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CPS1 / Carbamoyl-phosphate synthase [ammonia], mitochondrial · IHC design guide
Design Immunohistochemistry for CPS1
Plan CPS1 staining in paraffin sections using liver hepatocytes as a positive reference and granular cytoplasmic staining as the expected pattern (HPA tissue IHC). The guide covers fixation consistency, controls and interpretation of chromogenic signal.
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CPS1 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 in hepatocytes and small intestine (HPA tissue IHC) | |
| Staining pattern | Granular cytoplasmic staining in hepatocytes and intestinal endocrine cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01320-2) | |
| Positive control | Duodenum+2 more · see all | |
| Negative control | Adipose tissue+4 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 | Endogenous peroxidase can add DAB signal in liver (standard IHC practice) | |
| Regulation | Liver-enriched expression (HPA RNA specificity) | |
| Isoform / epitope | 3 isoforms; mature chain begins at residue 39; epitope coverage is unknown (UniProt) |
Section 1
Recommended CPS1 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol with published CPS1 staining in gastric tissue (PMC8045184) and liver sections (PMC8888708).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A01320-2) |
| Fixation | Image fixative and duration unreported (datasheet A01320-2); 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 A01320-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01320-2) |
| Primary antibody | Rabbit anti-CPS1, 2-5 μg/ml (datasheet A01320-2) |
| Primary incubation | Overnight at 4 °C (datasheet A01320-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A01320-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CPS1-positive staining in endocrine cells of duodenum (HPA tissue IHC: High). HPA tissue profile: Selective granular cytoplasmic expression in small intestine and hepatocytes. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet A01320-2); citrate retrieval was used for gastric tissue (PMC8045184).
Section 2
What Is the Expected CPS1 Staining Pattern?
CPS1 should show selective granular cytoplasmic staining in hepatocytes and small-intestinal endocrine cells (HPA tissue IHC: Enhanced; high in these cells). Its mitochondrial localization fits that pattern (UniProt P31327 localization). UniProt also reports nucleolar and hepatocyte cell-surface localization, despite no transmembrane segment; those annotations do not change the expected dominant IHC pattern (UniProt P31327 localization and topology).
| Strong, granular cytoplasmic staining in hepatocytes, with staining in small-intestinal endocrine cells. | This matches the reported positive cell types and pattern (HPA tissue IHC: high in hepatocytes and small-intestinal endocrine cells; Enhanced). Judge the fraction of cells and intensity alongside localization; signal elsewhere in the section should not be counted as equivalent CPS1 staining (standard IHC interpretation). |
| Predominantly nuclear, nucleolar, or membrane-only staining, without the expected granular cytoplasm. | This is discordant with the principal tissue IHC pattern and warrants an artefact check (HPA tissue IHC: selective granular cytoplasm). Do not automatically discard focal nucleolar or hepatocyte surface signal: both have localization support, while nucleolar evidence comes chiefly from ICC-IF (UniProt P31327 localization; HPA subcellular ICC-IF: supported nucleoli). |
| Strong staining in a cell population listed as undetected, such as adipocytes in adipose tissue. | Treat this as a possible false positive, including cross-reactivity or endogenous detection activity, until controls resolve it (HPA tissue IHC: adipocytes not detected; standard IHC practice). A tissue-level negative comparison must be assessed in the specified cell type, not inferred from every cell in that tissue. |
| Broad, diffuse color over tissue, stroma, and blank areas, with little cell-level contrast. | This does not reproduce selective granular staining (HPA tissue IHC: selective granular cytoplasm). Background can arise from nonspecific binding, detection chemistry, or incomplete washing (standard IHC practice). Assess clean areas and a negative reagent control before assigning CPS1 positivity. |
| No convincing signal in hepatocytes on a liver section. | A failed positive control is more likely than an interpretable negative result, because hepatocytes are reported high (HPA tissue IHC: high in hepatocytes). Check tissue integrity, the IHC-validated antibody and detection controls, and the laboratory's established paraffin-section workflow before scoring the specimen (standard IHC practice). |
💡Expected CPS1 appearanceCall a positive when hepatocytes or small-intestinal endocrine cells show high, selective granular cytoplasmic staining; widespread diffuse or wrong-cell staining is suspect (HPA tissue IHC: Enhanced; high in those cells).
| Cell type and tissue selection | Liver hepatocytes and small-intestinal endocrine cells are reported high, while adipose adipocytes are not detected (HPA tissue IHC). Compare the named cell populations; a whole-section average can obscure the selective pattern (standard IHC interpretation). |
| Compartment used for IHC scoring | Granular cytoplasm is the reported tissue IHC pattern (HPA tissue IHC). Mitochondrial, nucleolar, and hepatocyte surface localizations are annotated separately (UniProt P31327 localization); these annotations alone do not establish that every compartment will stain in paraffin sections. |
| Antibody evidence | HPA021400 and CAB003781 each have Enhanced IHC status (HPA antibodies). Enhanced reflects agreement between staining and independent antibody or orthogonal evidence (HPA antibody validation). It supports the reference pattern but does not validate every reagent or staining run. |
| IF evidence and its scope | Nucleoli and nucleoli rim are supported in ICC-IF; sperm mid piece and principal piece are additional approved locations (HPA subcellular ICC-IF). These observations answer the IF localization question, but do not supply an IHC-P protocol or replace the tissue IHC scoring pattern. |
| Isoforms and epitope coverage | Three CPS1 isoforms are listed (UniProt P31327 isoforms). No epitope map or isoform-specific IHC result is supplied, so do not infer which isoforms the catalog antibody detects or explain a negative section by isoform choice alone. |
| Situation | Likely cause | Next action |
|---|---|---|
| Liver positive control is blank. | The staining run may have failed; hepatocytes are expected to stain strongly (HPA tissue IHC: high in hepatocytes). | Confirm tissue integrity, reagent identity, detection performance, and the established retrieval workflow with a valid positive control (standard IHC practice). No CPS1-specific fixation sensitivity is supplied. |
| Signal is weak in expected positive cells. | Weak signal can reflect a suboptimal general IHC workflow; the record does not identify a CPS1-specific retrieval or fixation effect (standard IHC practice; supplied UniProt/HPA scope). | Review the validated antibody conditions, retrieval, incubation, and detection controls; compare with liver hepatocytes in the same run before changing interpretation (standard IHC practice; HPA tissue IHC: high in hepatocytes). |
| Color appears in a no-primary control. | The detection system or endogenous tissue activity can generate color independently of primary-antibody binding (standard chromogenic IHC practice). | Identify the background source with reagent controls and apply the detection system's appropriate blocking step; reassess CPS1 only after control signal is resolved (standard IHC practice). |
| Diffuse staining obscures cell boundaries. | Nonspecific binding or inadequate washing can reduce contrast with granular cytoplasm (standard IHC practice; HPA tissue IHC: granular cytoplasm). | Review blocking, washing, and antibody concentration within the validated workflow; retain settings that recover cell-restricted staining and clean negative controls (standard IHC practice). |
| A negative-reference cell type stains strongly. | Cross-reactivity or endogenous detection activity is possible; adipose adipocytes are listed as not detected (HPA tissue IHC: adipocytes not detected; standard IHC practice). | Check the no-primary control, compare with the liver positive control, and score the specified cell type before accepting the signal (standard IHC practice; HPA tissue IHC: high in hepatocytes). |
| Only nucleolar or surface staining is visible. | Those locations have separate evidence, but a compartment-only result does not match the principal granular cytoplasmic tissue pattern (HPA subcellular ICC-IF; UniProt P31327 localization; HPA tissue IHC). | Check whether a liver control also lacks granular hepatocyte cytoplasm, then review antibody and detection controls. Record the unusual compartment separately rather than scoring it as the expected IHC pattern (standard IHC interpretation). |
Experiment evidence
IHC & IF images showing CPS1 staining
A01320-2 · IHCIHC analysis of CPS1 using anti-CPS1 antibody (A01320-2). CPS1 was detected in a paraffin-embedded section of human liver cancer tissue. Hea
A01320-2 · IHCIHC analysis of CPS1 using anti-CPS1 antibody (A01320-2). CPS1 was detected in a paraffin-embedded section of mouse colon tissue. Heat media
A01320-2 · IFIF analysis of CPS1 using anti-CPS1 antibody (A01320-2). CPS1 was detected in an immunocytochemical section of Hela cells. Enzyme antigen re
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000021826-CPS1/tissue/cerebral+cortex#imid_1204752
HPA · Small intestineHuman Protein Atlas IHC, Small intestine. Source: https://www.proteinatlas.org/ENSG00000021826-CPS1/tissue/small+intestine#imid_5741881
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000021826-CPS1/tissue/colon#imid_1204678
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000021826-CPS1/tissue/liver#imid_1204679
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA021400; green = CPS1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA021400; green = CPS1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CPS1 IHC & IF
🧪Run liver first: hepatocytes should stain (HPA: High in hepatocytes). Use adipose tissue as the negative tissue, where adipocytes are not detected (HPA: Not detected in adipocytes); on the liver slide, nonhepatocyte stromal cells should provide an internal background reference.
Positive control tissue: Duodenum (Endocrine cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CPS1 in A-431, U-251MG, U2OS, Sperm, with annotated localisation: Nucleoli (supported), Nucleoli rim (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) slide, an isotype control matched to the primary antibody’s host species and class, and CPS1-knockout tissue as a biological negative (standard IHC controls). For liver sections developed with the caption’s biotin-based DAB system, quench endogenous peroxidase and control for endogenous biotin (selected-SKU tissue-IHC caption: biotinylated secondary, SABC and DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the fixative in the selected-SKU tissue-IHC caption is unreported. The paraffin-section example uses heat-mediated retrieval in EDTA at pH 8.0, so retrieval should be checked when transferring the method to new specimens (selected-SKU tissue-IHC caption). Paraffin-section IHC has a supplied example; the evidence does not establish that frozen sections or IF are easier, and endogenous biotin can complicate interpretation of the caption’s biotin-based liver staining (selected-SKU tissue-IHC caption; standard IHC practice).
HPA tissue IHC evidence for CPS1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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 |
|---|---|---|---|---|
| Duodenum | Endocrine cells | High | Protein (IHC) | HPA → |
| Liver | Hepatocytes | High | Protein (IHC) | HPA → |
| Small intestine | Endocrine cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | Endocrine cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced CPS1 IHC Tips
Troubleshoot CPS1 staining in paraffin sections using the catalog antibody’s tissue IHC evidence and the expected cell and compartment patterns.
What retrieval should I try first when CPS1 staining is weak?
Start with heat-mediated EDTA pH 8.0 retrieval for paraffin sections (datasheet A01320-2). The catalog antibody detected CPS1 in a paraffin section of human liver cancer after this retrieval, followed by 2 μg/ml primary antibody overnight at 4°C (datasheet A01320-2). Keep antibody concentration and detection conditions consistent while adjusting heating duration within your laboratory’s validated retrieval range (standard IHC practice). Compare the result with hepatocytes, where granular cytoplasmic staining is expected, and an omission control to distinguish improved signal from increased background (HPA tissue IHC; standard IHC practice).
Could fixation explain weak or uneven CPS1 staining?
Target-specific CPS1 sensitivity to fixation is unknown from the supplied evidence; the catalog image describes a paraffin section but does not state its fixative (datasheet A01320-2). Record the actual fixative and fixation interval for each specimen, and compare sections processed together before attributing differences to CPS1 biology (standard IHC practice). Use the documented EDTA pH 8.0 retrieval and 2 μg/ml primary incubation as a consistent starting point (datasheet A01320-2). Check tissue preservation and staining across the section, then assess hepatocyte staining against the reported granular cytoplasmic pattern (standard IHC practice; HPA tissue IHC).
How should I assess cytoplasmic, nucleolar, or surface CPS1 staining?
In tissue IHC, selective granular cytoplasmic staining in hepatocytes and small-intestinal cells provides the clearest reference pattern (HPA tissue IHC). CPS1 is also annotated in mitochondria, nucleoli, and at the hepatocyte cell surface, despite having no transmembrane segment (UniProt P31327). Nucleolar localisation has separate support from subcellular IF images, so assess a nucleolar IHC pattern against tissue morphology and controls before interpreting it (HPA subcellular; standard IHC practice). Score cytoplasmic, nucleolar, and apparent surface staining separately, and verify that the pattern follows intact cells rather than section edges or damaged tissue (standard IHC practice).
Could CPS1 isoforms or epitope changes alter the IHC pattern?
CPS1 has 3 annotated isoforms, but the supplied catalog caption does not identify the antibody epitope or establish isoform selectivity (UniProt P31327; datasheet A01320-2). Its annotated domains span residues 219–404, 551–743, 1093–1284, and 1355–1500, providing landmarks only if an epitope is later documented (UniProt P31327). Annotated glycosylation and lysine modifications make epitope accessibility a question to test, not an established cause of altered staining (UniProt P31327). If specimens disagree, compare retrieval and processing first, then use a second antibody with a documented, distinct epitope if available (standard IHC practice).
How can I check CPS1 localisation by multiplex IF?
Pair CPS1 with a validated hepatocyte marker when examining liver, and inspect each channel independently before interpreting overlap (HPA tissue IHC; standard IF practice). Choose fluorophores and filter sets after checking unstained tissue autofluorescence, particularly where tissue background overlaps the chosen emission range (standard IF practice). For the expected mitochondrial signal, use permeabilisation that admits antibody to intracellular epitopes; assess any proposed surface signal under conditions appropriate to an accessible extracellular epitope (UniProt P31327; standard IF practice). Because this antibody’s epitope and IF performance are not established by the supplied IHC caption, validate the IF staining with appropriate controls (datasheet A01320-2; standard IF practice).
What should I check if DAB staining looks diffuse?
The documented tissue image used a biotinylated secondary, a streptavidin–biotin complex, and DAB, so evaluate background in that detection sequence (datasheet A01320-2). Include a primary-omission control and a detection control suited to the tissue to reveal nonspecific secondary or chromogen signal (standard IHC practice). Block endogenous peroxidase before DAB development, and assess endogenous biotin background when using biotin-based detection (standard IHC practice). Compare suspect staining with the selective granular cytoplasmic hepatocyte pattern, while checking whether pigment, damaged areas, or section edges create a similar appearance (HPA tissue IHC; standard IHC practice).
How should I quantify CPS1 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored cell population before measurement: hepatocytes are strongly positive in liver reference tissue, while adipocytes in adipose tissue are reported as undetected (HPA tissue IHC). For chromogenic sections, record the percentage of positive target cells and an intensity-weighted H-score using the same scoring thresholds across specimens (standard IHC practice). Normalise positive-cell counts to the number of evaluable target cells, or report positive-cell density per mm² of evaluable tissue when cell counts are impractical (standard IHC practice). Exclude necrosis and processing artefacts, and score cytoplasmic and nucleolar signals separately because their evidence comes from different localisation assays (standard IHC practice; HPA tissue IHC; HPA subcellular).
How do I distinguish genuine CPS1 staining from artefact?
Look first for selective granular cytoplasmic staining in intact hepatocytes or the reported small-intestinal cell populations, with suitable negative tissue and reagent controls (HPA tissue IHC; standard IHC practice). Treat staining restricted to section edges, folds, or necrotic areas as suspect and compare it with adjacent well-preserved tissue (standard IHC practice). Nucleolar staining needs separate assessment because subcellular IF supports nucleolar localisation, whereas the tissue IHC reference pattern is granular cytoplasmic (HPA subcellular; HPA tissue IHC). Check primary-omission and detection controls before assigning diffuse DAB signal to CPS1, particularly with the documented biotin-based detection method (standard IHC practice; datasheet A01320-2).
Boster reagents
Best CPS1 / Carbamoyl-phosphate synthase [ammonia], mitochondrial IHC Antibodies
A01320-2 has IHC images of human liver cancer and mouse and rat colon paraffin sections, plus HeLa cell IF imagery (catalog image captions); M01320-1 lists IHC and IF/ICC applications (catalog applications).
Real IHC data
Anti-CPS1 Antibody ®
Cat # A01320-2
A01320-2 has IHC images from human liver cancer and mouse and rat colon paraffin sections, and an IF image from HeLa cells (catalog image captions). M01320-1 lists IHC and IF/ICC applications and human, mouse and rat reactivity, but has no IHC or IF image in the supplied catalog (catalog applications/reactivity; catalog image captions).
Which to pick: Choose A01320-2 for tissue IHC when an image of the relevant species and sample type matters: its captions show human liver cancer and mouse and rat colon paraffin sections (catalog IHC captions). For IF/ICC, A01320-2 has HeLa cell IF imagery; M01320-1 is a rabbit monoclonal option listed for IF/ICC, without a supplied IF image (catalog IF caption; catalog clone/applications). A01320-2 has the broader listed reactivity, including monkey, although its IHC images cover human, mouse and rat; the captions report paraffin embedding but do not report the fixative (catalog reactivity; catalog IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P31327 (CPSM_HUMAN, Carbamoyl-phosphate synthase [ammonia], mitochondrial).
- Human Protein Atlas. CPS1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CPS1 subcellular location (ICC-IF): Mainly localized to the nucleoli and nucleoli rim. In addition localized to the mid piece and principal piece..
- Human Protein Atlas. CPS1 antibody validation summary (2 antibodies).
- Aberrant expression and distribution of enzymes of the urea cycle and other ammonia metabolizing pathways in dogs with congenital portosystemic shunts. PloS one 2014 — PMC4063766.
- Expression profiling of CPS1 in Correa's cascade and its association with gastric cancer prognosis. Oncology letters 2021 — PMC8045184.
- A constitutive knockout of murine carbamoyl phosphate synthetase 1 results in death with marked hyperglutaminemia and hyperammonemia. Journal of inherited metabolic disease 2019 — PMC6728231.
- Liver injury in non-alcoholic fatty liver disease is associated with urea cycle enzyme dysregulation. Scientific reports 2022 — PMC8888708.
- PubMed PMID:1840546 — UniProt-cited evidence.
- PubMed PMID:9711878 — UniProt-cited evidence.
- PubMed PMID:12853138 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CPS1 (Carbamoyl-phosphate synthase [ammonia], mitochondrial). Expected localisation Granular cytoplasm in hepatocytes and small intestine (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A01320-2). Validated IHC antibody: A01320-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Duodenum (Endocrine cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A01320-2); 2. Fixation: Image fixative and duration unreported (datasheet A01320-2); 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 A01320-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A01320-2); 8. Primary antibody: Rabbit anti-CPS1, 2-5 μg/ml (datasheet A01320-2); 9. Primary incubation: Overnight at 4 °C (datasheet A01320-2). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Endogenous peroxidase can add DAB signal in liver (standard IHC practice); Isoform / epitope: 3 isoforms; mature chain begins at residue 39 ; epitope coverage is unknown (UniProt); Regulation: Liver-enriched expression (HPA RNA specificity). Evidence: UniProt P31327, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the nucleoli and nucleoli rim. In addition…, Datasheet A01320-2, PMC8045184, PMC8888708. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CPS1/immunohistochemistry-ihc-guide.