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Simple Summary: Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is time consuming though still may yield poor digestion efficiency. While raising the temperature should theoretically accelerate the digestion, it also destabilizes the enzyme and promotes trypsin de-activation. We therefore questioned whether elevated temperature is beneficial for improving tryptic digestion. Here, we quantify protein digestion kinetics at elevated temperatures for calcium-stabilized trypsin and enforce the critical importance of calcium ions to preserve the enzyme. We quantitatively demonstrate that 1 h at 47 °C provides a superior digest when compared to conventional (overnight, 37 °C) processing of the proteome. The practical impact of our enhanced digestion protocol is shown through bottom-up mass spectrometry analysis of a complex proteome mixture. Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency. [ABSTRACT FROM AUTHOR]

Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency.

The effect of increasing the trypsin amount in bottom-up based targeted protein analysis is evaluated. By applying an increased trypsin-to-protein ratio (1:1 (w/w)) after heat denaturation (60 °C), reduction and alkylation, the digestion time could be reduced profoundly compared to conventional digestion conditions (ratio 1:40, overnight) without compromising method sensitivity or digestion repeatability. The procedure was obtained after a systematic evaluation of trypsin level and trypsin quality using a set of three model proteins: human chorionic gonadotropin (hCG), bovine serum albumin (BSA) and cytochrome C (CytC). All peptides monitored were produced at similar or higher levels after 45 min at trypsin-to-protein ratio 1:1, compared to conventional overnight digestion (exception: CytC using modified trypsin, required up to 4 h (at 1:1 ratio) in order achieve this). Peptide decay due to chymotryptic activity was observed at longer digestion times, but the effect was circumvented using digestion times <4 h. The accelerated digestion protocol (1:1 (w/w), 45 min) was applied to realistic human serum samples containing the biomarker protein hCG to demonstrate its applicability. [ABSTRACT FROM AUTHOR]

A simple, fast digestion procedure for fresh and dried foods, using high-power pulsed UV photolysis in the presence of hydrogen peroxide, is being developed. The homogenized food samples were mixed with H2O2 or with a mixture of H2O2 and HNO3, and irradiated for short times with a 248-nm UV excimer laser. After centrifugation, a clear, colorless solution was obtained and aliquots were deposited on Teflon filters for XRF and/or PIXE analyses. Standard reference materials (NIST Peach Leaves; Typical Diet) were also analyzed to compare recoveries and detection limits. Improvements in detection limits were observed, but a few trace elements (<1 ppm) were not reproducibly detected (Fe, Sr). This method proved to be practical for the accelerated digestion of food samples and preparing analytes in short-time intervals. In combination with PIXE and XRF, it allows high-sensitivity multi-elemental analyses for screening the nutritional elements and for food safety purposes regarding the potential presence of toxic elements. Further development to optimize and validate this procedure for a broader range of analytes is in progress. [Copyright &y& Elsevier]

• It is important to monitor effect of process changes on PTMs in mAb proteins. • A good LC-MS peptide mapping is required to semi-quantitate PTMs. • Artifact PTMs induced by sample preparation result in overestimation of PTMs. • Peptide mapping should minimize artifact PTMs induced by sample preparation. • PCT-assistant sample preparation significantly reduces artifact PTMs. Peptide mapping by liquid chromatography-mass spectrometry (LC-MS) is a common method for characterizing primary sequences of monoclonal antibodies (mAbs) and their post-translational modifications (PTMs). Most methods prepare digests by incubating samples with proteases from several hours to overnight. This often induces artifacts of some modifications such as deamidation and isomerization, resulting in overestimated product-related modifications levels. Hour-long-digestion can generate complicate chromatographic profiles due to semi-cleavages or other unnecessary reactions, interfering with the quantitation of peaks of interest. On the other hand, shortening digestion-time can cause incomplete peptide cleavages, thus low sequence coverage and poor repeatability. This study applied pressure cycling technology (PCT) to tryptic digestion and PNGase F deglycosyaltion. A 0.5-h PCT assistant tryptic digestion, by alternating cycles of 10-s atmospheric pressure and 50-s high pressure (30 kpsi) at 37 °C, was evaluated and compared with two conventional digestions, 4-h and 18-h (i.e., overnight) incubations at 37 °C under atmospheric pressure. The 0.5-h PCT assistant deglycosylation was also assessed using the same conditions as those by PCT tryptic digestion. The results demonstrated the application of a 0.5-h PCT to tryptic digestion minimized modification artifacts and reduced interference with quantitation by providing a clean chromatographic profile. The 0.5-h PCT assistant deglycosylation completely removed the N-glycans from the Asn 301 in the heavy chains of monoclonal antibody with no impact on the chromatographic profile of the tryptic digests. [ABSTRACT FROM AUTHOR]

Proteolytic digestion is a time consuming and critical step in bottom-up proteomic analysis. The most widely used protease, trypsin, has high specificity and generates peptides that are considered to be ideally suited for bottom-up LC-MS technology. By exploiting key factors affecting enzymatic activity we obtained a simple, straightforward, and rapid in-solution digest protocol that performed better than the conventional overnight digestion method in terms of amino acid coverage of proteins, number of peptides generated, and peptide ion abundances. Prolonged digestion time, such as overnight digestion, leads to decline in protein amino acid coverage and loss of tryptic peptides. This was found to be caused by complete digestion by trypsin leading to an increased number of small peptides that are not LC-MS detectable. Slow-rate nontryptic digestion of peptides is a contributing factor for loss of peptide ion intensities during extended digestion time. Our work demonstrates that for both qualitative and quantitative bottom-up proteomic studies it is beneficial to prevent trypsin digestion to go to completion by reducing treatment time from the conventional several hours to a few minutes cleavage time., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)