Can the Fragment Analyzer tell us if and what contaminants are in the sample (phenol, salt, protein)? If not, do you know of another way to detect what contaminants may be in the sample?

The Fragment Analyzer cannot tell which contaminants may be in a sample. Check out this very quick read in the following link about determining DNA and RNA purity based on 260/230 ratios.

The Significance of the 260/230 Ratio in Determining Nucleic Acid Purity