This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
PXMP4 / Peroxisomal membrane protein 4 · IHC design guide
Design Immunohistochemistry for PXMP4
Plan chromogenic PXMP4 IHC in paraffin sections using renal tubules and type II alveolar cells as high-staining references (HPA tissue IHC). The catalog antibody has an IHC dilution range of 1:100–1:300 (datasheet A13147); spleen red-pulp cells are reported as unstained (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PXMP4 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Expected peroxisome membrane (UniProt); observed granular cytoplasm (HPA tissue IHC) | |
| Staining pattern | Granular cytoplasm in renal tubules and type II alveolar cells (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A13147) | |
| Positive control | Bronchus+4 more · see all | |
| Negative control | Spleen |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections and controls. (selected-SKU IHC image A13147) | |
| Caveat | Tissue staining has medium consistency with RNA expression (HPA tissue IHC) | |
| Regulation | Expression varies with androgen sensitivity (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope side is unannotated (UniProt) |
Section 1
Recommended PXMP4 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet A13147) is accompanied by one published PXMP4 IHC protocol in hepatocellular carcinoma tissue (PMC11077113).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A13147) |
| Fixation | Image fixative and duration unreported (datasheet A13147); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Tris-EDTA pH 9.0 (datasheet A13147); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-PXMP4, 1:100-1:300 (datasheet A13147) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PXMP4-positive staining in respiratory epithelial cells of bronchus (HPA tissue IHC: High). HPA tissue profile: Granular cytoplasmic expression in most tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated Tris-EDTA at pH 9.0 (datasheet A13147); the published protocol used citric acid retrieval (PMC11077113).
Section 2
What Is the Expected PXMP4 Staining Pattern?
PXMP4 is a peroxisomal membrane protein with 2 transmembrane segments (UniProt Q9Y6I8 topology). In paraffin IHC, expect granular cytoplasmic staining in appropriately expressing cells, including kidney tubular cells, bronchial respiratory epithelial cells and lung type II alveolar cells (HPA tissue IHC). HPA rates the tissue staining Approved, with medium consistency between staining and RNA expression (HPA tissue IHC).
| Discrete cytoplasmic granules in kidney tubular cells or bronchial respiratory epithelial cells, with readily visible chromogen. | This matches the reported granular cytoplasmic pattern and High staining in those cells (HPA tissue IHC). At light-microscope resolution, the granules are consistent with peroxisome-associated PXMP4; IHC alone does not prove each granule is a peroxisome (UniProt Q9Y6I8 subcellular location; HPA tissue IHC). |
| Predominantly uniform nuclear, surface-membrane or extracellular staining, without discernible cytoplasmic granules. | This differs from the expected paraffin IHC pattern (HPA tissue IHC). Consider nonspecific staining or a detection artefact. HPA also reports nucleoli fibrillar-center localization by ICC-IF; that separate observation does not establish uniform nuclear staining as the expected IHC result (HPA subcellular ICC-IF). |
| Strong signal in a cell population where the chosen reference image shows little or no staining. | Check cell identity and morphology before calling it PXMP4: HPA reports low tissue specificity, so an unexpected cell type is not automatically negative (HPA tissue IHC). If the pattern persists without matching granules, investigate antibody cross-reactivity or endogenous detection activity (general IHC practice). |
| Diffuse chromogen over the section, including extracellular spaces or many unrelated cells. | A broad haze obscures the reported granular cytoplasmic pattern (HPA tissue IHC). Review background in a control section and assess blocking, antibody concentration, washing and chromogen development as general IHC variables (general IHC practice). |
| No staining in kidney tubular cells despite preserved tissue morphology and a functioning counterstain. | Kidney tubular cells are reported High by HPA, so this result warrants a technical check (HPA tissue IHC). A counterstain confirms tissue is present, but does not verify primary-antibody binding or detection; check those steps with appropriate assay controls (general IHC practice). |
💡Expected PXMP4 appearanceCall a result positive when distinct cytoplasmic granules are visible in a reported High population such as kidney tubular cells (HPA tissue IHC); uniform nuclear or diffuse extracellular color is discordant with that IHC pattern (HPA tissue IHC).
| Reference tissue and cell population | HPA reports High staining in bronchial respiratory epithelium, Purkinje cells, endometrial and epididymal glandular cells, kidney tubules, lung type II alveolar cells, parathyroid glandular cells and rectal glandular cells (HPA tissue IHC). Score the identified population within its tissue, not the entire section. |
| Low-signal comparator | HPA reports Not detected specifically in spleen red-pulp cells, while several other listed populations are Low (HPA tissue IHC). Use those labels for their named cells only; neither label establishes that every cell in the tissue must be blank. |
| Topology and epitope uncertainty | The protein has 2 transmembrane segments at residues 97–117 and 153–173 (UniProt Q9Y6I8 topology). The supplied record does not identify the IHC antibody's epitope, so topology cannot determine which antigen-retrieval condition will work. |
| Antibody evidence and localization | HPA lists antibody HPA050077 as Approved for IHC and ICC; tissue IHC has medium staining-to-RNA consistency (HPA antibody validation; HPA tissue IHC). Peroxisomes are the main approved ICC-IF location, with an additional nucleoli fibrillar-center location (HPA subcellular ICC-IF). |
| Protein variants and modifications | UniProt lists 2 isoforms and glycosylation sites at residues 57 and 206 (UniProt Q9Y6I8). Without an epitope map or variant-specific staining data, these annotations cannot predict an IHC intensity difference or a missing signal. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known High reference population is blank. | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. | Confirm cell identity, run assay controls, and review antigen retrieval, primary-antibody incubation and detection as general IHC steps (general IHC practice). |
| Reference tissue stains weakly or unevenly. | Variable tissue processing or reagent delivery can produce uneven IHC staining (general IHC practice); HPA levels describe observed populations, not guaranteed intensity on every section (HPA tissue IHC). | Compare well-preserved regions and a concurrent reference section; review retrieval consistency, reagent coverage and development time (general IHC practice). |
| Granules disappear into widespread brown haze. | Excess background can conceal the granular cytoplasmic pattern (HPA tissue IHC; general IHC practice). | Inspect a no-primary control, then review blocking, antibody concentration, washing and chromogen development (general IHC practice). |
| Nuclei appear uniformly positive in paraffin IHC. | Uniform nuclear staining is discordant with HPA's granular cytoplasmic tissue pattern; HPA's additional nucleolar localization comes from ICC-IF (HPA tissue IHC; HPA subcellular ICC-IF). | Compare a reference tissue and detection controls; assess nuclear background before treating the IHC signal as specific (general IHC practice). |
| Spleen red-pulp cells stain strongly. | HPA reports PXMP4 Not detected in that specific population (HPA tissue IHC); endogenous detection activity or cross-reactivity may account for unexpected color (general IHC practice). | Verify the stained cells are in red pulp, examine a no-primary control, and compare the pattern with a High reference population (HPA tissue IHC; general IHC practice). |
| Prostate sections differ between samples. | UniProt reports expression in normal prostate epithelial and androgen-sensitive adenocarcinoma cells, but not androgen-insensitive adenocarcinoma cells (UniProt Q9Y6I8 tissue specificity). This is not a guaranteed IHC result for any given specimen. | Document the sampled cell population and assay controls before interpreting a difference; use the HPA tissue images as the staining-pattern reference (HPA tissue IHC; general IHC practice). |
Experiment evidence
IHC & IF images showing PXMP4 staining
A13147 · IHCImmunohistochemical analysis of paraffin-embedded human tonsil. 1, Antibody was diluted at 1:200 (4° overnight). 2, Tris-EDTA, pH9.0 was use
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000101417-PXMP4/tissue/cerebral+cortex#imid_13772893
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000101417-PXMP4/tissue/colon#imid_13772819
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000101417-PXMP4/tissue/liver#imid_13772820
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000101417-PXMP4/tissue/kidney#imid_13772821
HPA · ICC-IF CACO-2Human Protein Atlas immunofluorescence, CACO-2, antibody HPA050077; green = PXMP4, blue = nucleus, red = microtubules.
HPA · ICC-IF CACO-2Human Protein Atlas immunofluorescence, CACO-2, antibody HPA050077; green = PXMP4, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PXMP4 IHC & IF
🧪Run kidney first and expect staining in tubular cells (HPA: High in cells in tubules); use spleen red pulp as the biological tissue negative (HPA: Not detected in cells in red pulp). On the kidney slide, cells outside the positive tubules should show only background staining, but their PXMP4 status is not specified by the supplied HPA rows.
Positive control tissue: Bronchus (Respiratory epithelial cells, HPA High)
Negative control tissue: Spleen (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PXMP4 in CACO-2, MCF-7, U2OS, with annotated localisation: Peroxisomes (approved) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) control, a host-species- and clonality-matched isotype control, and a PXMP4 knockout or validated peptide-block control (standard IHC practice). For chromogenic kidney IHC, quench endogenous peroxidase and account for tubular endogenous biotin if using avidin–biotin detection (standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported in the supplied evidence, and the selected paraffin-section caption does not state its fixative (A13147 caption: fixative unreported). The catalog antibody example uses Tris–EDTA at pH 9.0 for retrieval and a 1:200 primary dilution, but a PXMP4-specific retrieval dependency is unreported (A13147 caption). Frozen sections or IF are not established as easier; IF/ICC can assess peroxisomal localization (HPA: peroxisomes approved), while kidney tubular endogenous biotin may complicate avidin–biotin IHC detection (standard IHC practice).
HPA tissue IHC evidence for PXMP4
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Spleen | Cells in red pulp | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PXMP4 IHC Tips
Troubleshoot PXMP4 staining in paraffin sections by checking retrieval, compartment, cellular context, and controls before comparing signal across samples.
How should I retrieve PXMP4 in paraffin sections with weak staining?
Use heat-mediated Tris-EDTA pH 9.0 antigen retrieval for paraffin sections (datasheet A13147). The catalog antibody’s human tonsil image used this buffer, primary antibody at 1:200 overnight at 4°C, and secondary antibody at 1:200 for 30 minutes at room temperature (caption A13147). Keep retrieval conditions consistent across comparison slides and inspect tissue integrity after heating (standard IHC practice). If staining remains weak, vary heating duration on serial sections before trying another buffer or pH as a fallback (standard IHC practice). Judge improvement by discrete cytoplasmic granules rather than diffuse staining, consistent with the reported tissue profile (HPA tissue IHC).
Could fixation explain absent or uneven PXMP4 staining?
PXMP4-specific sensitivity to fixation is unknown: the catalog image identifies paraffin-embedded human tonsil but does not state its fixative (caption A13147). Record each sample’s fixative and processing history, then compare sections processed alike before attributing a difference to PXMP4 biology (standard IHC practice). For troubleshooting, stain serial sections together using Tris-EDTA pH 9.0 retrieval and the documented 1:200 primary dilution (datasheet A13147; caption A13147). Include a tissue control with an expected staining pattern and inspect morphology, section edges, and counterstain for processing variation (HPA tissue IHC; standard IHC practice). Do not use tissue staining patterns to infer a PXMP4-specific fixation effect.
What staining pattern should I expect, and how should I assess nuclear signal?
In chromogenic sections, look for granular cytoplasmic staining, the reported pattern across most tissues (HPA tissue IHC). PXMP4 is assigned to the peroxisome membrane (UniProt Q9Y6I8), and its main approved subcellular location is peroxisomes (HPA subcellular). HPA also reports an approved additional location in the nucleoli fibrillar center, so a nuclear focus warrants careful review rather than automatic rejection (HPA subcellular). Compare it with granular cytoplasmic signal on the same slide and with primary-omission and isotype controls where appropriate (standard IHC practice). Broad, uniform nuclear staining without the expected granules needs independent confirmation before being scored as PXMP4 (HPA tissue IHC; standard IHC practice).
How do isoforms and membrane topology affect a negative PXMP4 result?
PXMP4 has 2 annotated isoforms and transmembrane segments at residues 97–117 and 153–173 (UniProt Q9Y6I8). Its recorded glycosylation sites are residues 57 and 206 (UniProt Q9Y6I8). Check the catalog antibody’s documented immunogen or epitope against both isoforms before treating absent staining as absent protein; an epitope location is not supplied here (standard antibody validation practice). In paraffin sections, compare retrieval conditions on serial sections because epitope accessibility can depend on processing and retrieval (standard IHC practice). The documented starting conditions are Tris-EDTA pH 9.0 and primary antibody 1:200 (datasheet A13147; caption A13147).
How can IF help investigate an uncertain chromogenic PXMP4 pattern?
Use IF as a separate validation experiment and compare puncta with a peroxisome marker, reflecting PXMP4’s assigned membrane location (UniProt Q9Y6I8; HPA subcellular). Multiplex with a marker for the expected cell population, such as respiratory epithelial cells in bronchus, then assess overlap within identified cells (HPA tissue IHC). Choose fluorophores after checking tissue autofluorescence and include single-stain controls to assess channel bleed-through (standard IF practice). Because the epitope and its side of the peroxisome membrane are unspecified here, determine epitope orientation before selecting permeabilisation strength (UniProt Q9Y6I8 topology; standard IF practice). HPA reports approved peroxisomal and additional nucleolar localisation in its subcellular images (HPA subcellular).
How do I distinguish diffuse PXMP4 staining from chromogenic background?
Start by comparing stained sections with a primary-omission control and checking whether signal remains granular within cytoplasm, as reported for PXMP4 (HPA tissue IHC; standard IHC practice). Examine edges, folds, necrotic areas, and residual endogenous peroxidase activity before assigning diffuse DAB to antigen (standard chromogenic IHC practice). Apply a peroxidase block, appropriate protein blocking, and thorough washes as general chromogenic workflow steps (standard IHC practice). If signal is excessive, titrate from the documented 1:200 primary dilution while holding Tris-EDTA pH 9.0 retrieval constant (caption A13147; datasheet A13147). Compare changes in background and expected cytoplasmic granules on adjacent sections processed in the same run (HPA tissue IHC; standard IHC practice).
What should I score when comparing PXMP4 across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region before scoring, then record the percentage of cells with convincing granular cytoplasmic signal and its intensity (HPA tissue IHC; standard IHC practice). An H-score can combine intensity and percentage, while puncta density per mm² can supplement it when segmentation is reliable (standard image analysis practice). Normalise density to analysed tissue area and, when cell abundance varies, to the number of eligible cells in that area (standard image analysis practice). Exclude folds, necrosis, and edges using the same rules for every slide (standard IHC practice). Report retrieval, primary dilution, detection settings, and scoring thresholds so comparisons can be reproduced (standard IHC practice).
When is a PXMP4-positive IHC result biologically credible?
A credible result shows discrete cytoplasmic granules in intact cells, matching the reported tissue pattern and peroxisomal location (HPA tissue IHC; UniProt Q9Y6I8). Check cell identity: HPA reports high staining in kidney tubule cells and staining not detected in spleen red-pulp cells (HPA tissue IHC). Treat an unexpected cell distribution as a prompt to verify identity and controls, since HPA rates agreement between antibody staining and RNA expression as medium (HPA tissue IHC). Review diffuse nuclear staining, edge effects, necrosis, and signal persisting in a primary-omission control for artefact or endogenous enzyme activity (standard IHC practice). A focal nucleolar signal needs separate assessment because HPA also reports that location (HPA subcellular).
Boster reagents
Best PXMP4 / Peroxisomal membrane protein 4 IHC Antibodies
A13147 is listed for human and monkey IHC and IF (catalog: applications, reactivity). Its supplied figure shows paraffin-section IHC of human tonsil (A13147 IHC image caption).
Real IHC data
Anti-Pmp24 Antibody
Cat # A13147
A13147 will render with a human tonsil paraffin-section IHC figure (A13147 IHC image caption). IF is listed as an application for human and monkey samples, but no IF figure is supplied (catalog: applications, reactivity, if_image_alts).
Which to pick: For tissue IHC, choose A13147, a rabbit polyclonal listed for IHC (catalog: host, dilution_raw, applications); its own caption reports 1:200 antibody dilution and Tris-EDTA retrieval at pH 9.0 in paraffin-embedded human tonsil, with fixative unreported (A13147 IHC image caption). For IF, A13147 is listed, but ICC-specific validation and an IF figure are unreported (catalog: applications, if_image_alts). For monkey samples, A13147 lists monkey reactivity, while its supplied IHC figure shows human tissue only (catalog: reactivity; A13147 IHC image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9Y6I8 (PXMP4_HUMAN, Peroxisomal membrane protein 4).
- Human Protein Atlas. PXMP4 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. PXMP4 subcellular location (ICC-IF): Mainly localized to the peroxisomes. In addition localized to the nucleoli fibrillar center..
- Human Protein Atlas. PXMP4 antibody validation summary (1 antibodies).
- High Expression of PXMP4 in Hepatocellular Carcinoma Tissues. Asian Pacific journal of cancer prevention : APJCP 2024 — PMC11077113.
- PubMed PMID:10366717 — UniProt-cited evidence.
- PubMed PMID:11230166 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PXMP4 (Peroxisomal membrane protein 4). Expected localisation Expected peroxisome membrane (UniProt); observed granular cytoplasm (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A13147). Validated IHC antibody: A13147 at 1:100-1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Bronchus (Respiratory epithelial cells); negative Spleen. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A13147); 2. Fixation: Image fixative and duration unreported (datasheet A13147); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: Tris-EDTA pH 9.0 (datasheet A13147); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-PXMP4, 1:100-1:300 (datasheet A13147); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across paraffin sections and controls. (selected-SKU IHC image A13147); Caveat: Tissue staining has medium consistency with RNA expression (HPA tissue IHC); Isoform / epitope: 2 isoforms ; epitope side is unannotated (UniProt); Regulation: Expression varies with androgen sensitivity (UniProt). Evidence: UniProt Q9Y6I8, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the peroxisomes. In addition localized to the…, Datasheet A13147, PMC11077113. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PXMP4/immunohistochemistry-ihc-guide.