Fungal biotechnology has been well established in food and healthcare sector, and now being explored for lignocellulosic biorefinery due to their great potential to produce a wide array of extracellular enzymes for nutrient recycling. Due to global warming, environmental pollution, green house gases emission and depleting fossil fuel, fungal enzymes for lignocellulosic biomass refinery become a major focus for utilizing renewal bioresources. Proteomic technologies tender better biological understanding and exposition of cellular mechanism of cell or microbes under particular physiological condition and are very useful in characterizing fungal secretome. Hence, in addition to traditional colorimetric enzyme assay, mass-spectrometry-based quantification methods for profiling lignocellulolytic enzymes have gained increasing popularity over the past five years. Majority of these methods include two dimensional gel electrophoresis coupled to mass spectrometry, differential stable isotope labeling and label free quantitation. Therefore, in this review, we reviewed more commonly used different proteomic techniques for profiling fungal secretome with a major focus on two dimensional gel electrophoresis, liquid chromatography-based quantitative mass spectrometry for global protein identification and quantification. We also discussed weaknesses and strengths of these methodologies for comprehensive identification and quantification of extracellular proteome.
Recent developments in MS-based glycomics and glycoproteomics have rapidly advanced the field and pushed the boundaries of glyco-analysis into new territories. This review will lay out current workflows and strategies for characterization of the glycoproteome, including (in order of increasing complexity and information content) preliminary site mapping, compositional glycan profiling, isomer-specific glycan profiling, glycosite-specific glycopeptide profiling, and finally, glycoproteomic profiling.
Headspace solid phase micro-extraction gas chromatography/flame ionization detection (HS-SPME-GC/FID) method was compared with headspace gas chromatography/mass selective detection (HS-GC/MS). Organic solvent-spiked urine as well as urine samples from workspace was analyzed under optimal condition of each method. Detection limit of each compound by HS-SPME-GC/FID was 3.4-9.5 μg/L, which enabled trace analysis of organic solvents in urine. Linear range of each organic solvent was 10-400 μg/L, with fair correlation coefficient between 0.992 and 0.999. The detection sensitivity was 4 times better than HS-GC/MS in selected ion monitoring (SIM) mode. Accuracy and precision was confirmed using commercial reference material, with accuracy around 90% and precision less than 4.6% of coefficient of variance. Among 48 urine samples from workplace, toluene was detected from 45 samples in the range of 20-324 μg/L, but no other solvents were found. As a method for trace analysis, SPME HS GC/FID showed high sensitivity for biological monitoring of organic solvent in urine.
The effects of trifluoroacetic acid (TFA) were evaluated on the generation of multiply charged ions of cytochrome c in a 2-nitrophloroglucinol (2-NPG) matrix in high-vacuum, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The presence of 1% TFA in the 2-NPG matrix solution was more effective in generating multiply charged protein ions than matrix solutions containing 0.1% or 0% TFA. Regarding the matrix itself, with 1% TFA, 2-NPG was significantly more effective in generating multiply charged ions than 2,5-dihydroxybenzoic acid (2,5-DHB). The maximum charge state of cytochrome c was +8 when using a 2-NPG matrix containing 1% TFA.