Integrated Sample Processing System Involving On-Column Protein Adsorption, Sample Washing, and Enzyme Digestion for Protein Identification by LC−ESI MS/MS

A protein processing filter method for bacterial identification by mass spectrometry-based proteomics

A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposable filter unit placed inside a centrifuge vial for processing and digestion of bacterial proteins. Each processing stage allows filtration of excess reactants and unwanted byproduct while retaining the proteins. Upon addition of trypsin, the peptide mixture solution is passed through the filter while retaining the trypsin enzyme. The peptide mixture is then analyzed by LC-MS/MS with an in-house BACid algorithm for a comparison of the experimental unique peptides to a constructed proteome database of bacterial genus, specie, and strain entries. The concentration of bacteria was varied from 10 × 10(7) to 3.3 × 10(3) cfu/mL for analysis of the effect of concentration on the ability of the sample processing, LC-MS/MS, and data analysis methods to identify bacteria. The protein processing method and dilution procedure result in reliable identification of pure suspensions and mixtures at high and low bacterial concentrations.

A facile microdialysis interface for on-line desalting and identification of proteins by nano-electrospray ionization mass spectrometry

The adverse effect of salts, especially inorganic salts, on electrospray ionization mass spectrometry (ESI-MS) is one of the most serious obstacles that might limit its application. Among the numerous desalting approaches, the microdialysis technique is favorable for large molecules, such as proteins. In this work, employing a hollow fiber membrane of cellulose acetate (MWCO 3000 Da), a simple, facile and efficient microdialysis interface with the dead volume of less than 1 microL was constructed for the on-line desalting and identification of proteins dissolved in high salt concentration buffer by nano-ESI-MS. Furthermore, with counterflow added, the desalting procedure was accelerated, and could be finished within 1 min. This system was successfully applied to the analysis of myoglobin dissolved in either high concentration ammonium acetate or sodium chloride buffer. The experimental results showed that, by using such a microdialysis interface, the salt concentration, even as high as 1 M, could be decreased by at least 2 orders of magnitude, while sample loss was less than 10%, demonstrating the potential of such an interface in broadening the application of nano-ESI-MS in the analysis of large molecules.

Development of an open-tubular trypsin reactor for on-line digestion of proteins

A study was initiated to construct a micro-reactor for protein digestion based on trypsin-coated fused-silica capillaries. Initially, surface plasmon resonance was used both for optimization of the surface chemistry applied in the preparation and for monitoring the amount of enzyme that was immobilized. The highest amount of trypsin was immobilized on dextran-coated SPR surfaces which allowed the covalent coupling of 11 ng mm⁻² trypsin. Fused-silica capillaries were modified in a similar manner and the resulting open-tubular trypsin-reactors having a pH optimum of pH 8.5, display a high activity when operated at 37 °C and are stable for at least two weeks when used continuously. Trypsin auto-digestion fragments, sample carry-over, and loss of signal due to adsorption of the protein were not observed. On-line digestion without prior protein denaturation, followed by micro-LC separation and photodiode array detection, was tested with horse-heart cytochrome C and horse skeletal-muscle myoglobin. The complete digestion of 20 pmol μL⁻¹ horse cytochrome C was observed when the average residence time of the protein sample in a 140 cm ×50 μm capillary immobilized enzyme reactor (IMER) was 165 s. Mass spectrometric identification of the injected protein on the basis of the tryptic peptides proved possible. Protein digestion was favorable with respect to reaction time and fragments formed when compared with other on-line and off-line procedures. These results and the easy preparation of this micro-reactor provide possibilities for miniaturized enzyme-reactors for on-line peptide mapping and inhibitor screening.

Advances in hyphenated analytical techniques for shotgun proteome and peptidome analysis--a review

Proteomics is defined as the analysis of part or all of the protein components of a complex biological system (a cell, organ or tissue) at a given moment. Due to the huge number of proteins encoded by the genome, novel analytical techniques must be developed to meet the need of large scale analysis. This has led to the hyphenation of multiple techniques to achieve this object. Here current status of the hyphenated analytical techniques of one-dimensional and multidimensional liquid chromatography-mass spectrometry for shotgun proteomic analysis is reviewed, and on-line techniques for automated sample preparation and injection are also covered. In addition, the hyphenated techniques for peptidome analysis are also covered.

The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells

Mass spectrometry (MS) coupled to affinity purification is a powerful approach for identifying protein-protein interactions and for mapping post-translational modifications. Prior to MS analysis, affinity-purified proteins are typically separated by gel electrophoresis, visualized with a protein stain, excised, and subjected to in-gel digestion. An inherent limitation of this series of steps is the loss of protein sample that occurs during gel processing. Although methods employing in-solution digestion have been reported, they generally suffer from poor reaction kinetics. In the present study, we demonstrate an application of a microfluidic processing device, termed the Proteomic Reactor, for enzymatic digestion of affinity-purified proteins for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Use of the Proteomic Reactor enabled the identification of numerous ubiquitinated proteins in a human cell line expressing reduced amounts of the ubiquitin-dependent chaperone, valosin-containing protein (VCP). The Proteomic Reactor is a novel technology that facilitates the analysis of affinity-purified proteins and has the potential to aid future biological studies.

The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis

Gel-free proteomics has emerged as a complement to conventional gel-based proteomics. Gel-free approaches focus on peptide or protein fractionation, but they do not address the efficiency of protein processing. We report the development of a microfluidic proteomic reactor that greatly simplifies the processing of complex proteomic samples by combining multiple proteomic steps. Rapid extraction and enrichment of proteins from complex proteomic samples or directly from cells are readily performed on the reactor. Furthermore, chemical and enzymatic treatments of proteins are performed in 50 nL effective volume, which results in an increased number of generated peptides. The products are compatible with mass spectrometry. We demonstrated that the proteomic reactor is at least 10 times more sensitive than current gel-free methodologies with one protein identified per 440 pg of protein lysate injected on the reactor. Furthermore, as little as 300 cells can be directly introduced on the proteomic reactor and analyzed by mass spectrometry.

Monolithic Column HPLC Separation of Intact Proteins Analyzed by LC-MALDI Using On-Plate Digestion: An Approach To Integrate Protein Separation and Identification

A method is developed to integrate a protein separation by monolithic capillary reversed-phase high-performance liquid chromatography to on-probe tryptic digestion for subsequent analyses by MALDI-TOF MS and MALDI-TOF/TOF MS. The method provides a means of directly interfacing separations to MALDI-MS, reducing the amount of time required for traditional procedures involving in-solution enzymatic digestion and sample cleanup prior to MALDI-MS analysis. When used with pI-based fractionation as a first dimension, it provides a means of analyzing complex mixtures of proteins with minimal sample handling and cleanup. The use of monolithic capillary columns sufficiently resolved intact proteins so that peptide mass fingerprinting analysis by MALDI-TOF MS resulted in the identification of close to 40 unique proteins from 120 ng of sample obtained from a prefractionated MCF10 cell line at pH 6.34, where the identifications of several of these proteins were also confirmed by intact MW and tandem mass spectrometric analysis. The reproducibility of this method has been demonstrated to be sufficient for the purpose of protein identifications. Experimental values of protein intact MW are obtained and compared to that expected for each protein identified.

Multilayer-Assembled Microchip for Enzyme Immobilization as Reactor Toward Low-Level Protein Identification

A microchip reactor has been developed on the basis of a layer-by-layer approach for fast and sensitive digestion of proteins. The resulting peptide analysis has been carried out by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Natural polysaccharides, positively charged chitosan (CS), and negatively charged hyaluronic acid (HA) were multilayer-assembled onto the surface of a poly(ethylene terephthalate) (PET) microfluidic chip to form a microstructured and biocompatible network for enzyme immobilization. The construction of CS/HA assembled multilayers on the PET substrate was characterized by AFM imaging, ATR-IR, and contact angle measurements. The controlled adsorption of trypsin in the multilayer membrane was monitored using a quartz crystal microbalance and an enzymatic activity assay. The maximum proteolytic velocity of the adsorbed trypsin was approximately 600 mM/min mug, thousands of times faster than that in solution. BSA, myoglobin, and cytochrome c were used as model substrates for the tryptic digestion. The standard proteins were identified at a low femtomole per analysis at a concentration of 0.5 ng/muL with the digestion time <5s. This simple technique may offer a potential solution for low-level protein analysis.