The complete sequence of the genome of many organisms including the human is available today. However, our knowledge on the proteins, functional products of the genes, is very limited. Proteins give more accurate information about the dynamic condition of the cells, tissues or organs. For this reason, a concept called "proteome" has emerged and became important. The word proteome can be defined as "all the proteins synthesized by the cell or whole organism" or "all the proteins synthesized by a particular cell at particular time". Parallelly, the discipline of "proteomics" includes all the methods to investigate proteomes and can be defined as "the qualitative and quantitative comparison of proteomes under different conditions". Proteomics workflow can be grouped main titles: Protein isolation, protein seperation and expression analyses, protein identification, protein interactions and structures. Two dimensional gel electrophoresis (2D-PAGE) has an important role in protein seperation and fractionation. Mass spectrometry (MS) (i.e. MALDI-TOF, ESI Q-TOF) is one of the most informative methods for studying proteomics. Protein identification is achieved by matching the cleavaged peptides to the database masses with this approach. Proteomics also allow for identification of the protein changes caused by the disease process in a relatively high-throughput manner, because it permits an analysis of thousands of modified or unmodified proteins simultaneously. Thus, together with microarray analysis it is increasingly becoming popular in identifying biomarkers for cancer diagnosis, progression, as well as therapeutic targets. In this section microarray and proteome results of midkine and HIF-1 silenced/overexpressed alveolar macrophage cells will be discussed. This study was supported by TUBITAK-BMBF (SBAG108S262)