MSRA / Mitochondrial peptide methionine sulfoxide reductase · IHC design guide

Design Immunohistochemistry for MSRA

Plan MSRA IHC-P using kidney tubules and bone marrow hematopoietic cells as tissues with medium staining (HPA tissue IHC). Start the IHC-validated antibody at 1:10–1:50 (datasheet: A04413-1 IHC-P), then assess cellular staining with chromogenic detection.

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for MSRA (IHC for MSRA): expected localisation Mitochondrial matrix expected; tissue IHC compartment unassigned (UniProt), antibody A04413-1, validated IHC image, and IHC protocol steps
Printable MSRA IHC protocol sheet — expected localisation Mitochondrial matrix expected; tissue IHC compartment unassigned (UniProt), antibody A04413-1, controls and protocol steps. Open the full MSRA IHC guide →

MSRA 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 Mitochondrial matrix expected; tissue IHC compartment unassigned (UniProt)
Staining pattern Medium in kidney tubules and marrow cells (HPA tissue IHC)
Antigen retrieval Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen)
Positive control ⓘ Appendix+4 more · see all
Negative control ⓘ Adipose tissue+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Use formalin-fixed paraffin sections (selected-SKU IHC image A04413-1); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A04413-1)
Caveat Low staining–RNA consistency; splice discrepancy (HPA tissue IHC)
Regulation Kidney and liver RNA tissue enhanced (HPA tissue RNA)
Isoform / epitope 5 isoforms; N-terminal epitope coverage unknown (UniProt; datasheet: A04413-1)
Section 1

Recommended MSRA IHC & IF Protocols

Compare the catalog antibody’s IHC-P protocol with published MSRA staining methods for rat skin (PMC6393874), aortic valves (PMC12972393), and paraffin tissue (PMC9391305).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleFFPE human hepatocarcinoma tissue (datasheet A04413-1)
FixationImage formalin-fixed; duration unreported (datasheet A04413-1); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyRabbit anti-MSRA, 1:10-1:50 (datasheet A04413-1)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultMSRA-positive staining in glandular cells of appendix (HPA tissue IHC: Medium). HPA tissue profile: Expression in several tissues, including bone marrow and kidney. No signal in the no-primary control.
💡Decision noteStart with Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval rule); citrate pH 6 is a published alternative (PMC9391305).
Section 2

What Is the Expected MSRA Staining Pattern?

MSRA is annotated in the mitochondrial matrix, cytoplasm and nucleus, with no transmembrane segment (UniProt Q9UJ68). In tissue IHC, expect staining in kidney tubule cells, bone marrow hematopoietic cells and several glandular or respiratory epithelial populations (HPA tissue IHC: Medium). Treat these as guides to interpretation: HPA rates its tissue IHC evidence Approved but reports low consistency between antibody staining and RNA expression, with a possible splice or transcript discrepancy.

What am I looking at on my slide?
Kidney tubule cells or bone marrow hematopoietic cells stain above adjacent background.This fits the reported cell-level pattern (HPA tissue IHC: Medium in both populations). Cytoplasmic or nuclear staining can fit the annotated locations (UniProt Q9UJ68); a mitochondrial component is also plausible (UniProt Q9UJ68). Judge the stained cells against tissue structure, because a positive region alone does not show which cells contain the signal.
A sharp cell-surface outline dominates, with little intracellular staining.Recheck specificity and detection before calling this the expected pattern. MSRA has no annotated transmembrane segment, although membrane is among its listed locations (UniProt Q9UJ68). HPA ICC-IF instead reports mainly nucleoplasmic and cytosolic signal (HPA subcellular: supported). A surface-dominant IHC result therefore needs corroboration; it is not, by itself, proof of an artefact.
Adipocytes stain strongly while the expected positive cells are weak or unstained.Adipocytes are reported as Not detected, whereas kidney tubule cells and bone marrow hematopoietic cells are Medium (HPA tissue IHC). Consider cross-reactivity or endogenous detection activity, and compare the signal with controls processed using the same detection steps. HPA non-detection is a reference observation, not proof that every adipocyte sample must be negative.
Brown color spreads across cells and surrounding tissue without a clear cell pattern.Diffuse background cannot establish MSRA localization. Check whether signal persists in a control omitting the primary antibody, then review blocking, washes and chromogen development as general IHC troubleshooting steps. Interpret any residual cell-specific signal cautiously because HPA reports low consistency between tissue staining and RNA expression (HPA tissue IHC: reliability note).
No convincing signal appears in kidney tubule cells or bone marrow hematopoietic cells.These are useful reference populations because both were scored Medium (HPA tissue IHC). First verify tissue preservation, the detection run and antibody performance with an appropriate control. A negative run alone cannot establish absent MSRA: HPA flags staining–RNA inconsistency and a possible splice or transcript discrepancy (HPA tissue IHC: reliability note).
💡Expected MSRA appearanceCall a result positive when kidney tubule or bone marrow hematopoietic cells show discernible intracellular staining consistent with the reported Medium level (HPA tissue IHC) and annotated cytoplasmic, nuclear or mitochondrial locations (UniProt Q9UJ68); uniform background or dominant cell-surface outlining needs investigation.
How each factor affects the staining
Tissue and cell choiceKidney tubule cells and bone marrow hematopoietic cells offer reported Medium IHC reference patterns; adipocytes are reported Not detected (HPA tissue IHC). Compare the specified cells within each tissue, since a tissue-wide average can hide a cell-specific result.
Location evidenceUniProt places MSRA in mitochondria, cytoplasm and nucleus and annotates no transmembrane segment (UniProt Q9UJ68). HPA ICC-IF supports mainly nucleoplasm and cytosol (HPA subcellular). These sources support intracellular interpretation but do not establish a required chromogenic texture in paraffin sections.
Transcript variation and evidence limitsFive isoforms are listed (UniProt Q9UJ68). HPA notes low staining–RNA consistency and a possible splice or transcript discrepancy despite an Approved IHC reliability rating (HPA tissue IHC). Avoid treating disagreement between one stain and RNA data as a settled biological difference.
Mitochondrial processingUniProt annotates a mitochondrial chain spanning residues 24–235 (UniProt Q9UJ68). This establishes processing in the record, but the supplied sources give no antibody epitope or isoform coverage; they cannot predict whether processing changes this IHC antibody's staining.
Antibody validation scopeHPA023804 and HPA075766 are Approved for IHC; HPA053069 has no listed IHC status (HPA antibodies). HPA's overall tissue IHC rating is Approved with a reliability caveat (HPA tissue IHC). Apply those statuses to the named antibodies only; no catalog antibody identity is supplied.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected positive cells are unstained.The detection run, antibody conditions or section quality may be limiting; the supplied sources give no MSRA-specific retrieval setting.Check an appropriate positive control and the detection reagents, then optimize retrieval and antibody dilution as general IHC practice. Use kidney tubule or bone marrow hematopoietic cells as reported Medium references (HPA tissue IHC), while retaining HPA's reliability caveat.
Color appears where the primary antibody was omitted.A primary-independent detection contribution is possible; the observation does not identify MSRA.Review endogenous enzyme blocking, secondary reagent behavior and chromogen development as general chromogenic IHC checks. Repeat with the same omission control and assess whether the cell-specific signal remains.
Adipocytes show prominent staining.This conflicts with the reported Not detected adipocyte pattern (HPA tissue IHC); cross-reactivity or detection background is possible.Inspect the omission control and compare cell-level staining with kidney tubule cells or bone marrow hematopoietic cells, reported Medium (HPA tissue IHC). Do not infer target abundance from chromogen intensity alone.
Only a crisp membrane rim is visible.A surface-dominant pattern has limited support: MSRA has no transmembrane segment (UniProt Q9UJ68), while HPA ICC-IF mainly supports nucleoplasm and cytosol (HPA subcellular).Check morphology and background controls, then seek independent antibody or localization evidence before assigning the rim to MSRA. UniProt also lists membrane localization, so the rim alone cannot settle specificity (UniProt Q9UJ68).
Tissue staining and RNA abundance disagree.HPA explicitly reports low consistency and a possible splice or transcript discrepancy (HPA tissue IHC); UniProt lists five isoforms (UniProt Q9UJ68).Report the stained cell population and the discordance separately. Confirm antibody identity and its IHC validation status before comparison; HPA lists IHC approval for HPA023804 and HPA075766 (HPA antibodies).
Can IF/ICC resolve an uncertain compartment?Chromogenic tissue IHC may leave compartment boundaries ambiguous; HPA ICC-IF reports supported nucleoplasmic and cytosolic localization (HPA subcellular).Use the separate IF/ICC guide for that application and compare its localization result with the IHC section. Treat the HPA ICC-IF pattern as supporting evidence, while retaining UniProt's mitochondrial annotation (UniProt Q9UJ68).

Sample controls for MSRA IHC & IF

🧪Run bone marrow first: hematopoietic cells should stain (HPA: Medium in bone marrow hematopoietic cells). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); adipocytes within the marrow section can serve as an internal background reference, but their status in marrow must be checked because the HPA negative observation comes from adipose tissue.
Positive control tissue: Appendix (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show MSRA in GAMG, U2OS, SiHa, NIH 3T3, with annotated localisation: Nucleoplasm (supported), Cytosol (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) control, a nonimmune immunoglobulin control matched to the catalog antibody’s host species and class as appropriate to its clonality, and MSRA-knockout material or immunizing-peptide competition if available (standard IHC practice). Quench endogenous peroxidase before HRP/DAB detection in bone marrow, where hematopoietic cells can contribute peroxidase background (standard IHC practice).
⚠️Feasibility: The selected A04413-1 caption explicitly reports formalin-fixed, paraffin-embedded tissue with peroxidase/DAB detection (selected-SKU tissue-IHC caption), but reports no fixation window or fixation effect; a target-specific fixation window is unreported. Antigen-retrieval dependence is unreported, so retrieval conditions need empirical optimization (supplied target/application evidence). HPA has ICC-IF images for MSRA, while frozen-section suitability and whether IF is easier than IHC-P are unreported (HPA subcellular); endogenous marrow peroxidase is a practical IHC artefact to control (standard IHC practice).

HPA tissue IHC evidence for MSRA

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Caution, Splice and/or transcript discrepancy exists.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
Appendix Glandular cells Medium Protein (IHC) HPA →
Bone marrow Hematopoietic cells Medium Protein (IHC) HPA →
Bronchus Respiratory epithelial cells Medium Protein (IHC) HPA →
Colon Glandular cells Medium Protein (IHC) HPA →
Duodenum Glandular cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Cervix Glandular cells Not detected Protein (IHC) HPA →
Esophagus Squamous epithelial cells Not detected Protein (IHC) HPA →
Fallopian tube Glandular cells Not detected Protein (IHC) HPA →
Section 3

Advanced MSRA IHC Tips

Use the IHC observations, MSRA localisation data and matched controls to troubleshoot chromogenic staining; interpret tissue patterns with the reported HPA consistency warning.

How should I retrieve MSRA in paraffin sections when staining is weak?
Start with Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval setting). Allow slides to cool in retrieval buffer, then compare a stained test section with a matched section processed without primary antibody (standard IHC practice). If signal remains weak, vary heating time in small increments while keeping section thickness, antibody concentration and detection conditions constant (standard IHC practice). Assess whether the change improves cellular staining in kidney tubules, which show medium MSRA staining, without increasing diffuse background (HPA tissue IHC). Record retrieval conditions for each run so that a stronger signal can be checked for reproducibility (standard IHC practice).
Could fixation explain weak or patchy MSRA staining?
The selected antibody has been shown on formalin-fixed, paraffin-embedded human hepatocarcinoma with DAB detection (A04413-1 tissue-IHC caption). That image establishes an IHC example, but MSRA-specific sensitivity to fixation duration or delayed fixation is unknown from the supplied evidence (A04413-1 tissue-IHC caption). For troubleshooting, compare sections with documented fixation histories using identical retrieval, antibody incubation and detection settings (standard IHC practice). Inspect morphology and staining together, because damaged or unevenly processed areas can complicate interpretation of a weak signal (standard IHC practice). Include a matched no-primary control and a consistently staining reference section in the same run (standard IHC practice).
Which cellular compartments should show credible MSRA staining?
Assess cytoplasmic and nuclear staining separately, because MSRA is annotated in mitochondria, cytoplasm and nucleus (UniProt Q9UJ68 subcellular record). Mitochondrial matrix localisation is also annotated, while HPA IF places its main detectable signal in nucleoplasm and cytosol (UniProt Q9UJ68 subcellular record; HPA subcellular). A fine cytoplasmic pattern can therefore be plausible, but chromogenic resolution alone cannot establish mitochondrial localisation (UniProt Q9UJ68 subcellular record; standard IHC practice). Score the compartment and cell type rather than treating all brown signal as equivalent (standard IHC practice). Compare with kidney tubular cells or bone-marrow hematopoietic cells, both reported at medium staining, while checking matched controls (HPA tissue IHC; standard IHC practice).
Can MSRA isoforms or epitope placement alter the apparent IHC pattern?
MSRA has 5 annotated isoforms, so establish which sequences the antibody can recognize before comparing staining across specimens (UniProt Q9UJ68 isoforms; standard IHC practice). The selected tissue image identifies its antibody as N-terminal, but does not map the precise epitope or establish isoform coverage (A04413-1 tissue-IHC caption). MSRA also has an annotated processed chain spanning residues 24–235, making epitope position relevant when evaluating precursor and processed forms (UniProt Q9UJ68 processing). Check the antibody's documented immunogen or epitope against isoform sequences, if that information is available (standard IHC practice). Interpret discordant staining cautiously because HPA reports low consistency between antibody staining and RNA expression, with a splice or transcript discrepancy warning (HPA tissue IHC).
How should I investigate the MSRA pattern with multiplex immunofluorescence?
On the separate IF/ICC guide, pair MSRA with a marker that identifies the expected cell type, such as kidney tubular cells when assessing kidney (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores and place a dimmer signal in a channel with lower tissue autofluorescence, verified using an unstained section (standard IF practice). Compare nuclear and cytosolic signal directly, since these are the main HPA IF locations for MSRA (HPA subcellular). Use permeabilisation appropriate for intracellular epitopes; access to a mitochondrial matrix epitope may require membrane permeabilisation, while the antibody's exact epitope side remains unreported (UniProt Q9UJ68 subcellular record; standard IF practice). Check single-stain and no-primary controls before interpreting overlap (standard IF practice).
What should I change when MSRA DAB staining is diffuse?
First compare the stained slide with a no-primary control and inspect whether brown deposits follow tissue edges, damaged areas or cellular structures (standard IHC practice). Block endogenous peroxidase before peroxidase-based detection and check the blocking and wash steps if background persists (standard IHC practice). The selected tissue example used a peroxidase-conjugated secondary antibody followed by DAB, so its brown signal alone does not establish specificity (A04413-1 tissue-IHC caption; standard IHC practice). Titrate the catalog antibody and shorten DAB development systematically while holding retrieval at pH 9.0 and 20 min for the initial comparison (page retrieval setting; standard IHC practice). Retain only settings that preserve cellular contrast in a reference section (standard IHC practice).
How can I score MSRA IHC across specimens consistently? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, and keep exposure to DAB and counterstain consistent across slides (standard IHC practice). For cellular expression, record the percentage of positive cells and an H-score using intensity categories 0–3, giving a possible range of 0–300 (standard IHC practice). Where cell counts vary substantially, report positive-cell density per mm² of viable tissue and specify the counted area (standard IHC practice). Normalise comparisons to the same cell type or compartment and viable area, rather than total section area (standard IHC practice). Report kidney tubular-cell results separately from other cells because HPA assigns that population medium staining (HPA tissue IHC).
How do I distinguish genuine MSRA signal from staining artefacts?
A credible result follows identifiable cells and a plausible intracellular compartment: MSRA is annotated in mitochondria, cytoplasm and nucleus (UniProt Q9UJ68 subcellular record). HPA reports medium staining in kidney tubular cells and bone-marrow hematopoietic cells, offering tissue-level references rather than proof for an individual slide (HPA tissue IHC). Treat edge-only signal, necrotic regions and staining shared by a no-primary control as suspect (standard IHC practice). Check endogenous peroxidase when DAB signal appears independently of primary antibody, and compare morphology on the counterstained section (standard IHC practice). Avoid equating stain intensity with enzyme activity or clinical relevance; HPA warns of low staining–RNA consistency, and the selected tissue caption has no clinical evaluation (HPA tissue IHC; A04413-1 tissue-IHC caption).
Boster reagents

Best MSRA / Mitochondrial peptide methionine sulfoxide reductase IHC Antibodies

The catalog includes antibodies with IHC-P data in human hepatocarcinoma and IF/ICC data in SIHA cells; listed reactivity spans human, mouse, and rat (catalog image captions; catalog reactivity).

Real IHC data Formalin-fixed and paraffin-embedded human hepatocarcinoma reacted with MSRA Antibody (N-term), which was peroxidase-conjugated to the secondary antibody, followed by DAB staining. This data demonstrates the use of this antibody for immunohistochemistry; clinical relevance has not been evaluated.
Anti-MSRA Antibody (N-term)
Cat # A04413-1
Real IF data IF analysis of MSRA using anti-MSRA antibody (A04413-2) and anti-Beta Tubulin antibody (M01857-3). MSRA was detected in an immunocytochemical section of SIHA cells. Enzyme antigen retrieval was performed using IHC enzyme antigen retrieval reagent (AR0022) for 15 mins. The cells were blocked with 10% goat serum. And then incubated with 5 μg/mL rabbit anti-MSRA Antibody (A04413-2) and mouse anti-Beta Tubulin antibody (M01857-3) overnight at 4°C. DyLight®488 Conjugated Goat Anti-Rabbit IgG (BA1127) and Cy3 Conjugated Goat Anti-Mouse IgG (BA1031) were used as secondary antibody at 1:500 dilution and incubated for 30 minutes at 37°C. The section was counterstained with DAPI. Visualize using a fluorescence microscope and filter sets appropriate for the label used.
Anti-MSRA Antibody ®
Cat # A04413-2

A04413-1 lists IHC-P and IF for human and mouse, with DAB IHC data from formalin-fixed, paraffin-embedded human hepatocarcinoma (catalog applications; catalog reactivity; A04413-1 image caption). A04413-2 lists IF/ICC for human, mouse, and rat, with IF data from SIHA cells (catalog applications; catalog reactivity; A04413-2 image caption).

Which to pick: Choose A04413-1 for tissue IHC: it lists IHC-P at 1:10–1:50, and its own DAB image documents formalin-fixed, paraffin-embedded human hepatocarcinoma (catalog applications; catalog dilution; A04413-1 image caption). Choose A04413-2 for IF/ICC when SIHA-cell data are useful; it lists 5 μg/ml for IF/ICC, while A04413-1 also lists IF, and both are rabbit polyclonals (A04413-2 image caption; catalog dilutions; catalog applications; catalog clonality). For rat samples, A04413-2 lists reactivity and IF/ICC, whereas A04413-1 lists human and mouse reactivity with IHC-P (catalog reactivity; catalog applications).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q9UJ68 (MSRA_HUMAN, Mitochondrial peptide methionine sulfoxide reductase).
  2. Human Protein Atlas. MSRA tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. MSRA subcellular location (ICC-IF): Mainly localized to the nucleoplasm and cytosol..
  4. Human Protein Atlas. MSRA antibody validation summary (3 antibodies).
  5. Relation of Redox and Structural Alterations of Rat Skin in the Function of Chronological Aging. Oxidative medicine and cellular longevity 2019 — PMC6393874.
  6. Age-associated methionine sulfoxide reductase A protects against valvular interstitial cell senescence and valvular calcification. GeroScience 2026 — PMC12972393.
  7. Methionine oxidation activates pyruvate kinase M2 to promote pancreatic cancer metastasis. Molecular cell 2022 — PMC9391305.
  8. Dopamine D(2) receptor function is compromised in the brain of the methionine sulfoxide reductase A knockout mouse. Journal of neurochemistry 2010 — PMC2933736.
  9. PubMed PMID:10452521 — UniProt-cited evidence.
  10. PubMed PMID:16364291 — UniProt-cited evidence.
  11. PubMed PMID:14702039 — UniProt-cited evidence.