•PRM enabled the qualitative and quantitative analysis of mAbs and its glycosylation.•Absolute quantitation of mAbs and their glycoforms was achieved in serum and tissues.•HILIC enrichment enabled the in-depth analysis of low abundant glycopeptides.Monoclonal antibodies (mAbs), are one of the most important protein drugs have attracted increasing attention. However, the pharmacokinetics of mAbs has not been fully investigated due to the complexity of protein drugs. Traditonal immuno-based approaches can not recognize the proteoforms of mAbs because of the long development cycles, prohibitive cost, and interactions between different proteins. Therefore, reliable qualitative and quantitative analysis of the proteoforms of mAbs in biological samples is of crucial importance. Herein, a novel method was developed for absolute quantitation of mAbs and their glycoforms in complex biological samples such as serum and tissues. With the combination of HILIC enrichment and parallel reaction monitoring by high resolution mass spectrometry, most of the glycoforms can be accurately quantified at the fmol level through the use of the model mAb of bevacizumab. More importantly, the structural confirmation can be achieved simultaneously without the need for additional experiments. This strategy can be readily applied to the pharmacokinetic study of glycosylation modification and biomarker discovery for clinical applications.

•Human urine peptides were selectively enriched by mesoporous nanoparticles.•The extracted peptides were pre-fractionated by size exclusion chromatography.•The pH of urine should be kept at its native state to avoid protein proteolysis.Peptides in urine are excreted by kidney from the blood and tissues, which are composed of a large amount of hormones, cytokines, regulatory factors and the metabolized fragments of proteins. The peptide distribution in urine will reflect the physiological and pathophysiological processes in body. In past, limited information was reported about the composition of the peptides in urine. One possible reason is that the peptides in urine are fairly low abundant and there are high concentrations of salts and organic metabolites in the urine. In this report, we extracted the peptides from human urine by highly ordered mesoporous silica particles with the pore size of 2 nm, which will exclude the high molecular weight proteins over 12 kDa. The extracted peptides were then separated into fractions according to their molecular weight by size exclusion chromatography. Each of the fractions was further analyzed by MALDI-TOF MS and μRPLC–MS/MS. Totally, 193 peptides were identified by two-dimensional SEC/μRPLC–MS/MS analysis. By analyzing the progenitor protein of the peptides; we found that two-thirds of the proteins differed from the reported urine proteome database, and the high abundant proteins in urine proteome were less detected in the urine peptidome. The developed extraction and separation methods were efficient for the profiling of the endogenous peptides in human urine. The peptidome in human urine was complementary to the human urinary proteome and may provide an emerging field for biomarker discovery.

A strategy for the absolute quantitation of metabolic enzymes in rat liver microsomes was developed based on shotgun-based proteomics approach. Rat liver microsomes were digested with trypsin, and drug metabolizing enzymes were determined by liquid chromatography tandem mass spectrometry (LC-MS/MS) using standard curves based on custom synthesized specific peptides for each enzyme. The assays for cytochrome P450 (CYP450) and uridine diphosphoglucuronosyl transferase (UGT) showed good linearity (r > 0.995) with lower limits of quantitation of 10 nM. A synthetic isotope labeled specific peptide was then used as internal standard to determine UGT1A1 by stable isotope dilution method. The labeled peptide behaved similarly to the unlabeled peptide in LC-MS/MS and the assay was linear in matrix solution. The UGT1A1 concentration was detected by the labeled peptide method to be 18.2 pmol mg−1 protein compared with 17.3 pmol mg−1 protein obtained by the standard curve method. Although the consistent results were achieved by the two methods, the stable isotope dilution method was more convenient and more suitable for high throughput determinations in complex systems.Specific peptides from seven P450 and UGT isoforms were selected for the absolute protein quantification in rat liver microsomes by shotgun-based proteomic approach.

•A simple system was established for on-line extraction of peptides from serum.•SCX-RAM materials were used for the selective enrichment of serum peptides.•2D-LC-MS was explored for the separation and identification of endogenous peptides.The selective extraction of endogenous serum peptides has been a challenge due to the high abundant proteins present in serum. Here a simple on-line extraction of peptides from human serum using strong cation-exchange diol silica restricted-access materials (SCX-RAM) coupled with two-dimensional RP–RP liquid chromatography mass spectrometry was developed. The operation of the on-line extraction system is simple to use and does not need complex equipments. The two-dimensional RP–RP was proved to be orthogonal and efficient to separate peptides extracted from human serum.