Multidimensional chemical detection and identification based on phase shaped femtosecond laser pulses coupled to mass spectrometry is demonstrated. The method based on binary phase shaping (BPS) takes into account the accuracy and precision standards required by analytical chemistry. It couples multiphoton intrapulse interference of ultrashort laser pulses with time-of-flight mass spectrometry (TOF-MS). We demonstrate that BPS-MS provides a rigorous multidimensional technique for the detection and identification of analogues to chemical agents and mixtures in real time. Experimental results on dimethyl phosphite and pyridine illustrate the new approach toward the real-time accurate detection and identification of chemical compounds including isomers.