An enormous complexity of eukaryotic proteomes, in which tens of thousands of different genes give rise to millions of protein products, brings about new demands and challenges on the sensitivity, dynamic range, and robustness of analytical approaches employed for their analysis. The technologies behind the modern proteomics of eukaryots rely on a combination of microscale separation techniques and powerful detection methods, first of all by mass spectrometry. Analysis of other classes of natural compounds such as carbohydrates or lipids requires the development of innovative strategies several of which are described in this review. The analytical methods resulted in the acquisition of a wealth of information that needs to be sorted, presented, and cataloged using modern tools of current bioinformatics.