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How do SST products in *.L2_LAC_SST and *.L2_LAC files differ?
"The SST-specific files have two advantages: 1) they were produced with the most up-to-date algorithm coefficients and quality-assessment logic (until the ocean color products are reprocessed), and 2) they contain the quality-level information that allows the user to select the quality of interest (0=best, 3=worst). The idea is that if you are just looking for structure and can accept some cloud contamination, you can select lower-quality data."
For more MODIS SST product details see: http://oceancolor.gsfc.nasa.gov/DOCS/modis_sst/