Notes
Raman spectrometers vary greatly in the capabilities and features. Below are a few key notes to keep in mind when applying Raman to coral skeletons.
Fluorescence: Unless you are interested in organics, you want to avoid fluorescence as much as possible. This is relatively easy to do by (1) using a 785 nm (infrared) laser, and (2) bleaching your skeleton samples. Both of these are essential. If there are trace amounts of organics stuck to your skeleton surface, you will get a huge fluorescence signal, regardless of laser wavelength. Likewise, if you use a 532 nm (green) laser, you will probably get a large fluorescence signal even on bleached samples because there are tiny amounts of organic molecules preserved with coral skeletal crystals.
Resolution: This is probably the most important parameter to optimize. Generally, you will want to do everything possible to maximize spectral resolution (i.e. the bins in the x-axis, or Raman Shift). Spectral resolution depends a lot on the hardware you have, but often the one way to adjust it is by changing the grating (if your instrument has more than one to choose from) - select the largest grating (i.e. the most slits per mm). We have typically used a 1200/mm grating on a WITec instrument. The changes in peak width (FWHM) of coral skeleton samples is very small, and therefore requires as high of spectral resolution as possible to quantify any changes. Often, maximizing spectral resolution will come at the cost of a narrow spectral range. For example, on the WITec instrument with the high-resolution grating, we could include the ~705 /cm and 1085 /cm peaks of aragonite, but not the ~150 and ~200 /cm peaks. This was fine, since the ~705 /cm peak is sufficient to identify the sample as aragonite, and the 1085 /cm peak is the one used for peak width (FWHM) measurements.
Standardization: It is common for Raman users to standardize their data by calibrating to measurements of a silicon chip. This works well for standardizing the peak positions, but not the peak widths. To properly standardize coral skeleton peak width measurements, you really need aragonite standards. The best way to do this is using the JCp-1 coral since it is an international standard used for geochemistry by many labs around the world. See the below Biogeosciences paper for JCp-1 results to standardize against. We also have abiogenic aragonite samples that were used to develop our calibration between peak width and aragonite saturation state. We are willing to share subsets of these samples - just ask!
Fluorescence: Unless you are interested in organics, you want to avoid fluorescence as much as possible. This is relatively easy to do by (1) using a 785 nm (infrared) laser, and (2) bleaching your skeleton samples. Both of these are essential. If there are trace amounts of organics stuck to your skeleton surface, you will get a huge fluorescence signal, regardless of laser wavelength. Likewise, if you use a 532 nm (green) laser, you will probably get a large fluorescence signal even on bleached samples because there are tiny amounts of organic molecules preserved with coral skeletal crystals.
Resolution: This is probably the most important parameter to optimize. Generally, you will want to do everything possible to maximize spectral resolution (i.e. the bins in the x-axis, or Raman Shift). Spectral resolution depends a lot on the hardware you have, but often the one way to adjust it is by changing the grating (if your instrument has more than one to choose from) - select the largest grating (i.e. the most slits per mm). We have typically used a 1200/mm grating on a WITec instrument. The changes in peak width (FWHM) of coral skeleton samples is very small, and therefore requires as high of spectral resolution as possible to quantify any changes. Often, maximizing spectral resolution will come at the cost of a narrow spectral range. For example, on the WITec instrument with the high-resolution grating, we could include the ~705 /cm and 1085 /cm peaks of aragonite, but not the ~150 and ~200 /cm peaks. This was fine, since the ~705 /cm peak is sufficient to identify the sample as aragonite, and the 1085 /cm peak is the one used for peak width (FWHM) measurements.
Standardization: It is common for Raman users to standardize their data by calibrating to measurements of a silicon chip. This works well for standardizing the peak positions, but not the peak widths. To properly standardize coral skeleton peak width measurements, you really need aragonite standards. The best way to do this is using the JCp-1 coral since it is an international standard used for geochemistry by many labs around the world. See the below Biogeosciences paper for JCp-1 results to standardize against. We also have abiogenic aragonite samples that were used to develop our calibration between peak width and aragonite saturation state. We are willing to share subsets of these samples - just ask!
