We present time alignment based on blank measurement as analytical approach for reduction of time shift in high performance liquid chromatography - mass spectrometry (HPLC-MS). Our approach is based on the measurement and comparison of the distinct features of the blank and the analyzed sample. Blank measurement based time alignment (BBTA) utilizes solvent contaminants and other important events detectable both in blank run and the compared experiment for alignment of multiple 2D chromatograms. Several metrics for comparison of mass spectra were evaluated. Marker selection works efficiently even when no peaks are detected. It is capable of analyzing the baseline contribution in analyte measurement when the knowledge of blank behavior is limited. Finally, BBTA because of its simplicity has the potential to be widely used in HPLC-MS data treatment.