Fast on-column protein digestion with subsequent peptide mapping using tandem mass spectrometry with information dependent acquisition

Mass spectrometric analysis of peptides from an immobilized lipase: focus on oxidative modifications

Liquid chromatography/tandem mass spectrometry (LC/MS/MS) was used to study the primary structure of immobilized Candida antarctica lipase B (Novozym(R)435) without detaching the enzyme from the carrier. The immobilized enzyme packed in a miniature column was subjected to proteolysis and the peptides released were injected into the mass spectrometer for analysis. The set-up was utilized to determine amino acid oxidation after treatment of the biocatalyst with hydrogen peroxide. In total, sequence coverage of more than 90% was obtained, containing almost all of the amino acids sensitive to oxidation. Oxidation of methionine, tryptophan and cystine residues was observed. The flow system also allowed evaluation of the enzyme activity prior to peptide analysis. The developed method is general and should be applicable to other immobilized enzyme systems and to different treatments.

Miniaturized on-line digestion system for the sequential identification and characterization of protein analytes

A miniaturized on-column digestion system constructed for the sequential analysis of semi-purified protein analytes is presented. By utilizing fused silica capillary (diameter 150microm) packed with a zone of trypsin-modified Eupergit C beads and a second zone of reversed-phase C18 material, a linear column set-up was constructed. The protein analytes (pmol amounts) were first digested in the 600nl trypsin reactor portion of the system. Next, the generated peptides were trapped in the C18 column shaped as an electrospray emitter. Finally, after washing the matrix free from salts and other hydrophilic impurities present in the sample, peptides were eluted. A stepwise increased concentration profile of organic solvent, created by a dual syringe pump system, promoted the release of bound peptides, which were identified by electrospray ionization MS/MS. This approach proved to be very efficient, achieving almost complete digestion of the proteins studied, with suitable operational stability maintained for more than 1 week. Further, a small nebulizer was designed and fitted to the electrospray emitter. A significant improvement of the spray stability was observed and droplet build-up on the capillary was avoided, even at flow rates well above 1500nl/min. The proteins chloroperoxidase, staphylococcal enterotoxin B and protein A (injection volume 0.3microl, salt concentration 0.2-1M) were sequentially digested, desalted, eluted, detected and conclusively identified by bioinformatics web tools with an analytical cycle time of 10min.

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.