Mingming Dong

Synthesis and characterization of a new boronate affinity monolithic capillary for specific capture of cis-diol-containing compounds

Boronate affinity chromatography (BAC) is an important tool for specific capture and separation of cis-diol-containing compounds such as glycoproteins, RNA and carbohydrates. Only a few reports on monolithic column-based BAC have appeared. In this paper, boronate functionalized monolithic capillary column was synthesized by in situ free radical polymerization for the first time. The prepared column was first characterized in terms of morphology, pore properties, capacity and retention mechanisms. The column exhibited uniform open channel network and high capture capacity. Systematical investigation on the retention mechanism revealed that multiple intermolecular interactions occur between the analytes and the boronate affinity monolith, including boronate affinity, reversed-phase, cation-exchange and hydrogen bonding interactions, depending on the conditions used. In addition, the presence of Lewis base such as fluoride ion in the mobile phase was found to be favorable to the complexation between cis-diol-containing compounds with the boronic acid ligand under less basic conditions. On the basis of these fundamental investigations, the prepared monolithic column was then applied to the capture of adenosine and flavin adenine dinucleotide. The investigations in this study provide sound understanding not only on how to manipulate the separation selectivity through selection of appropriate mobile phase composition on the currently prepared columns but also on how to design next-generation columns with desired properties and functions.

An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome

UNLABELLED Protein phosphorylation is one of the most common post-translational modifications. It plays key roles in regulating diverse biological processes of liver tissues. To better understand the role of protein phosphorylation in liver functions, it is essential to perform in-depth phosphoproteome analysis of human liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid chromatography (RP-RPLC) approach with both RPLC separations operated with optimized acidic mobile phase was developed. High orthogonal separation was achieved by trypsin digestion of the Glu-C generated peptides in the fractions collected from the first RPLC separation. The phosphoproteome coverage was further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526 nonredundant phosphoproteins were finally identified from normal human liver tissues. Of these sites, 15,229 sites were confidently localized with Ascore≥13. This dataset was the largest phosphoproteome dataset of human liver. It can be a public resource for the liver research community and holds promise for further biology studies. BIOLOGICAL SIGNIFICANCE The enzyme assisted approach enabled the two RPLC separations operated both with optimized acidic mobile phases. The identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. The largest phosphoproteome dataset of human liver was generated.

Coupling Strong Anion-Exchange Monolithic Capillary with MALDI-TOF MS for Sensitive Detection of Phosphopeptides in Protein Digest

Protein phosphorylation is one of the most biologically relevant and ubiquitous post-translational modifications. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the analysis of protein phosphorylation by detection of phosphopeptides in phosphoprotein digest. Enrichment of phosphopeptides by immobilized metal ion affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC) followed with MALDI analysis is the common approach. However, the pH for loading and elution of phosphopeptides is incompatible with protein digestion as well as the preparation of the MALDI matrix solution. Therefore, some pretreatment steps, such as pH adjustment and desalting, are required, which make the approach tedious and insensitive. In this study, a strong anion-exchange (SAX) capillary monolith was prepared to enrich phosphopeptides from protein digest for MALDI-TOF MS analysis. It was found that phosphopeptides could be specifically retained on the SAX column at high pH around 8 and could be eluted by 5% formic acid. Thus, the protein digests without any pretreatment could be loaded onto the SAX column under basic pH condition; after removing nonphosphopeptides by washing, the bound phosphopeptides could be eluted directly onto a MALDI target and analyzed by MALDI-TOF MS. This approach significantly simplified the analytical procedures and reduced the sample loss. Because of the excellent MALDI MS compatible procedure and the microscale SAX column, a detection limit as low as 50 amol for the analysis of phosphopeptides from beta-casein digest was achieved. To circumvent the inconvenience of the sample loading, a new simple sample introducing method based on capillary action was proposed, which further reduced the detection limit to 10 amol.

Global Screening of CK2 Kinase Substrates by an Integrated Phosphoproteomics Workflow

Due to its constitutive activity and ubiquitous distribution, CK2 is the most pleiotropic kinase among the individual members of the protein kinase superfamily. Identification of CK2 substrates is vital to decipher its role in biological processes. However, only a limited number of CK2 substrates were identified so far. In this study, we developed an integrated phosphoproteomics workflow to identify the CK2 substrates in large scale. First, in vitro kinase reactions with immobilized proteomes were combined with quantitative phosphoproteomics to identify in vitro CK2 phosphorylation sites, which leaded to identification of 988 sites from 581 protein substrates. To reduce false positives, we proposed an approach by comparing these in vitro sites with the public databases that collect in vivo phosphorylation sites. After the removal of the sites that were excluded in the databases, 605 high confident CK2 sites corresponding to 356 proteins were retained. The CK2 substrates identified in this study were based on the discovery mode, in which an unbiased overview of CK2 substrates was provided. Our result revealed that CK2 substrates were significantly enriched in the spliceosomal proteins, indicating CK2 might regulate the functions of spliceosome.

Capture and Dimethyl Labeling of Glycopeptides on Hydrazide Beads for Quantitative Glycoproteomics Analysis

Incorporation of isotopic tag onto peptides via chemical labeling is a popular approach for quantitative proteomics. Chemical labeling via solution based methods usually lead to a tedious process and sample loss because several sample preparation steps including buffer exchange and desalting are performed. In this study, a solid phase based labeling approach by integration of glycopeptide enrichment and stable isotope labeling on hydrazide beads was developed for relative quantification of protein glycosylation, by which enrichment, washing, labeling, and release of the glycopeptides were all performed on the hydrazide beads sequentially. This approach was proved to be accurate in quantitative glycoproteome analysis and have good linearity range with 2 orders of magnitude for quantification of glycopeptides. Compared with dimethyl labeling conventionally performed in solution, the developed approach has better enrichment recovery (10-330% improvement) and high detection sensitivity in which 42% of annotated glycosites (vs 26%) still can be quantified using only 10 μg of four standard glycoprotein mixtures and 400 μg of bovine serum album interference as starting sample. The applicability of the approach for quantitative glycopeptide profiling was also explored by differential analysis of glycoproteome between human normal serum and liver cancer serum.

Depletion of acidic phosphopeptides by SAX to improve the coverage for the detection of basophilic kinase substrates.

The Ser/Thr protein kinases fall into three major subgroups, pro-directed, basophilic, and acidophilic, on the basis of the types of substrate sequences that they preferred. Despite many phosphoproteomics efforts that have been taken for global profiling of phosphopeptides, methodologies focusing on analyzing a particular type of kinase substrates have seldom been reported. Selective enrichment of phosphopeptides from basophilic kinase substrates is difficult because basophilic motifs are cleaved by trypsin during digestion. In this study, we develop a negative enrichment strategy to enhance the identification of basophilic kinase substrates. This method is based on an observation that high pH strong anion exchange (SAX) chromatography can separate tryptic phosphopeptides according to the number of acidic amino acidic residues that they have. Thus, SAX was applied to deplete acidic phosphopeptides from the phosphopeptide mixture, which improved the coverage for the detection of basophilic kinase substrates. The SAX depletion approach was further combined with online SCX-RP separation for large-scale analysis of mouse liver phosphoproteome, which resulted in the identification of 6944 phosphorylated sites. It was found that motifs associated with basophilic kinases prevail for these identified phosphorylated sites.

Determination of CK2 Specificity and Substrates by Proteome-Derived Peptide Libraries

Understanding the specificity of kinases enables prediction of their substrates and uncovering kinase functions in signaling pathways. Traditionally synthesized peptide libraries are used to determine the kinase specificity. In this study, a proteomics-based method was developed to determine the specificity of kinase by taking the advantages of proteome-derived peptide libraries and quantitative proteomics. Proteome-derived peptide libraries were constructed by digesting proteins in total cell lysate followed with dephosphorylation of the resulting peptides. After incubating the peptide libraries with/without CK2 for in vitro kinase assay, stable isotopic labeling based quantitative phosphoproteomics was applied to distinguish the in vitro phosphosites generated by CK2. By using the above approach, 404 CK2 in vitro phosphosites were identified by 1D LC-MS/MS. Those sites allowed the statistic determination of the CK2 specificity. In addition to the easy construction of the proteome-derived peptide library, another significant advantage of this method over the method with synthesized peptide libraries is that the identified phosphosites could be directly mapped to proteins for the screening of putative kinase substrates. It was found that the confidence for substrate identification could be significantly improved by comparing the in vitro CK2 sites with the in vivo sites identified by phosphoproteomics analysis of the same cell lines. By applying this integrated strategy, 138 phosphosites from 105 putative CK2 substrates of high confidence were determined.

N‐Terminal Labeling of Peptides by Trypsin‐Catalyzed Ligation for Quantitative Proteomics

Labeling tryptic peptides with stable isotopes is one of the most important methods for quantitative proteomics, and many ingenious chemical labeling strategies have been developed. Incorporation of one isotopically labeled tag onto a peptide terminus represents an ideal labeling approach, as it would simplify the interpretation of mass spectra. Moreover, the absence of labels on the side chains would facilitate the quantification of post-translational modifications (PTMs). However, to date all the reported chemical labeling strategies, including dimethyl labeling, iTRAQ (isobaric tags for absolute and relative quantification), and ICAT (isotope-coded affinity tags), result in the modification of side chains. One promising method to achieve the incorporation of a single tag is enzymatic labeling. Proteolytic O labeling can specifically label tryptic peptide termini without modification of side chains, but the small change in mass and O/O back-exchange, i.e. the exchange of O with O after the labeling process hinder its wide application in quantitative proteomics. Herein, we report a novel enzymatic labeling approach, in which trypsin is used as a ligase to specifically incorporate amino acids labeled with stable isotopes onto the N termini of peptides for quantitative analysis. Trypsin is a serine protease that specifically hydrolyzes peptide bonds in proteins after arginine and lysine residues. However, trypsin also catalyses peptide synthesis in organic solvents. Therefore, it is possible to covalently link isotopically labeled amino acids to tryptic peptides by using trypsin as a ligase. In this study, arginine, the prototype substrate for trypsin, was used as an acyl moiety donor. The primary amine group of arginine was protected with a benzoyl group (Bz) to prevent the formation of dipeptides or oligopeptides, and the carboxy group was esterified with ethanol to activate the acyl donor (see the Supporting Information, Figure S1). The final product, Na-benzoyl-l-arginine ethyl ester (Bz–R–OEt), was used as a substrate for the trypsin-catalyzed ligation. The quantitative proteomics workflow based on the trypsincatalyzed N-terminal labeling is shown in Figure 1a. Trypsin was first used as a protease to digest proteins in an aqueous solution (1m urea/50 mm Tris-HCl, pH 8.0). Then, the generated tryptic peptides were lyophilized and transferred to an ethanol solution containing 4% aqueous buffer (0.1m TrisHCl, pH 8.0). Next, trypsin immobilized on magnetic nanoparticles (IM-trypsin) and Bz–R–OEt were added to the ethanol solution for the N-terminal labeling of peptides with Bz–R based on a kinetically controlled mechanism (see the Supporting Information). Finally, quantification of the proteins was achieved by the differential labeling of two samples by using Bz–R–OEt (light label) and Bz–(C6)R–OEt (bearing six C atoms; heavy label), the incorporation of which are indicated by mass shifts of 260 and 266 Da, respectively. We first validated the protease and ligase activities of trypsin by using the synthetic peptide VGKANEELAGVVAEVQK (Figure 1b; m/z= 1740.86), which contains one trypsin cleavage site. In aqueous solution, treatment with IMtrypsin generated a shorter peptide ANEELAGVVAEVQK (Figure 1b, m/z= 1456.82). Treatment of the obtained peptide with an ethanol solution containing Bz–R–OEt and IMtrypsin gave an N-terminus labeled peptide Bz–RANEELAGVVAEVQK (Figure 1b, m/z= 1716.9). Similar results were also obtained for three other synthetic peptides that contained one trypsin cleavage site (Supporting Information, Figure S2). These examples clearly illustrate that trypsin functions as a protease in an aqueous solution whereas it acts as an N-terminus ligase in an ethanol solution. Thus, these results imply that this enzymatic labeling approach can be used to label peptides generated by trypsin digestion of a proteome sample. In this study, free trypsin was used for the digestion of proteins, as is conventional in proteomics analysis, whereas IM-trypsin (trypsin from the same source) was used for ligation because it is more tolerant to organic solvents and it is readily removed using magnetism. We tested whether the labeling of side-chain primary amino groups would also be facilitated by trypsin ligase. A synthetic peptide VIFIEHAKRKG, containing two sidechain amino groups and one terminal primary amino group, was labeled by trypsin. The Arg tag was incorporated only onto the terminal primary amino group and not onto the sidechain amino groups (see the Supporting Information, Figure S3a). These results are markedly different from those of other amine labeling approaches. For example, for labeling [*] Y. Pan, Prof. Dr. M. Ye, Dr. L. Zhao, K. Cheng, M. Dong, C. Song, H. Qin, Dr. F. Wang, Prof. Dr. H. Zou CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 (China) E-mail: mingliang@dicp.ac.cn hanfazou@dicp.ac.cn

Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy

The diversity of O-linked glycan structures has drawn increasing attention due to its vital biological roles. However, intact O-glycopeptides with different glycans are typically not well elucidated using the current methods. In this work, an integrated strategy was developed for comprehensive analysis of O-GalNAc glycosylation by combining hydrophilic interaction chromatography (HILIC) tip enrichment, beam-type collision induced decomposition (beam-CID) detection, and in silico deglycosylation method for spectra interpretation. In this strategy, the intact O-GalNAc glycopeptides were selectively enriched and the original spectra obtained by time-of-flight (TOF)-CID were preprocessed using an in silico deglycosylation method, enabling direct searching without setting multiple glycosylation modifications, which could significantly decrease the search space. This strategy was applied to analyze the O-GalNAc glycoproteome of human serum, leading to identification of 407 intact O-GalNAc glycopeptides from 93 glycoproteins. About 81% of the glycopeptides contained at least one sialic acid, which could reveal the microheterogeneity of O-GalNAc glycosylation. Up until now, this is the largest data set of intact O-GalNAc glycoforms from complex biological samples at the proteome level. Furthermore, this method is readily applicable to study O-glycoform heterogeneity in other complex biological systems.

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.