Interactions between proteins and humic substances affect protein identification by mass spectrometry

Soil proteomics is facing problems such as low yields of protein extraction from soil and low protein identification rates as compared to theoretical estimates of soil proteome. This work aimed to evaluate the effect of soilborne humic substances (HS) on the identification of model proteins with different properties, such as myoglobin (Mb), α-glucosidase (αG), and β-glucosidase (βG), by using electrophoretic and ESI- and MALDI-mass spectrometry (MS) methodologies. Results showed that the contact between proteins and HS did not alter protein electrophoretic mobility but led to protein modifications that affected protein identification by MS. The decrease in protein identification parameters was more evident for Mb than for αG and βG, probably due to its lower molecular weight and less complex molecular structure. Analysis of MS data indicated that hydrophobic interactions could be responsible for the observed effects of contact between proteins and HS.