A multidimensional liquid chromatography-tandem mass spectrometry platform to improve protein identification in high-throughput shotgun proteomics.

A new on-line multidimensional system for sequential trapping and individual elution and separation of peptides based on their molecular weight is described. By sequentially using two chemically different trapping columns, a polymethacrylate monolith and a packed C18 one, peptides from complex samples can be on-line trapped and divided into two fractions, containing respectively mainly medium-large peptides and smaller peptides. Then, by means of two switching valves working in parallel, the two fractions were individually separated by reversed phase chromatography. The whole gradient consisted of two subgradients, with the first one dedicated to the separation of smaller peptides and the second one to the separation of larger peptides. Such configuration allowed to identify up to 1476 proteins in a standard E. coli tryptic digest, with improved performance, increased average sequence coverage and reduced single unique peptide identifications compared to a conventional shotgun proteomics configuration comprising only the C18 trapping column and the analytical column.

Capillary methacrylate-based monoliths by grafting from/to γ-ray polymerization on a tentacle-type reactive surface for the liquid chromatographic separations of small molecules and intact proteins.

Capillary methacrylate-based monoliths were prepared for the high performance liquid chromatography (HPLC) separation of both small molecules and large biomolecules. An efficient grafting from/to synthetic approach was adopted introducing a network of activated sites in the inner wall surface using the new silanization agent (N-trimethoxysilylpropyl)-polyethylenimine. Copolymerization of lauryl methacrylate monomer and 1,6-hexanediol dimethacrylate cross-linker in the presence of porogenic solvents was obtained under continuous γ-ray exposure with high conversion yield. The morphology and porous structure of the resulting monoliths have been investigated by Scanning Electron Microscopy (SEM) and 1H NMR cryoporosimetry. By chromatographic investigation, the new capillary columns attested high kinetic performance (with efficiency larger than 100,000 theoretical plate/m for small molecules at optimum mobile phase linear velocity of about 0.5mm/s) and also excellent mechanical stability and repeatability. The new methacrylate-based monolithic capillary columns have been successfully employed for efficient reversed-phase separation of intact proteins and peptides.

Separation of intact proteins on γ-ray-induced polymethacrylate monolithic columns: A highly permeable stationary phase with high peak capacity for capillary high-performance liquid chromatography with high-resolution mass spectrometry.

Polymethacrylate-based monolithic capillary columns, prepared by γ-radiation-induced polymerization, were used to optimize the experimental conditions (nature of the organic modifiers, the content of trifluoroacetic acid and the column temperature) in the separation of nine standard proteins with different hydrophobicities and a wide range of molecular weights. Because of the excellent permeability of the monolithic columns, an ion-pair reversed-phase capillary liquid chromatography with high-resolution mass spectrometry method has been developed by coupling the column directly to the mass spectrometer without a flow-split and using a standard electrospray interface. Additionally, the high working flow and concomitant high efficiency of these columns allowed us to employ a longer column (up to 50 cm) and achieve a peak capacity value superior to 1000. This work is motivated by the need to develop new materials for high-resolution chromatographic separation that combine chemical stability at elevated temperatures (up to 75°C) and a broad pH range, with a high peak capacity value. The advantage of the γ-ray-induced monolithic column lies in the batch-to-batch reproducibility and long-term high-temperature stability. Their proven high loading capacity, recovery, good selectivity and high permeability, moreover, compared well with that of a commercially available poly(styrene-divinylbenzene) monolithic column, which confirms that such monolithic supports might facilitate analysis in proteomics.

Evaluation of two sub-2 µm stationary phases, core-shell and totally porous monodisperse, in the second dimension of on-line comprehensive two dimensional liquid chromatography, a case study: separation of milk peptides after expiration date.

Milk is a rich source of bioactive peptides of great interest for their healthy properties. These peptides are usually encrypted in the sequences of proteins and are released after time dependent proteolysis as very complex hydrolysates. In order to separate and identify the bioactive sequences, we developed an on-line comprehensive two dimensional liquid chromatography approach using the high performance combined with the ultra high performance conditions. A microbore reversed phase (C18 silica, 5 µm) column was employed in first dimension, while, in second dimension, two different UHPLC columns, packed with C18 silica, were tested: a new column based on monodisperse sub-2 µm fully porous particles with high surface area (50 mm × 3.0 mm, 1.9 µm d.p., from Supelco), and a column based on sub-2 µm core-shell particles (50 mm × 3.0 mm, 1.7µm d.p, from Phenomenex(®)). Both set-ups were compared, showing high peak capacity values with respect to a high efficiency monodimensional method, maintaining the same analysis time. Satisfactory selectivity was obtained through the use of different pH between the two dimension, while a very fast continuous shifted gradient in second dimension ensured a good employment of the 2D separation space.

Toward enantioselective nano ultrahigh-performance liquid chromatography with Whelk-O1 chiral stationary phase.

In this study, a Whelk-O1 chiral stationary phase immobilized on 2.5 µm silica particles was employed in nanoLC. Two nanocolumns (180 and 250 mm long, 75 µm id) with a single polymeric organic monolithic outlet frit were packed under high-pressure ultrasonic-assisted packing procedure. The monolithic outlet frit was prepared by thermal polymerization of methacrylate-based monomers affording high-mechanical stability and high-pressure resistance. Very efficient enantioseparations with more than 70 000 plates/m were achieved in normal phase mode by eluting (+/-) acenaphthenol. Nanocolumns were also tested in RP mode by using on-line MS detection with nano-spray ESI ion source. Kinetic performances of columns in RP mode were comparable to those in normal phase-conditions.

Analysis of bovine milk caseins on organic monolithic columns: an integrated capillary liquid chromatography-high resolution mass spectrometry approach for the study of time-dependent casein degradation.

Casein proteins constitute approximately 80% of the proteins present in bovine milk and account for many of its nutritional and technological properties. The analysis of the casein fraction in commercially available pasteurized milk and the study of its time-dependent degradation is of considerable interest in the agro-food industry. Here we present new analytical methods for the study of caseins in fresh and expired bovine milk, based on the use of lab-made capillary organic monolithic columns. An integrated capillary high performance liquid chromatography and high-resolution mass spectrometry (Cap-LC-HRMS) approach was developed, exploiting the excellent resolution, permeability and biocompatibility of organic monoliths, which is easily adaptable to the analysis of intact proteins. The resolution obtained on the lab-made Protein-Cap-RP-Lauryl-γ-Monolithic column (270 mm × 0.250 mm length × internal diameter, L × I.D.) in the analysis of commercial standard caseins (αS-CN, ß-CN and κ-CN) through Cap-HPLC-UV was compared to the one observe using two packed capillary C4 columns, the ACE C4 (3 µm, 150 mm × 0.300 mm, L × I.D.) and the Jupiter C4 column (5 µm, 150 mm × 0.300 mm, L × I.D.). Thanks to the higher resolution observed, the monolithic capillary column was chosen for the successive degradation studies of casein fractions extracted from bovine milk 1-4 weeks after expiry date. The comparison of the UV chromatographic profiles of skim, semi-skim and whole milk showed a major stability of whole milk towards time-dependent degradation of caseins, which was further sustained by high-resolution analysis on a 50-cm long monolithic column using a 120-min time gradient. Contemporarily, the exact monoisotopic and average molecular masses of intact αS-CN and ß-CN protein standards were obtained through high resolution mass spectrometry and used for casein identification in Cap-LC-HRMS analysis. Finally, the proteolytic degradation of ß-CN in skim milk and the contemporary formation of low-molecular-weight proteose-peptones (PP) with exact monoisotopic Mr between 9444.0989 Da and 14098.9861 Da was confirmed through the deconvolution of high resolution mass spectra and literature data.