High confidence compound identification by liquid chromatography-mass spectrometry

A method of characterizing a sample, comprising:

• providing the sample to a liquid chromatography system capable of sample separation to generate separated sample components;
• analyzing separated sample components by multiplexed targeted selected ion monitoring (SIM) to select a plurality of precursor ions;
• and
• performing iterative mass spectral data-dependent acquisition (DDA) on the plurality of precursor ions,
• wherein preforming iterative mass spectral data-dependent acquisition comprises utilizing an iterative inclusion list and an iterative exclusion list, wherein the iterative inclusion list comprises the plurality of precursor ions and the iterative exclusion list comprises a precursor ion that has been previously fragmented from the plurality of precursor ions, and
• wherein the sample comprises a cell culture medium from a mammalian cell-based antibody production system.