Ionic chemical background noise in LC-MS has been one of the major problems encountered in trace analysis. In this study, the typical negative background ions in ESI LC-MS are investigated exemplarily. It was carried out using tandem mass spectrometry to study the products and precursors of the major background ions to examine their structures and structure relationship. Various typical LC eluents with different compositions and additives such as ammonium formate/formic acid and ammonium acetate/acetic acid have been studied. Several types of negative noise ions are concluded, which include the cluster chemical background ions only from mobile phase components and additives. Furthermore, there are also abundant clusters resulting from the solvation of some typical individual contaminants (e.g. additives and degradation products from tubing, impurities in the mobile phase, etc.), accompanied by some minor contribution from contaminants. The elemental composition of some selected ions was confirmed using the FT-ICR accurate mass measurement. This work provides us insight into information about the structures and types of common negative background ions and will help to understand their formation and origins. More importantly, it will guide us to prevent chemical noise interference in practice and also contribute to develop methods for noise reduction based on selective ion-molecule reactions.