This chapter discusses liquid secondary ion mass spectrometry of phosphorylated and sulfated peptides and proteins. The phosphorylation and sulfation of amino acids are two of the most common posttranslational modifications known to occur in proteins and peptides, and are frequently critical to the function of these molecules by increasing or decreasing their activity. In the case of protein phosphorylation, enzymes called protein kinases are known to transfer the terminal γ-phosphate moiety in Adenosine triphosphate (ATP) to the nucleophilic hydroxyl group of a target serine, threonine, or tyrosine residue. These modifications are reversed by the action of protein phosphatases, a group of enzymes that catalyze the hydrolysis of these ester bonds in vivo. Despite the importance and widespread occurrence of phosphorylation and sulfation of hyroxyl amino acids in proteins and peptides, the methodology for determining their presence and sequence positions has been less than adequate. For example, a frequent method of determining phosphorylation stoichiometries in vivo is to label cells or tissues to steady state by incubation with radiolabeled inorganic [32p] phosphate.