This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
MIPEP / Mitochondrial intermediate peptidase · IHC design guide
Design Immunohistochemistry for MIPEP
Plan chromogenic IHC for MIPEP in paraffin sections using the catalog antibody’s 2–5 μg/ml range (datasheet A05926-1). Compare granular cytoplasmic staining in kidney tubule cells with adipocytes, where staining was not detected (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
MIPEP 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 | Granular cytoplasm (HPA tissue IHC); mitochondrial matrix (UniProt) | |
| Staining pattern | General granular cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A05926-1) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+2 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Low tissue RNA specificity (HPA tissue RNA) | |
| Isoform / epitope | No isoforms annotated; mature chain begins at 36 (UniProt) |
Section 1
Recommended MIPEP IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet: A05926-1) with the published canine mammary tumour IHC protocol below (PMC3750412).
| Sample | Paraffin-embedded human placenta tissue; fixative not specified (datasheet A05926-1) |
| Fixation | Image fixative and duration unreported (datasheet A05926-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A05926-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A05926-1) |
| Primary antibody | Rabbit anti-MIPEP, 2-5 μg/ml (datasheet A05926-1) |
| Primary incubation | Overnight at 4 °C (datasheet A05926-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A05926-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | MIPEP-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression with a granular pattern. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet: A05926-1); the published canine protocol used citrate pH 6.0 (PMC3750412).
Section 2
What Is the Expected MIPEP Staining Pattern?
MIPEP is a mitochondrial matrix protein with no transmembrane segment (UniProt Q99797: localization and topology). In paraffin-section IHC, expect granular cytoplasmic staining (HPA: tissue IHC profile), especially in kidney tubular cells, intestinal glandular cells, and bone marrow hematopoietic cells (HPA: High). HPA rates the tissue IHC profile Approved, with medium consistency between antibody staining and RNA expression (HPA: reliability).
| Granular cytoplasmic signal in kidney tubules or duodenal glands (HPA: High; granular cytoplasmic profile). | This fits the reported IHC pattern and mitochondrial matrix location (HPA: tissue IHC profile; UniProt Q99797: localization). Score the named cells and the granular compartment together; a tissue-wide positive label alone loses that distinction (general IHC interpretation). |
| Dominant nuclear or cell-surface signal, with little granular cytoplasmic staining. | That compartment conflicts with the reported mitochondrial localization and granular IHC profile (UniProt Q99797: localization; HPA: tissue IHC profile). Treat it as suspect staining and compare it with a known-positive tissue and detection controls before assigning MIPEP (general IHC practice). |
| Strong staining in adipocytes, ovarian stromal cells, or soft-tissue fibroblasts (HPA: Not detected). | These are reported negative cell populations, so strong signal warrants a specificity check (HPA: tissue IHC). Cross-reactivity or endogenous chromogen activity are possibilities, not diagnoses from appearance alone; compare antibody and detection controls (general IHC practice). |
| Diffuse, uniform color obscures cell borders and any granular pattern. | The expected tissue profile is granular cytoplasmic staining (HPA: tissue IHC profile). Uniform haze limits compartment scoring; inspect background in adjacent cells and a no-primary control, then review blocking, washes, and detection chemistry (general IHC practice). |
| No signal in kidney tubular cells or small-intestinal glandular cells (HPA: High). | An absent signal in a reported high-staining population makes that run hard to interpret (HPA: tissue IHC). Check tissue preservation, primary-antibody and detection steps, and an established positive control before calling the specimen negative (general IHC practice). |
💡Expected MIPEP appearanceCall an IHC result positive when named high-staining cells show clear granular cytoplasmic signal—such as kidney tubular cells (HPA: High; granular profile)—while dominant nuclear, surface, or uniform background color is suspect (UniProt Q99797: mitochondrial matrix; general IHC interpretation).
| Compartment and topology | MIPEP resides in the mitochondrial matrix and has no transmembrane segment (UniProt Q99797). Granular cytoplasmic IHC is therefore coherent with its location (HPA: tissue IHC profile); a membrane outline is not the reported pattern. |
| Cell-specific tissue expression | HPA reports High staining in several glandular populations, kidney tubules, and bone marrow hematopoietic cells, but Not detected in adipocytes, ovarian stromal cells, and soft-tissue fibroblasts (HPA: tissue IHC). Interpret each cell population separately. |
| Strength of IHC evidence | The tissue IHC profile is Approved, with medium consistency between antibody staining and RNA expression (HPA: reliability). The listed staining levels guide control selection; they do not make every discrepant specimen a technical failure. |
| Processing and epitope position | The annotated mature chain spans residues 36–713 (UniProt Q99797: processing). The payload gives no antibody epitope, so it cannot establish whether maturation affects recognition by the IHC-validated antibody; avoid an epitope-specific prediction. |
| Does IF/ICC support the compartment call? | Yes: HPA reports mitochondrial localization by ICC-IF and lists A-431, U-251MG, and U2OS image lines (HPA: subcellular). This supports the location interpretation; it does not supply an IF protocol or establish how any paraffin section will stain. |
| Situation | Likely cause | Next action |
|---|---|---|
| A reported high-staining cell population is blank (HPA: High). | The run may have a primary-antibody, detection, or tissue-quality problem (general IHC practice); HPA staining levels alone cannot identify which. | Check an established positive section processed in the same run, reagent steps, and tissue integrity before scoring the specimen negative (general IHC practice). |
| Color is concentrated in nuclei or along cell borders. | This differs from mitochondrial matrix localization and the granular cytoplasmic profile (UniProt Q99797; HPA: tissue IHC). | Compare compartment staining in a known-positive section and review antibody and detection controls; withhold a MIPEP-positive call if the discordant pattern persists (general IHC practice). |
| Staining is prominent in HPA-listed negative cell populations. | Specificity or endogenous detection activity may be involved (general IHC practice); HPA reports these populations as Not detected (HPA: tissue IHC). | Run a no-primary detection control and compare the suspected cells with reported high-staining cells in the same workflow (general IHC practice; HPA: tissue IHC). |
| Diffuse chromogen obscures the expected granules (HPA: granular profile). | Background from the staining workflow can mask cell-level localization (general IHC practice). The appearance alone does not identify its source. | Inspect the no-primary control, then review blocking, wash steps, and detection development against the validated workflow (general IHC practice). |
| Some glandular cells stain while neighboring cells do not. | HPA reports cell-specific levels across tissues, with low tissue RNA specificity overall (HPA: tissue IHC); uneven color alone does not establish assay failure. | Score the named cell population and compartment, and compare an internal or parallel positive population before changing assay conditions (HPA: tissue IHC; general IHC practice). |
| The observer wants to infer a paraffin-section result from IF images. | HPA ICC-IF supports mitochondrial localization, while HPA tissue IHC separately describes granular cytoplasmic staining (HPA: subcellular; tissue IHC). | Use the IF result to check compartment plausibility, then judge IHC against its own tissue profile and same-run controls (HPA: subcellular; tissue IHC; general IHC practice). |
Experiment evidence
IHC & IF images showing MIPEP staining
A05926-1 · IHCIHC analysis of MIPEP using anti-MIPEP antibody (A05926-1). MIPEP was detected in a paraffin-embedded section of human placenta tissue. Heat
A05926-1 · IHCIHC analysis of MIPEP using anti-MIPEP antibody (A05926-1). MIPEP was detected in a paraffin-embedded section of human placenta tissue. Heat
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000027001-MIPEP/tissue/cerebral+cortex#imid_8168168
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000027001-MIPEP/tissue/colon#imid_8175294
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000027001-MIPEP/tissue/liver#imid_8175287
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000027001-MIPEP/tissue/kidney#imid_8175288
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA030676; green = MIPEP, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA030676; green = MIPEP, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for MIPEP IHC & IF
🧪Run kidney first and expect staining in tubular cells (HPA: High in kidney cells in tubules). Run adipose tissue as a negative comparator (HPA: Not detected in adipocytes); on the kidney slide, use visibly unstained neighboring cells to judge background without assuming a specific renal cell type is MIPEP-negative.
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show MIPEP in A-431, U-251MG, U2OS, with annotated localisation: Mitochondria (enhanced) (HPA subcellular).
Technical controls: Include a no-primary secondary-only control, a rabbit IgG isotype control matched to the catalog primary’s clonality where known, and a MIPEP knockout or peptide-block control (selected-SKU tissue-IHC caption: rabbit primary). Quench endogenous peroxidase for chromogenic detection; if using biotin-based detection, block endogenous biotin in kidney tissue (standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the exact selected-SKU paraffin-section caption leaves the fixative unreported (selected-SKU tissue-IHC caption: fixative not stated). Heat retrieval in EDTA at pH 8.0 is a documented IHC starting condition, but its necessity for kidney has not been established (selected-SKU tissue-IHC caption: placenta retrieval). The supplied evidence does not establish whether frozen sections or IF are easier; IF can assess the expected mitochondrial localization (HPA subcellular: mitochondria), while biotin-based kidney IHC requires attention to endogenous biotin (standard IHC practice).
HPA tissue IHC evidence for MIPEP
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 |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
Section 3
Advanced MIPEP IHC Tips
These questions address chromogenic MIPEP staining in paraffin sections, with one companion question on IF/ICC and its separate validation needs.
Which retrieval conditions should I try when MIPEP staining is weak in paraffin sections?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A05926-1). The selected antibody stained human placenta after that retrieval, followed by 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet A05926-1). If staining remains weak, vary heating time on matched sections while keeping section thickness, antibody concentration and DAB development constant (standard IHC practice). Compare granular cytoplasmic signal with no-primary controls before accepting a stronger condition, since excessive retrieval can damage morphology or raise background (HPA: general cytoplasmic granular pattern; standard IHC practice). Record the retrieval time and cooling conditions so the result can be reproduced (standard IHC practice).
How should I assess whether fixation is suppressing MIPEP staining?
Target-specific MIPEP sensitivity to fixation is unknown: the selected paraffin-section caption does not state a fixative (datasheet A05926-1). Record the fixative and exposure time for each specimen, then compare sections processed together with the same EDTA pH 8.0 retrieval and antibody conditions (datasheet A05926-1; standard IHC practice). Include a previously staining control section in each run to distinguish a specimen-processing problem from a failed detection run (standard IHC practice). Assess preserved morphology alongside granular cytoplasmic signal; tissue staining patterns alone cannot establish a MIPEP-specific fixation effect (HPA: general cytoplasmic granular pattern; standard IHC practice). Avoid assigning a fixation threshold without a direct comparison under controlled conditions (standard IHC practice).
What cellular pattern should count as plausible MIPEP staining?
Expect a granular cytoplasmic pattern consistent with mitochondrial matrix localisation, while remembering that chromogenic IHC does not resolve the matrix itself (HPA: general cytoplasmic granular pattern; UniProt Q99797: mitochondrial matrix; standard IHC practice). MIPEP has no annotated transmembrane segment, so a crisp cell-surface outline is discordant with the recorded topology (UniProt Q99797 topology). Inspect staining within identifiable cells at sufficient magnification and compare its distribution with a no-primary section (standard IHC practice). Kidney tubular cells and several glandular cell populations have high reported IHC staining and can provide contextual comparisons (HPA: kidney cells in tubules; breast glandular cells). Treat diffuse extracellular deposit or isolated nuclear staining as a reason to investigate specificity (standard IHC practice).
Could processing or epitope position explain discordant MIPEP IHC results?
MIPEP is recorded as a 713-residue precursor with a mature chain spanning residues 36–713, and no isoforms are annotated (UniProt Q99797 processing and isoforms). Check the antibody's documented immunogen or epitope before attributing discordance to processing; the supplied tissue-IHC caption does not identify that epitope (datasheet A05926-1). An epitope within the removed amino-terminal region could behave differently from one within the mature chain, but that possibility requires epitope information and experimental confirmation (UniProt Q99797 processing; standard IHC practice). MIPEP has an annotated acetyllysine at residue 126; its effect on this antibody's staining is unknown (UniProt Q99797 modified residues). Compare matched sections under one retrieval and detection workflow before invoking an epitope explanation (standard IHC practice).
How can IF/ICC help evaluate a puzzling MIPEP IHC pattern?
Use IF/ICC as a separate validation experiment when chromogenic IHC shows a disputed compartment or cell population (standard IHC/IF practice). Multiplex MIPEP with a marker for the expected cell type and a mitochondrial marker in distinguishable channels; mitochondrial localisation has independent subcellular support (HPA: mitochondria enhanced; standard IF practice). Choose fluorophores and controls after checking specimen autofluorescence in each channel, because background can mimic punctate signal (standard IF practice). MIPEP resides in the matrix, so antibody access requires permeabilisation across mitochondrial membranes; optimise this against preserved mitochondrial morphology and the antibody's epitope accessibility (UniProt Q99797: mitochondrial matrix; standard IF practice). Do not transfer the paraffin-section retrieval or incubation conditions to IF/ICC as a validated protocol (datasheet A05926-1; standard IF practice).
How do I reduce granular background without losing plausible MIPEP signal?
First compare no-primary and secondary-only controls with the test section to locate background from detection reagents (standard IHC practice). In a peroxidase/DAB workflow, apply and verify an endogenous peroxidase block before interpreting brown deposits; this is a general chromogenic step, not evidence specific to MIPEP (standard IHC practice). The selected caption used 10% goat serum and 2 μg/ml primary antibody overnight at 4°C, providing a documented starting condition (datasheet A05926-1). If controls are clean but nonspecific staining persists, optimise primary concentration and washing on adjacent sections while preserving the EDTA pH 8.0 retrieval baseline (datasheet A05926-1; standard IHC practice). Judge retained signal by its intracellular granular pattern and intact morphology (HPA: general cytoplasmic granular pattern; standard IHC practice).
What is a defensible way to quantify MIPEP across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and anatomical region before scoring, because MIPEP staining differs among reported tissue compartments (HPA: tissue IHC profile; standard IHC practice). For cell-based comparisons, report the percentage of positive cells and an H-score using fixed intensity categories; for spatial counts, report positive cells per mm² of viable tissue (standard IHC practice). Normalise each score to the number of evaluable cells or the measured viable area, and keep retrieval, antibody incubation, DAB development and image settings consistent (standard IHC practice). Exclude folds, edges and necrotic areas using a prespecified rule (standard IHC practice). Interpret small differences cautiously because HPA rates agreement between antibody staining and RNA expression as medium (HPA: Approved, medium consistency).
When should an apparent MIPEP-positive cell be considered artefactual?
A credible positive shows intracellular granular cytoplasmic staining in an intact cell, consistent with the reported pattern and mitochondrial matrix location (HPA: general cytoplasmic granular pattern; UniProt Q99797: mitochondrial matrix). Staining confined to nuclei, cell borders, section edges or necrotic material warrants review against morphology and control slides (UniProt Q99797 topology; standard IHC practice). Check the cell identity: kidney tubular cells are reported high, whereas adipocytes and ovarian stromal cells are reported undetected in the HPA tissue survey (HPA: kidney tubules high; adipocytes and ovarian stroma not detected). Brown signal that survives omission of primary antibody points toward detection background, including endogenous peroxidase, rather than demonstrated MIPEP binding (standard IHC practice). Resolve unexpected positives with an independent specificity control before making a biological claim (standard IHC practice).
Boster reagents
Best MIPEP / Mitochondrial intermediate peptidase IHC Antibodies
The catalog antibody A05926-1 has real IHC data from paraffin sections of human placenta and thyroid papillary carcinoma (IHC image captions). No IF data are shown (catalog: IF images absent).
Real IHC data
Anti-MIPEP Antibody ®
Cat # A05926-1
A05926-1 was used for IHC on paraffin sections of human placenta and thyroid papillary carcinoma (IHC image captions). Its listed reactivity is human, mouse and rat, while the supplied IHC images show human tissue only (catalog reactivity; IHC image captions).
Which to pick: Choose A05926-1 for paraffin-section IHC: its rabbit antibody has an IHC application listing and was used at 2 μg/ml after EDTA pH 8.0 heat retrieval in the supplied images; the fixative is unreported (catalog; IHC image captions). There is no IF/ICC-validated SKU in this payload (catalog applications; IF images absent). For mouse or rat tissue, A05926-1 lists reactivity with those species, but its supplied IHC evidence is human tissue, so validate staining in the intended species (catalog reactivity; IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q99797 (MIPEP_HUMAN, Mitochondrial intermediate peptidase).
- Human Protein Atlas. MIPEP tissue IHC expression (reliability: Approved).
- Human Protein Atlas. MIPEP subcellular location (ICC-IF): Localized to the mitochondria..
- Human Protein Atlas. MIPEP antibody validation summary (3 antibodies).
- ESF1 and MIPEP proteins promote estrogen receptor-positive breast cancer proliferation and are associated with patient prognosis. Clinical proteomics 2024 — PMC11247778.
- Five markers useful for the distinction of canine mammary malignancy. BMC veterinary research 2013 — PMC3750412.
- PubMed PMID:9073519 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15057823 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for MIPEP (Mitochondrial intermediate peptidase). Expected localisation Granular cytoplasm (HPA tissue IHC); mitochondrial matrix (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A05926-1). Validated IHC antibody: A05926-1 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human placenta tissue; fixative not specified (datasheet A05926-1); 2. Fixation: Image fixative and duration unreported (datasheet A05926-1); 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: EDTA pH 8.0 (datasheet A05926-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A05926-1); 8. Primary antibody: Rabbit anti-MIPEP, 2-5 μg/ml (datasheet A05926-1); 9. Primary incubation: Overnight at 4 °C (datasheet A05926-1). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: No isoforms annotated; mature chain begins at 36 (UniProt); Regulation: Low tissue RNA specificity (HPA tissue RNA). Evidence: UniProt Q99797, HPA tissue IHC · Approved, HPA ICC-IF · mitochondria., Datasheet A05926-1, PMC3750412. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/MIPEP/immunohistochemistry-ihc-guide.