Rationale Retroactive analysis of previously tested urine samples has become an important sports anti‐doping tool. Retroactive reprocessing of old data files acquired from a generic screening procedure can reveal detection of initially unknown substances, like illegal drugs and newly identified metabolites. Methods To be able to efficiently search through hundreds to thousands of liquid chromatography high‐resolution full‐scan Orbitrap mass spectrometry data files of anti‐doping samples, a combination of MetAlign and HR_MS_Search software has been developed. MetAlign reduced the data size ca 100‐fold making possible local storage of a massive volume of data. Results The newly developed HR_MS_Search module can search through the reduced data files for new compounds (mass or isotope pattern) defined by mass windows and retention time windows. A search for 33 analytes in 940 reduced data files lasted 10 s. The output of the automatic search was compared to the standard manual routine evaluation. The results of searching were evaluated in terms of false negatives and false positives. The newly banned b2‐agonist higenamine and its metabolite coclaurine were successfully searched in reduced data files originating from a testing period for which these substances were not banned, as an example of retroactive analysis. Conclusions The freeware MetAlign software and its automatic searching module HR_MS_Search facilitated the retroactive reprocessing of reduced full‐scan high‐resolution liquid chromatography/mass spectrometry screening data files and created a new tool in anti‐doping laboratories' network.