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PCMT1 / Protein-L-isoaspartate(D-aspartate) O-methyltransferase · IHC design guide
Design Immunohistochemistry for PCMT1
Plan chromogenic PCMT1 IHC around its general cytoplasmic tissue pattern (HPA tissue IHC). Use reported positive neuronal and glandular cells and vaginal squamous epithelial cells with no detected staining to help assess the result (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PCMT1 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 | Cytoplasmic tissue staining (HPA tissue IHC); cytosolic protein (UniProt) | |
| Staining pattern | General cytoplasmic staining across varied cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A04579-2) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Vagina |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A04579-2) | |
| Caveat | Staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | Two isoforms; epitope coverage unspecified (UniProt) |
Section 1
Recommended PCMT1 IHC & IF Protocols
The catalog antibody protocol and two published PCMT1 IHC protocols provide starting conditions for paraffin sections (datasheet A04579-2; PMC9459589; PMC12000267).
| Sample | Paraffin-embedded human thyroid papillary carcinoma tissue; fixative not specified (datasheet A04579-2) |
| Fixation | Image fixative and duration unreported (datasheet A04579-2); 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 A04579-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A04579-2) |
| Primary antibody | Rabbit anti-PCMT1, 2-5 μg/ml (datasheet A04579-2) |
| Primary incubation | Overnight at 4 °C (datasheet A04579-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A04579-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PCMT1-positive staining in lymphoid tissue of appendix (HPA tissue IHC: Medium). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet A04579-2). The cervical tissue protocol used microwave-heated sodium citrate instead (PMC9459589).
Section 2
What Is the Expected PCMT1 Staining Pattern?
PCMT1 should give predominantly cytoplasmic staining in paraffin-section IHC, consistent with its cytosolic localization and lack of a transmembrane segment (UniProt P22061; HPA: general cytoplasmic expression). Expect signal in neuronal cells, Purkinje cells, cardiomyocytes, hematopoietic cells, and some glandular cells (HPA: medium staining in the listed tissues). The tissue IHC profile is Approved, with medium consistency between staining and RNA expression (HPA: tissue IHC reliability).
| Cytoplasmic signal in cerebral cortex neurons or cerebellar Purkinje cells. | This fits the expected compartment and reported medium staining in those cells (UniProt P22061: cytosol; HPA: cerebral cortex and cerebellum IHC). Score the stained cells and their intensity; do not treat every unstained neighboring cell as a failed reaction. |
| Strong, sharply nuclear or membrane-restricted signal with little cytoplasmic staining. | That distribution conflicts with the supported cytosolic pattern (UniProt P22061: cytosol, no transmembrane segment; HPA: ICC-IF cytosol supported). Review morphology and control sections, then reassess staining specificity before calling it PCMT1. |
| Signal concentrated in a cell population outside the reported pattern. | Compare cell identity and compartment with the HPA tissue images; HPA reports selected cell populations, including breast glandular cells and bone-marrow hematopoietic cells (HPA: tissue IHC). An unexpected pattern warrants checks for antibody cross-reactivity or endogenous chromogenic activity (standard IHC practice). |
| Diffuse color covers tissue and background, obscuring cell boundaries. | A field-wide deposit cannot establish cytoplasmic PCMT1 staining (HPA: general cytoplasmic expression). Check the antibody-omission control and detection background, and compare a known-positive section processed in the same run (standard IHC practice). |
| No signal in cerebral cortex neurons or cerebellar Purkinje cells. | Those populations have reported medium staining, so a blank result calls for a technical review (HPA: cerebral cortex and cerebellum IHC). Check tissue integrity, retrieval, antibody application, detection, and counterstain on the same run (standard IHC practice). |
💡Expected PCMT1 appearanceA convincing positive is predominantly cytoplasmic staining, reaching the reported medium level in an HPA-listed cell population; a strong nuclear or membrane-only pattern, or uniform color without recognizable cells, is suspect (UniProt P22061: cytosol; HPA: tissue IHC; standard IHC practice).
| Compartment and topology | PCMT1 is assigned to the cytosol and has no transmembrane segment (UniProt P22061). Use cytoplasmic localization as the primary pattern check; membrane-restricted staining requires independent scrutiny. |
| Choice of comparison tissue | HPA reports medium staining in several cell populations, including cortex neurons, Purkinje cells, cardiomyocytes, and breast glandular cells (HPA: tissue IHC). Vaginal squamous epithelium is reported as not detected; that observation is not a universal negative-control claim (HPA: vagina IHC). |
| Strength of validation | The tissue profile is Approved but has medium consistency with RNA data, while HPA003239 is Approved for IHC (HPA: tissue reliability; HPA: antibody validation). Treat an unexpected distribution as a finding to verify rather than definitive PCMT1 expression. |
| IF/ICC: where should signal appear? | Predominantly in the cytosol: HPA calls cytosol its supported main location and lists ICC-IF images in A-431, U-251MG, and U2OS (HPA: subcellular). Those images support a compartment comparison; they do not establish an IHC staining level in those cell lines. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive tissue is blank. | The expected cell population may be absent from the section, or a run step may have failed (HPA: reported positive populations; standard IHC practice). | Confirm the cells are present, then review retrieval, primary-antibody application, detection reagents, and a same-run positive control (standard IHC practice). |
| Staining is nuclear or outlines cell membranes. | The dominant pattern is inconsistent with cytosolic PCMT1 (UniProt P22061; HPA: supported cytosol). | Check localization against an HPA-listed positive tissue and assess antibody-omission and detection controls before scoring the signal (HPA: tissue IHC; standard IHC practice). |
| Color appears in the antibody-omission control. | The signal may arise from endogenous detection activity or the detection system (standard chromogenic IHC practice). | Review the appropriate endogenous-activity block and detection reagents; interpret the test slide only after the control background is resolved (standard chromogenic IHC practice). |
| Diffuse haze obscures cytoplasmic detail. | Nonspecific background or excessive detection can obscure cell-level localization (standard IHC practice). | Compare control sections, then optimize blocking, washing, and antibody concentration within the validated IHC workflow (standard IHC practice). |
| Vaginal squamous epithelium stains strongly. | HPA reports PCMT1 as not detected in that cell population; strong staining is discordant with that observation (HPA: vagina IHC). | Check the compartment and controls, then seek independent support before assigning the staining to PCMT1 (HPA: cytoplasmic profile; standard IHC practice). |
| Only faint signal appears in an HPA-listed positive population. | Reported medium staining is a reference observation, not a guaranteed intensity in every section or run (HPA: tissue IHC). | Compare a same-run positive section and review tissue morphology, retrieval, antibody application, and detection before interpreting intensity differences (standard IHC practice). |
Experiment evidence
IHC & IF images showing PCMT1 staining
A04579-2 · IHCIHC analysis of PCMT1 using anti-PCMT1 antibody (A04579-2). PCMT1 was detected in a paraffin-embedded section of human thyroid papillary car
A04579-2 · IHCIHC analysis of PCMT1 using anti-PCMT1 antibody (A04579-2). PCMT1 was detected in a paraffin-embedded section of human glioblastoma tissue.
A04579-2 · IFIF analysis of PCMT1 using anti-PCMT1 antibody (A04579-2). PCMT1 was detected in an immunocytochemical section of SiHa cells. Enzyme antigen
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000120265-PCMT1/tissue/cerebral+cortex#imid_1112600
HPA · RectumHuman Protein Atlas IHC, Rectum. Source: https://www.proteinatlas.org/ENSG00000120265-PCMT1/tissue/rectum#imid_1112494
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000120265-PCMT1/tissue/liver#imid_1112535
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000120265-PCMT1/tissue/kidney#imid_1112528
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA003239; green = PCMT1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA003239; green = PCMT1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PCMT1 IHC & IF
🧪Run cerebellum first and look for staining in Purkinje cells (HPA: Medium in cerebellar Purkinje cells). Run vagina as the negative tissue (HPA: Not detected in vaginal squamous epithelial cells); on the cerebellum slide, treat morphologically intact cells without staining as an internal background reference, without assuming a particular neighboring cell type is PCMT1-negative.
Positive control tissue: Appendix (Lymphoid tissue, HPA Medium)
Negative control tissue: Vagina (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PCMT1 in A-431, U-251MG, U2OS, with annotated localisation: Cytosol (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a rabbit isotype control matched to the primary antibody, and PCMT1 knockout tissue or cells as a biological negative (selected caption: rabbit anti-PCMT1; standard IHC practice). Quench endogenous peroxidase for chromogenic detection, and check cerebellar autofluorescence if using IF (standard IHC/IF practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected A04579-2 paraffin-section caption does not state the fixative (selected caption). That caption uses heat retrieval in EDTA at pH 8.0, but does not establish that retrieval is required (selected caption). The evidence does not establish whether frozen sections or IF are easier; ICC-IF images support a cytosolic location, while neuronal lipofuscin may complicate cerebellar IF interpretation (HPA: Cytosol supported; standard IF practice).
HPA tissue IHC evidence for PCMT1
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 | Lymphoid tissue | Medium | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Vagina | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PCMT1 IHC Tips
Troubleshoot PCMT1 staining in paraffin sections using the catalog antibody’s tissue image and documented cytosolic expression (datasheet A04579-2; HPA tissue IHC; UniProt P22061).
What retrieval conditions should I start with for weak PCMT1 staining in paraffin sections?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A04579-2). The catalog image used this condition to detect PCMT1 in human thyroid papillary carcinoma tissue, followed by 2 μg/ml primary antibody overnight at 4°C (datasheet A04579-2). If staining is weak, check that sections were fully deparaffinized and that the retrieval bath reached and maintained the intended temperature (standard IHC practice). Compare a documented positive tissue alongside the test section, keeping retrieval and detection conditions matched (HPA tissue IHC; standard IHC practice). Adjust heating duration on adjacent sections only after checking these steps, because excessive retrieval can damage tissue morphology (standard IHC practice).
How should I troubleshoot fixation when PCMT1 staining varies between paraffin blocks?
PCMT1-specific sensitivity to fixation is unknown from the supplied evidence, and the catalog tissue caption does not state its fixative (datasheet A04579-2). Record each block’s fixative, fixation interval, and processing history before comparing staining intensity across specimens (standard IHC practice). Process a documented positive tissue beside the affected sections, using the same EDTA pH 8.0 retrieval and detection run (datasheet A04579-2; HPA tissue IHC; standard IHC practice). If differences persist, compare adequately preserved regions and repeat staining on adjacent sections to distinguish block-dependent signal loss from a run problem (standard IHC practice). Do not assign a PCMT1-specific fixation effect from tissue staining patterns alone (HPA tissue IHC).
Where should convincing PCMT1 chromogenic staining appear within positive cells?
Expect predominantly cytoplasmic staining, consistent with PCMT1’s cytosolic annotation and the reported general cytoplasmic tissue pattern (UniProt P22061; HPA tissue IHC). PCMT1 has no annotated transmembrane segment or signal peptide, so a sharply membrane-restricted pattern needs independent verification (UniProt P22061 topology and processing). Examine the DAB signal within intact cells against the counterstained nuclei, rather than scoring pigment in lumina or damaged areas as intracellular PCMT1 (standard IHC practice). HPA reports medium staining in cerebellar Purkinje cells and cerebral cortex neuronal cells, which can provide cellular context for a comparison section (HPA tissue IHC). Interpret unexpected nuclear-only signal cautiously and check controls before assigning a new localisation (UniProt P22061; standard IHC practice).
Can this stain distinguish PCMT1 isoforms or reveal epitope masking?
The supplied record lists 2 PCMT1 isoforms, but the catalog image does not identify the antibody’s epitope or establish isoform selectivity (UniProt P22061; datasheet A04579-2). Treat positive DAB staining as PCMT1 immunoreactivity without assigning it to isoform 1 or 2 (UniProt P22061; standard IHC interpretation). If signal changes with retrieval, compare adjacent sections under matched detection conditions before attributing the change to epitope exposure (standard IHC practice). PCMT1 has one annotated modified residue, N-acetylalanine at position 2, but the supplied evidence does not show whether that residue affects antibody binding (UniProt P22061). An independently mapped epitope would be needed to assess isoform coverage or a modification-dependent staining difference (standard antibody validation practice).
How can I adapt PCMT1 localisation checks to multiplex immunofluorescence?
For a separate IF experiment, pair PCMT1 with a marker identifying the expected cell type, such as a neuronal marker when examining the HPA-reported neuronal staining context (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores and inspect an unstained section so tissue autofluorescence is not mistaken for PCMT1 signal (standard IF practice). PCMT1 is cytosolic and lacks an annotated transmembrane segment, so permeabilisation must allow antibody access to the cytosol while preserving cell outlines (UniProt P22061; standard IF practice). HPA reports supported cytosolic localisation from ICC/IF, providing a compartment-level comparison for the multiplex image (HPA subcellular). Validate the IF antibody and fixation conditions separately; the paraffin-section caption reports neither IF performance nor its fixative (datasheet A04579-2).
What should I check when diffuse DAB obscures PCMT1 cytoplasmic staining?
First compare a no-primary control with the stained section to identify signal arising from detection reagents or endogenous tissue activity (standard IHC practice). The catalog image used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and an HRP/DAB detection sequence (datasheet A04579-2). Check peroxidase blocking, washing, and DAB development on matched sections before changing the primary antibody conditions (standard IHC practice). If background remains, compare shorter development or a lower primary concentration while retaining a documented positive tissue in the same run (standard IHC practice; HPA tissue IHC). Assess cytoplasmic signal in intact cells separately from diffuse staining over damaged or poorly preserved regions (UniProt P22061; standard IHC practice).
How should I quantify PCMT1 IHC across samples with different cell mixtures? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and tissue area before scoring, because HPA reports PCMT1 staining across several cell types and tissues (HPA tissue IHC; standard IHC practice). For intact target cells, record the percentage positive and intensity to calculate an H-score; use positive-cell density per mm² when cell abundance is the comparison of interest (standard IHC practice). Normalize the readout to eligible cells or evaluable tissue area, and exclude necrotic and damaged regions consistently (standard IHC practice). Keep EDTA pH 8.0 retrieval and DAB acquisition settings matched across the compared sections (datasheet A04579-2; standard IHC practice). Report compartment-specific cytoplasmic scoring and the threshold used to call a cell positive (UniProt P22061; standard IHC practice).
How can I distinguish true PCMT1 positivity from staining artefacts?
A credible positive has intracellular cytoplasmic signal in intact cells, matching PCMT1’s cytosolic annotation and HPA’s general cytoplasmic tissue pattern (UniProt P22061; HPA tissue IHC). Check that the stained cell type fits the comparison tissue: HPA reports medium staining in cerebellar Purkinje cells but no detection in vaginal squamous epithelial cells (HPA tissue IHC). Treat isolated membrane-only or nuclear-only staining as unresolved until supported by controls, since neither is the supplied principal localisation (UniProt P22061; HPA subcellular). Exclude edge staining and necrotic areas, and use a no-primary control to assess endogenous peroxidase or detection background (standard IHC practice). Interpret intensity conservatively because HPA rates agreement between antibody staining and RNA expression as medium (HPA tissue IHC).
Boster reagents
Best PCMT1 / Protein-L-isoaspartate(D-aspartate) O-methyltransferase IHC Antibodies
The anti-PCMT1 antibody has paraffin-section IHC images from human thyroid papillary carcinoma, human glioblastoma, and rat brain, plus IF data from SiHa cells (catalog image captions).
Real IHC data
Anti-PCMT1 Antibody ®
Cat # A04579-2
A04579-2 is shown in IHC on paraffin sections of human thyroid papillary carcinoma, human glioblastoma, and rat brain (catalog IHC captions). A04579-2 is also listed for IF/ICC and shown in SiHa cells (catalog applications and IF caption).
Which to pick: For tissue IHC, choose A04579-2: its rabbit antibody is shown on paraffin sections at 2 μg/ml; the fixative is unreported (catalog IHC captions). For IF/ICC, choose A04579-2 at 5 μg/ml for SiHa cells (catalog IF caption). For cross-species planning, A04579-2 lists Human, Mouse, and Rat reactivity, but its IHC images cover Human and Rat only; clonality is unreported (catalog reactivity, IHC captions, and clone field).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P22061 (PIMT_HUMAN, Protein-L-isoaspartate(D-aspartate) O-methyltransferase).
- Human Protein Atlas. PCMT1 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. PCMT1 subcellular location (ICC-IF): Localized to the cytosol..
- Human Protein Atlas. PCMT1 antibody validation summary (1 antibodies).
- [Prognostic Value of PCMT1 Expression in Gastric Cancer and Its Regulatory Effect on Spindle Assembly Checkpoints]. Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition 2023 — PMC10752781.
- Elevated expression of protein-L-isoaspartate O-methyltransferase-1 (PCMT1) in cervical cancer. Translational cancer research 2022 — PMC9459589.
- PCMT1 Is a Potential Prognostic Biomarker and Is Correlated with Immune Infiltrates in Breast Cancer. BioMed research international 2022 — PMC9078795.
- PCMT1 as a prognostic marker in breast cancer. Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico 2025 — PMC12000267.
- PubMed PMID:2684970 — UniProt-cited evidence.
- PubMed PMID:1339271 — UniProt-cited evidence.
- PubMed PMID:7592526 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PCMT1 (Protein-L-isoaspartate(D-aspartate) O-methyltransferase). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC); cytosolic protein (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A04579-2). Validated IHC antibody: A04579-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Lymphoid tissue); negative Vagina. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human thyroid papillary carcinoma tissue; fixative not specified (datasheet A04579-2); 2. Fixation: Image fixative and duration unreported (datasheet A04579-2); 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 A04579-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A04579-2); 8. Primary antibody: Rabbit anti-PCMT1, 2-5 μg/ml (datasheet A04579-2); 9. Primary incubation: Overnight at 4 °C (datasheet A04579-2). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A04579-2); Caveat: Staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: Two isoforms; epitope coverage unspecified (UniProt); Regulation: Low tissue specificity (HPA tissue RNA). Evidence: UniProt P22061, HPA tissue IHC · Approved, HPA ICC-IF · cytosol., Datasheet A04579-2, PMC9459589, PMC12000267. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PCMT1/immunohistochemistry-ihc-guide.