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. Author manuscript; available in PMC: 2021 Jun 23.
Published in final edited form as: Nat Protoc. 2021 Feb 24;16(4):1995–2022. doi: 10.1038/s41596-020-00477-y

Table 2 |.

Troubleshooting table

Step Problem Possible reason Solution

2–4 15N-labeling not detected Inadequate label dose or delivery Use controls to assess for absorption (urine) and/or incorporation into alternative cell types (WBCs)
Label is diluted away by ongoing proliferation during label free chase Increase dose of 15N-thymidine labeling or decrease chase period
27–40 Indeterminate cell type in NanoSIMS images Inadequate resolution or edge effect at margin of imaging field Reanalyze with NanoSIMS at higher resolution and with centering of the histologic feature of interest in the imaging field
Cannot resolve mass peaks for the N isotopes The MRP is not high enough Iteratively adjust Q, LF4, HEX and incrementally use smaller entrance and aperture slits
Insert the smallest exit slit (ExS 3) for the detector monitoring 15N
36 Long pre-sputtering time Primary ion beam intensity is too low Adjust the voltage (higher or lower) slightly on the L1 primary lens, in coordination with deflection plates C1x and C1y
Secondary ion intensity unstable Sample is not flat and/or smooth Inspect sample height with a microscope and readjust sample in NanoSIMS holder
Apply a thicker gold coat
55 Cardiomyocytes in oblique axis for binucleation quantification Review additional serial sections in the z-axis (sections are on glass slides) for a second nucleus
66 Over- or undersaturation of photomicrographs Decrease concentration of Hoechst staining or incubation time
Adjust the strength of the excitation light, the sensitivity of the emission light detector, and the exposure time