Tryptic Digestion Of Proteins Research Articles

Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures.

A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined. Thus, we investigated the reasons why was it so, to help to improve the identification success rate. Focusing on O-linked glycopeptides, we noticed that in EThcD, larger glycan oxonium ions better survive the activation than those in HCD. These fragments, combined with reducing terminal Y ions, provide important information about the glycan(s) present, so we investigated whether filtering the peaklists for glycan oxonium ions indicating the presence of a tetra- or hexasaccharide structure would help to reveal all molecules containing such glycans. Our study showed that intact glycans frequently do not survive even mild supplemental activation, meaning one cannot rely on these oxonium ions exclusively. We found that ETD efficiency is still a limiting factor, and for highly glycosylated peptides, the only information revealed in EThcD was related to the glycan structures. The limited overlap of results delivered by the two search engines draws attention to the fact that automated data interpretation of O-linked glycopeptides is not even close to being solved. Graphical abstract ᅟ.

Abstract 425: Resistin induced Differential Global Protein Expression in Human Macrophage

Background: Human resistin synthesized by macrophages is shown to be associated with insulin resistance, type 2 diabetes, atherosclerosis, and chronic inflammation. However, there are several missing links related to downstream targets and intracellular signaling pathways involving hyper-resistinemia-associated metabolic disorders. In this study, we used a comparative global protein expression profiling of human macrophage treated with resistin to identify some of these missing links. Methods: Human macrophage (Mϕ) derived from THP1 cells were treated with 10ng/ml of human resistin for 48 hrs. Samples of total protein tryptic digest of untreated control and resistin-treated Mϕ were analyzed by HPLC-ESI-MS/MS. Differentially expressed proteins were analyzed by using the Gene Ontology (GO), DAVID, and KEGG databases to characterize their potential functional roles and related pathways. Results: Proteins with significant (ρ < 0.05) differences in expression between control and resistin treated groups are shown in Table I. The differentially expressed proteins were mainly involved in metabolic process, cell-cell adhesion, MAPK cascade, protein polyubiquitination, autophagy, and NIK/NF-κB signaling. Majority of the differentially expressed proteins were located in the extracellular exosome, mitochondrion, nucleoplasm, and proteasome complex Table II & III. Conclusion: Resistin significantly changed the expression of ∼162 proteins in human macrophage. The differentially expressed proteins are involved in metabolic process, signal transduction pathways, immunological and inflammatory response, exosome and mitochondrial function. This work provides the foundation for future in-depth understanding of resistin-associated metabolic derangement.

Highly uniform porous silica layer open-tubular capillary columns produced via in-situ biphasic sol–Gel processing for open-tubular capillary electrochromatography

We report a highly uniform porous layer open tubular (PLOT) column for capillary electrochromatography (CEC) analysis. The PLOT column is easily fabricated using a single-step in-situ biphasic reaction, producing homogeneous porous-layer modified surface with ∼240 nm thickness in a 50 μm-id capillary. CEC performance of the PLOT column has been investigated and optimized under various experimental parameters. Using a mixture of naphthalene and biphenyl as the test sample, we show that the PLOT column exhibits good separation efficiency with resolution >3.0 and theoretical plate numbers over 6 × 104, as well as good intra-/inter-day repeatability and column-to-column repeatability. The column has been successfully applied for CEC analysis of three different types of samples without any further modification of the columns, including complicated peptide products from tryptic-digestion of proteins (lysozyme and BSA), β-blockers (basic samples) and polycyclic aromatic hydrocarbons (neutral samples). Efficient separation has been achieved, which could be attributed to the enhanced surface-to-volume ratio of the PLOT column that will increase the interaction between solid phase and mobile phase in CEC. In addition, base-line separation of neutral samples indicates the reversed phase chromatographic property of the PLOT column, which could be induced by the residue of hexadecyltrimethylammonium bromide used in the fabrication process. Our study show that the present PLOT column is a promising approach that can significantly enhance CEC separation efficiency and could be of potential value in analysis of various different samples.

Identification of proteins contained in aqueous extracts of wheat bran through a proteomic approach

Proteins of aqueous extracts of wheat bran are usually considered as the albumin fraction, and have been characterized in terms of molecular weight, amino acid content and functional properties. However, there are no reports on the variety of the extracted proteins and their amino acid sequence, despite this information would be useful if the extracts were used in distinct applications. In the present work, the proteins contained in the aqueous extracts of wheat bran were separated by SDS-PAGE. Nineteen bands with molecular weights in the range 8─93 kDa were revealed in the SDS-PAGE gels. After tryptic digestion of proteins, the resulting peptides were analyzed by tandem mass spectrometry. Database search against the Viridiplantae subset of the NCBInr protein database resulted in 39 unique proteins, 11 from which had not been previously identified in different sections of the wheat grain through proteomic analysis. Most of the proteins were metabolic and stress defense enzymes, with the storage proteins representing just a minor fraction.

Antigen 85B peptidomic analysis allows species-specific mycobacterial identification

BackgroundNontuberculous mycobacteria (NTM)-mediated infections are a growing cause of worldwide morbidity, but lack of rapid diagnostics for specific NTM species can delay the initiation of appropriate treatment regimens. We thus examined whether mass spectrometry analysis of an abundantly secreted mycobacterial antigen could identify specific NTM species.MethodsWe analyzed predicted tryptic peptides of the major mycobacterial antigen Ag85B for their capacity to distinguish Mycobacterium tuberculosis and three NTM species responsible for the majority of pulmonary infections caused by slow-growing mycobacterial species. Next, we analyzed trypsin-digested culture supernatants of these four mycobacterial species by liquid chromatography–tandem mass spectrometry (LC–MS/MS) to detect candidate species-specific Ag85B peptides, the identity of which were validated by LC–MS/MS performed in parallel reaction monitoring mode.ResultsTheoretical tryptic digests of the Ag85B proteins of four common mycobacterial species produced peptides with distinct sequences, including two peptides that could each identify the species origin of each Ag85B protein. LC–MS/MS analysis of trypsinized culture supernatants of these four species detected one of these species-specific signature peptides in each sample. Subsequent LC–MS/MS analyses confirmed these results by targeting these species-specific Ag85B peptides.ConclusionsLC–MS/MS analysis of Ag85B peptides from trypsin-digested mycobacterial culture supernatants can rapidly detect and identify common mycobacteria responsible for most pulmonary infections caused by slow-growing mycobacteria, and has the potential to rapidly diagnose pulmonary infections caused by these mycobacteria through direct analysis of clinical specimens.

Authentication of pork in meat mixtures using PRM mass spectrometry of myosin peptides.

Adulteration of meat products is a major concern not only for economic fraud, but also for ethical reasons. In this study, we presented a parallel reaction monitoring (PRM) mass spectrometry approach for detection of trace pork in meat mixtures (chicken, sheep, and beef). Specific peptides were identified and screened by a shotgun proteomic approach based on tryptic digests of certain protein. Five surrogate peptides from myosin were screened and then used for pork detection by PRM of Orbitrap MS. When the most sensitive peptide was selected, the LOD in mixed meat can be up to 0.5%. The RSD values between detected and designated pork levels (1%, 5% and 50%) were 4–15%. The targeted method developed can be applied to identify and quantify the pork in meat mixture.

Zinc Ion-immobilized Magnetic Microspheres for Enrichment and Identification of Multi-phosphorylated Peptides by Mass Spectrometry.

The selective isolation of phosphorylated peptides and subsequent analysis using mass spectrometry is important for understanding how protein kinase and phosphatase signals can precisely modulate the on/off states of signal transduction pathways. However, the isolation and detection of multi-phosphorylated peptides is still limited due to their distinct affinity to various materials and their poor ionization efficiency. Here, we report a highly efficient and selective enrichment of phosphorylated peptides using binuclear Zn2+-dipicolylamine complex-coated magnetic microspheres (ZnMMs). ZnMMs can utilize the rapid and selective isolation/enrichment of phosphorylated peptides and the subsequent mass spectrometric analysis, given the intrinsic magnetic property of magnetic microspheres and the highly selective binding ability of the binuclear Zn2+-dipicolylamine complex to phosphate groups. α-Casein and β-casein were chosen for a proof-of-concept demonstration. We contemplated that phosphopeptides were selectively isolated and enriched from both the tryptic digests of casein proteins and mixed samples with a high degree of sensitivity by facilitating ZnMMs. Especially, ZnMMs showed high efficiency with multi-phosphopeptides, which are in general difficult to be examined by mass analysis on account of their poor ionization efficiency. For the model protein α, β-casein mixture of the tryptic digest, 17 phosphopeptides were identified with ZnMMs and 82% of the enriched phosphopeptides were multi-phosphorylated peptides, indicating that ZnMMs have excellent enrichment efficiency and strong affinity towards multi-phosphorylated peptides.

Quantification of Cardiovascular Disease Biomarkers in Human Platelets by Targeted Mass Spectrometry.

Platelets are known to be key players in thrombosis and hemostasis, contributing to the genesis and progression of cardiovascular diseases. Due to their pivotal role in human physiology and pathology, platelet function is regulated tightly by numerous factors which have either stimulatory or inhibitory effects. A variety of factors, e.g., collagen, fibrinogen, ADP, vWF, thrombin, and thromboxane promote platelet adhesion and aggregation by utilizing multiple intracellular signal cascades. To quantify platelet proteins for this work, a targeted proteomics workflow was applied. In detail, platelets are isolated and lyzed, followed by a tryptic protein digest. Subsequently, a mix of stable isotope-labeled peptides of interesting biomarker proteins in concentrations ranging from 0.1 to 100 fmol is added to 3 μg digest. These peptides are used as an internal calibration curve to accurately quantify endogenous peptides and corresponding proteins in a pooled platelet reference sample by nanoLC-MS/MS with parallel reaction monitoring. In order to assure a valid quantification, limit of detection (LOD) and limit of quantification (LOQ), as well as linear range, were determined. This quantification of platelet activation and proteins by targeted mass spectrometry may enable novel diagnostic strategies in the detection and prevention of cardiovascular diseases.

Improvement of ubiquitylation site detection by Orbitrap mass spectrometry

Ubiquitylation is an important posttranslational protein modification that is involved in many cellular events. Immunopurification of peptides containing a K-ε-diglycine (diGly) remnant as a mark of ubiquitylation combined with mass spectrometric detection has resulted in an explosion of the number of identified ubiquitylation sites. Here, we present several significant improvements to this workflow, including fast, offline and crude high pH reverse-phase fractionation of tryptic peptides into only three fractions with simultaneous desalting prior to immunopurification and better control of the peptide fragmentation settings in the Orbitrap HCD cell. In addition, more efficient sample cleanup using a filter plug to retain the antibody beads results in a higher specificity for diGly peptides and less non-specific binding. These relatively simple modifications of the protocol result in the routine detection of over 23,000 diGly peptides from HeLa cells upon proteasome inhibition. The efficacy of this strategy is shown for lysates of both non-labeled and SILAC labeled cell lines. Furthermore, we demonstrate that this strategy is useful for the in-depth analysis of the endogenous, unstimulated ubiquitinome of in vivo samples such as mouse brain tissue. This study presents a valuable addition to the toolbox for ubiquitylation site analysis to uncover the deep ubiquitinome. SignificanceA K-ε-diglycine (diGly) mark on peptides after tryptic digestion of proteins indicates a site of ubiquitylation, a posttranslational modification involved in a wide range of cellular processes. Here, we report several improvements to methods for the isolation and detection of diGly peptides from complex biological mixtures such as cell lysates and brain tissue. This adapted method is robust, reproducible and outperforms previously published methods in terms of number of modified peptide identifications from a single sample. In-depth analysis of the ubiquitinome using mass spectrometry will lead to a better understanding of the roles of protein ubiquitylation in cellular events.

Polymer Analysis in the Second Dimension: Preliminary Studies for the Characterization of Polymers with 2D MS.

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FTICR MS or 2D MS) allows direct correlation between precursor and fragment ions without isolation prior to fragmentation. The method has been optimized for the analysis of complex mixtures and used so far for the analysis of small molecules and peptides obtained by tryptic digestion of proteins and entire proteins. In this work, a 2D MS method is developed to characterize complex mixtures of polymers using infrared multiphoton decay (IRMPD) and electron capture dissociation (ECD) as fragmentation techniques, and D-α-tocopheryl polyethylene glycol 1000 succinate (TPGS), Polysorbate 80, and poly(methyl methacrylate) (PMMA) as analytes. The use of 2D MS allowed generation of fragment m/z values for all the compounds in the mixture at once and allowed tandem mass spectrometry of species very close in m/z that would have been difficult to isolate with a quadrupole for standard MS/MS. Furthermore, the use of unique features of 2D MS such as the extraction of neutral-loss lines allowed the successful assignment of peaks from low abundant species that would have been more difficult with standard MS/MS. For all the samples, the amount of information obtained with 2D MS was comparable with what obtained with multiple 1D MS/MS experiments targeted on each individual component within each mixture but required a single experiment of about 20-40 min.

Synthesis of polymeric monoliths via thiol-maleimide polymerization reaction for highly efficient chromatographic separation

One-step thiol-maleimide polymerization reaction was firstly adopted for direct preparation of polymeric monoliths via alkaline-catalyzed reaction of 4,4′-bis(maleimidophenyl)methane (BMI) and trimethylolpropane tris(3-mercaptopropionate) (3SH)/pentaerythriol tetra(3-mercaptopropionate) (4SH) in the presence of a small amount of triethylamine (TEA). The polymerization could be performed within 3h, which was faster than thermal-initiated free radical polymerization. Two kinds of monoliths, poly(BMI-co-3SH) (marked as I) and poly(BMI-co-4SH) (marked as II), were characterized with scanning electron microscopy (SEM), attenuated total reflection Fourier-transformed infrared spectroscopy (ATR-FTIR), thermal gravimetric analysis (TGA) and mercury intrusion porosimetry (MIP). Satisfactory chromatographic separation ability and column efficiency were gained for analysis of small molecular compounds such as alkylbenzenes, polynuclear aromatic hydrocarbons (EPA 610) and phenols in reversed-phase capillary liquid chromatography (cLC). High column efficiency (180,500N/m) for butylbenzene was acquired on poly(BMI-co-3SH) column I-2, which was higher than those on most reported polymeric monoliths. A retention-independent efficient performance of small molecules was obtained by plotting of plate height (H) of alkylbenzenes versus the linear velocity (u). A term values in van Deemter equation of I-2 (1.72-0.24μm) and poly(BMI-co-4SH) column II-2 (5.28-4.14μm) were smaller than those of traditional organic/hybrid monoliths. Finally, as a practical application, 53 and 2184 unique peptides from the tryptic digests of bovine serum albumin (BSA) and HeLa cell proteins were positively identified with poly(BMI-co-3SH) monolith in cLC–MS.

Facile and Selective Enrichment of Intact Sialoglycopeptides Using Graphitic Carbon Nitride.

Combining powerful selectivity, high stability, convenient operation, mild condition, and eco-friendliness, a novel graphitic carbon nitride (g-C3N4)-based enrichment method of intact sialoglycopeptides (SGs) was developed. The intact SGs could be simply enriched and separated from protein tryptic digests by hydrogen bonding without damage of glycan structures due to the specific structure of g-C3N4. By optimizing the enrichment and elution conditions, 45 and 38 SGs were detected from the tryptic digests of bovine fetuin and transferrin, respectively. Under the synergistic effect of hydrogen bonding and electrostatic adsorption, the SGs could be enriched simply in less than 2 h with a detection limit of 50 fmol. The method is repeatable due to the high stability of g-C3N4 and the simple protocol of the method, indicating the potential application of g-C3N4 in efficient and selective enrichment of intact SGs.

Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides.

Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from ten pairs of monozygotic twins. Profiling using the protein tryptic digests revealed that samples from identical twins had typically an order of magnitude fewer protein expression differences than unrelated individuals. The data did not indicate that the degree of difference within twin pairs increased with age. In parallel, data from the digests were used to detect genetically variant peptides that result from common nonsynonymous single nucleotide polymorphisms in genes expressed in the hair follicle. Compilation of the variants permitted sorting of the samples by hierarchical clustering, permitting accurate matching of twin pairs. The results demonstrate that genetic differences are detectable by proteomic methods and provide a framework for developing quantitative statistical estimates of personal identification that increase the value of hair shaft evidence.

Preparation of open tubular capillary columns by in situ ring-opening polymerization and their applications in cLC-MS/MS analysis of tryptic digest

An open tubular (OT) column (25 μm i.d.) was prepared by in situ ring-opening polymerization of octaglycidyldimethylsilyl polyhedral oligomeric silsesquioxanes (POSS-epoxy) with 4-aminophenyl disulfide (APDS) in a binary porogenic system of ethanol/H2O. It was found that porogenic composition played an important role in the formation of OT stationary phases. The ratio of ethanol/H2O at 6/1 (v/v) would lead to the fabrication of hybrid monoliths, while the ratio of ethanol/H2O at 13/1 (v/v) would result in the synthesis of OT phases. In addition, the effects of precursor content and reaction duration on the thickness of OT stationary phases were investigated. Either lower precursor content or shorter reaction duration would produce thinner layer of OT column. The repeatability of OT columns was evaluated through relative standard deviation (RSD%) with benzene as the analyte. The run-to-run, column-to-column and batch-to-batch repeatabilities were 1.7%, 4.8% and 5.6%, respectively, exhibiting satisfactory repeatability of the OT column. Then tryptic digest of mouse liver proteins was used to evaluate the performance of the resulting OT columns (25 μm i.d. × 2.5 m in length) by cLC-MS/MS analysis, demonstrating their potential in proteome analysis.

One-pot preparation of mercaptotetrazole-silica hybrid monoliths by the thiol-ene click reaction for mixed-mode capillary liquid chromatography.

A novel mercaptotetrazole-silica hybrid monolithic column was prepared for capillary liquid chromatography, in which the thiol-end mercaptotetrazole was mixed with hydrolyzed γ-methacryloxypropyltrimethoxysilane and tetramethyloxysilane for the co-polycondensation and thiol-ene click reaction in a one-pot process. The effects of the molar ratio of silanes, the amount of mercaptotetrazole, and the volume of porogen on the morphology, permeability and pore properties of the as-prepared mercaptotetrazole-silica hybrid monoliths were investigated in detail. A series of test compounds including alkylbenzenes, amides and anilines were employed for evaluating the retention behaviors of the mercaptotetrazole-silica hybrid monolithic columns. The results demonstrated that the mercaptotetrazole-silica hybrid monoliths exhibited hydrophobic, hydrophilic as well as ion-exchange interaction. The run-to-run, column-to-column and batch-to-batch reproducibilities of the mercaptotetrazole-silica hybrid monoliths were satisfactory with the relative standard deviations less than 1.4 (n=5), 3.9 (n=3) and 4.0% (n=5), respectively. In addition, the mercaptotetrazole-silica hybrid monolith was further applied to the separation of sulfonamides, nucleobases and protein tryptic digests. These successful applications confirmed the promising potential of the mercaptotetrazole-silica hybrid monolith in the separation of complex samples.

Effect of centrifugation on tryptic protein digestion

This study investigated the effect of centrifugation on tryptic digestion. This was done by applying different centrifugation speeds (6,000, 8,000, 10,000, 20,000, and 30,000×g) over various durations (0, 10, 20, 30, 40, 50, and 60 min) to digest two model proteins - cytochrome c and myoglobin. The intact proteins and resulting peptides were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Centrifugation greatly improved the tryptic digestion efficiency of cytochrome c, where either an increase in centrifugation speed or in digestion duration significantly improved the digestion of cytochrome c. However, centrifugation did not noticeably improve the digestion of myoglobin; 16 h of centrifuge-assisted tryptic digestion at 30,000×g barely removed the myoglobin protein peak. Similar results were also obtained when using conventional tryptic digestion with gentle mixing. When acetonitrile (ACN) was added to make 10% ACN buffer solutions, the myoglobin protein peak disappeared after 6 h of digestion using both centrifuge-assisted and conventional tryptic digestions.

Pyridoxal 5′-phosphate mediated preparation of immobilized metal affinity material for highly selective and sensitive enrichment of phosphopeptides

Phosphorylation is a crucial post-translational modification, which plays pivotal roles in various biological processes. Analysis of phosphopeptides by mass spectrometry (MS) is intractable on account of their low stoichiometry and the ion suppression from non-phosphopeptides. Thus, enrichment of phosphopeptides before MS analysis is indispensable. In this work, we employed pyridoxal 5′-phosphate (PLP), as an immobilized metal affinity chromatography (IMAC) ligand for the enrichment of phosphopeptides. PLP was grafted onto several substrates such as silica (SiO2), oxidized carbon nanotube (OCNT) and silica coated magnetic nanoparticles (Fe3O4@SiO2). Then the metal ions Fe3+, Ga3+ and Ti4+ were incorporated for the selective enrichment of phosphopeptides. It is indicated that Fe3O4@SiO2-PLP-Ti4+ has a superior selectivity towards phosphopeptides under as much as 1000-fold interferences of non-phosphopeptides. Further, Fe3O4@SiO2-PLP-Ti4+ exhibited high efficiency in selective enrichments of phosphopeptides from complex biological samples, including human serum and tryptic digested non-fat milk. Finally, Fe3O4@SiO2-PLP-Ti4+ was successfully employed in the sample pretreatment for profiling phosphopeptides in a tryptic digest of rat brain proteins. Our experimental results evidenced a great potential of this new chelator-based material in phosphoproteomics study.

An immobilized titanium (IV) ion affinity chromatography adsorbent for solid phase extraction of phosphopeptides for phosphoproteome analysis

In this study, we developed a centrifugation assisted solid phase extraction (SPE) method for the selective enrichment of phosphopeptides using a new Ti4+-IMAC material synthesized in-house. This new material has the feature of big size and large specific surface area which makes it more suitable to enrich phosphopeptides in a SPE way. The spin tips loaded with the Ti4+-IMAC material were applied to enrich phosphopeptides from the complex protein digests. It was found that phosphopeptides can be specifically enriched from tryptic digest of bovine serum albumin and β-casein at a molar ratio up to 1000:1. And about 4700 unique phosphorylated peptides can be identified with the specificity as high as 99% from the tryptic digest of HeLa cell proteins. This tip was demonstrated to have good column-to-column reproducibility. Furthermore, it is fitted to analyze minute amount of sample. Compared with the conventional solution method, the SPE method facilitated the rapid and complete separation of the material with solution, which making it a time-saving and convenient method for phosphopeptide enrichment. Compared with the commercial TiO2 material, this new materials yielded much more phosphopeptide identifications and much higher enrichment specificity.

Application of paper EWOD (electrowetting-on-dielectrics) chip: Protein tryptic digestion and its detection using MALDI-TOF mass spectrometry

A paper-based open EWOD chip was used for protein tryptic digestion, and the resulting peptides were analyzed using MALDI-TOF mass spectrometry to identify the proteins. Although on-chip protein digestion was previously demonstrated on a glass-based EWOD platform, this is the first report to show that a paper-based EWOD can also be used for protein digestion and further analysis by mass spectrometry. A number of protein digestion processes, i.e., disulfide bond reduction, alkylation, buffering, and tryptic digestion, can be successfully conducted on the paper-based EWOD chip. Furthermore, a “Y”-shaped junction design was shown to be effective in successfully manipulating a droplet for protein digestion. A paper-based EWOD platform offers a cheap and versatile avenue for biological applications.

Functionalization of hybrid monolithic columns via thiol-ene click reaction for proteomics analysis

The vinyl-functionalized hybrid monolithic columns (75 and 150μm i.d.) were prepared via sol-gel chemistry of tetramethoxysilane (TMOS) and vinyltrimethoxysilane (VTMS). The content of accessible vinyl groups was further improved after the monolithic column was post-treated with vinyldimethylethoxysilane (VDMES). The surface properties of monolithic columns were tailored via thiol-ene click reaction by using 1-octadecanethiol, sodium 3-mercapto-1-propanesulfonate and 2,2′-(ethylenedioxy)diethanethiol/vinylphosphonic acid, respectively. The preparing octadecyl-functionalized monolithic columns were adopted for proteomics analysis in cLC–MS/MS. A 37-cm-long×75-μm-i.d. monolithic column could identify 3918 unique peptides and 1067 unique proteins in the tryptic digest of proteins from HeLa cells. When a 90-cm-long×75-μm-i.d. monolithic column was used, the numbers of unique peptides and proteins were increased by 82% and 32%, respectively. Furthermore, strong cation exchange (SCX) monolithic columns (4cm in length×150μm i.d.) were also prepared and coupled with the 37-cm-long×75-μm-i.d. octadecyl-functionalized monolithic column for two-dimensional SCX-RPLC–MS/MS analysis, which could identify 17114 unique peptides and 3211 unique proteins.