This dissertation focuses on the use of LC-MS for the analysis of related peptides and anions in the positive mode. Separating closely related peptides (those differing by one or two amino acids or the chirality of a single amino acid) can be challenging using reversed-phase liquid chromatography (LC), ion exchange LC, or using ion-pairing agents. Also, the mobile phases that give the best separations in these modes may not be electrospray ionization mass spectrometry (ESI-MS) compatible. Macrocyclic glycopeptide stationary phases were investigated as an alternative to the standard C18 stationary phase for the separation of related peptides. On the macrocyclic glycopeptide stationary phases, high selectivity was observed for single amino acid substitutions (achiral and chiral) regardless of the position of the substitution in the sequence for peptides of thirteen amino acids or less. Selectivity of the macrocyclic glycopeptide stationary phases for a series of diastereomers and larger peptides was also explored and compared to separations achieved on a standard C18 stationary phase. MS compatible mobile phases were used whenever possible.;Negative ion mode is often used for the detection of anions in LC-ESI-MS applications. However, operating in negative ion mode tends to be more problematic than positive ion mode. Singly charged anions can be detected in the positive ion mode if the anions are paired with a dicationic reagent to form a complex with the anion that retains an over all positive charge. This method was also expanded to divalent anions through the use of tricationic reagents. When the anion pairs with the tricationic reagent, an overall positive charge is retained and enables detection by ESI-MS in the positive mode. Different cationic reagents were found to vary tremendously in their ability to pair with anions and produce sensitive ESI-MS signals. The effect of these structural elements on the detection sensitivity of the complex is examined empirically. A comparision of signal to noise ratios achieved in positive and negative modes also is presented.