workflow choice, and case studies (sinoatrial node mapping, ten arrhythmogenic cardiomyopathy biopsies vs. controls) recovered known regional and disease-specific protein signatures from archival blocks stored up to 15 years.
Publication Whole-worm DIA-LC-MS/MS proteomics of C. elegans fed three E. coli diets reveals that bacterial ribonuclease-3-dependent RNA species drive an inter-tissue proteostasis program, up-regulating a 12-protein muscle-function cluster only in proteotoxically challenged animals. The authors used PIXUL to lyse flash-frozen whole worms in SDS/TCEP/TEAB before TCA precipitation and Orbitrap Exploris 480 analysis — resolving 194 significantly altered proteins that trace a dietary RNA cue from intestinal uptake through the RNAi machinery to body-wall muscle aggrephagy.
Publication A 96-well PIXUL workflow that extracts protein, DNA, and RNA in parallel from FFPE or fresh-frozen tissue — FFPE-to-frozen proteomic correlation reaches Pearson R² ≥ 0.95 across four mouse organs. Archived blocks become viable inputs for modern multi-omic analysis.
Publication Loss-of-function pph-7 mutants in C. elegans show severely reduced fertility and embryonic lethality at 26 degrees C, and PIXUL-prepared lysates enabled proteome and phosphoproteome profiling identifying ~5,500 proteins and ~6,500 phospho-peptides per sample. The analysis pinpointed nine consistently dysregulated proteins across both pph-7 alleles, including VHL-1 pathway targets (CLEC-209, MCT-2, C01B4.6), spermatogenesis proteins (SMZ-1, SSQ-1, MSP-3), and putative direct PPH-7 substrates phosphorylated >4-fold higher in mutants (PAT-12, PAT-2).
Publication SWATH-MS proteomic comparison of Huh7 cells transfected with HBV subgenotype A1 wildtype versus the G1862T precore mutant — protein extracted with PIXUL — identified 3,906 proteins and 247 vs. 123 differentially expressed proteins relative to vector control. G1862T uniquely dysregulated oxidative stress and cell cycle pathways and upregulated DNA-synthesis proteins PRIM2 and RPA more than 2-fold versus wildtype, connecting precore-mutation-driven ER stress to host pathways implicated in hepatocellular carcinoma.
Publication First comparative proteomic study of Huh7 cells transfected with sub-Saharan African HBV (sub)genotypes A1, D3, and E versus the non-African reference A2, using SWATH-MS to quantify 3,906 proteins. PIXUL multi-sample sonication was used for cell lysis and protein extraction, enabling the discovery that subgenotype A1 — the most hepatocarcinogenic strain — uniquely upregulates RHOC, Rap2B, and GNB1 to drive PI3K/Akt/mTOR and MAPK signalling.
Publication A PIXUL-prepared LC-MS/MS proteomics dataset from lysolecithin-induced demyelinated lesions in the corpus callosum of female Lewis rats, sampled at 3 and 11 days post-lesioning with either continuous vagus nerve stimulation or sham. The dataset identifies 8,271 proteins (8,172 reliably quantified) and resolves hundreds of differentially expressed proteins between the demyelination and remyelination timepoints, providing a reusable reference for groups studying CNS lesion repair, neuroinflammation, and remyelination biology.
Publication One PIXUL-Matrix workflow generates 8-dimensional multi-omic datasets — DNA, RNA, chromatin, and protein — in parallel from a single 96-well plate, validated across six mouse organs. FFPE-to-frozen RNA-seq Spearman correlations of 0.83–0.91 (including 1.5-year-old room-temperature blocks) and ~5,572 proteins quantified per organ on an Orbitrap Exploris 480 confirm that archived FFPE specimens are practical inputs for modern multi-omic studies. This preprint introduces MultiomicsTracks96, the 96-well-format toolbox unlocking the multiome of hundreds of millions of banked clinical tissues.
Integrated PIXUL chromatin shearing workflows, sonication recommendations, and partner technical notes for reproducible, high-throughput ChIP-seq sample preparation.
ChIP-seq, methylation, and chromatin profiling resources featuring PIXUL — covering chromatin shearing recommendations, integrated workflows, and validated protocols.