Trace metals such as copper, iron, zinc and manganese play important roles in several biochemical processes including respiration and photosynthesis. Using a label-free, quantitative proteomics strategy (MSE), we examined the impact of deficiencies of these micronutrients on the soluble proteome of Chlamydomonas reinhardtii. We quantified 1000 proteins with abundances within a dynamic range of 3-4 orders of magnitude and demonstrated statistically significant changes in approximately 200 proteins in each metal deficient growth condition relative to nutrient replete media. From analysis of the Pearson's coefficient we also examined the correlation between protein abundance and transcript abundance (as determined by RNA-Seq analysis) and found moderate correlations under all nutritional states. Interestingly, the correlation between the change in protein abundance and the change in transcript abundance in cells grown in metal replete and metal deficient conditions is even stronger. Examples of new discoveries highlighted in this work include the accumulation of O2 labile, anaerobiosis-related enzymes (Hyd1, Pfr1, and Hcp2) in copper deficient cells, loss of various stromal and lumenal, photosynthesis-related proteins including plastocyanin in iron limited cells, large accumulation (from undetectable amounts to over 1,000 zmol/cell) of two COG0523 domain-containing proteins in zinc deficient cells, and the preservation of photosynthesis proteins in manganese deficient cells despite known losses in photosynthetic function in this condition.