Shotgun proteomics reveals biochemistry of normal and acute respiratory distress syndrome bronchoalveolar lavage fluid proteome

Abstract

Recently, so-called label-free quantitative proteomic methods have gained acceptance for protein expression analysis via mass spectrometry (MS). These methods allow better experiment design by circumventing the need to establish pair-wise comparisons required by popular stable isotope dilution methods (for example, isotope coded affinity tag, isobaric tags for relative and absolute quantitation and stable-isotope labelling by amino acids in cell culture) and are thus fundamentally better suited for proteome studies where sample number is large. Here we discuss the use of shotgun proteomics (that is, no prior protein fractionation) and label-free quantitative methods to characterize human bronchoalveolar lavage fluid (BALF) proteomes of six normal healthy volunteers and three patients with acute respiratory distress syndrome (ARDS) [1].