Phase-shaped femtosecond laser pulses and mass spectrometry were implemented as a tool for improving molecular identification. We demonstrate that the specific lines in the mass spectra of several chemical warfare simulants are sensitive to the phase characteristics of the incident laser field. The deviation in the relative yield of fragment ions observed upon pulse shaping (enhancement or suppression) adds a new dimension to mass spectrometry that improves molecular identification and can be used to quantitatively analyze mixtures of isomers.