CaCO3–Poly(methyl methacrylate) Nanoparticles for Fast Enrichment of Low-Abundance Peptides Followed by CaCO3-Core Removal for MALDI-TOF MS Analysis

C18-functionalized magnetic nanocomposites fabricated by one-step aqueous coating of tailored oligopeptides for enrichment of low-abundance peptides

Screening and monitoring endogenous peptides from complicated biosamples is still a major challenge in mass spectrometry-based proteomics research, mainly due to their low concentration and the interference of high-abundance proteins and other contaminants in biological samples. Herein, a facile and novel approach was described for rapid fabrication of C₁₈-functionalized magnetic nanocomposites (C₁₈-MNCs) based on one-step aqueous coating of C₁₈-Val-Lys-Val-Lys-Val-Lys (C₁₈-VK-VI) for the highly selective enrichment of low-abundance endogenous peptides from biological samples. C₁₈-VK-VI can readily self-assemble into complete monolayers mainly composed of β-sheets with C₁₈ hydrophobic chains erecting on the surface of GO@Fe₃O₄ MNCs under the physiological conditions. The resulting C₁₈VK-VI-GO@Fe₃O₄ MNCs exhibited good performance for peptides enrichment from digests of standard protein (myoglobin, MYO) and human serum, such as high sensitivity (0.05 fmol μL^-1) and selectivity (mass ratio of MYO digests and MYO = 1:500), rapid separation, and good reproducibility. Such a simple mild and rapid one-step aqueous coating method on the basis of oligopeptides self-assembly showed great potential in surface functionalization of various nanoadsorbents for proteome/peptidome researches.

Eliminating sweet spot in MALDI-MS with hydrophobic ordered structure as target for quantifying biomolecules

In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), the analyte is usually distributed unevenly throughout the sample spot. The area with aggregated analyte molecules contributing abundant signal, is termed as "sweet spot", which results in poor detection reproducibility and makes it impossible to quantify analytes without internal standards. We proposed a strategy to eliminate sweet spot in MALDI-MS by using a hydrophobic ordered structure as target. The target is fabricated by creating a hydrophobic silicon nanopillar array and subsequently decorating it uniformly with poly(methyl methacrylate) nanodots for capturing analytes. The sweet spot is eliminated by distributing analyte molecules uniformly on this target, and then result in a uniform MS image, which demonstrates an ideal reproducibility. Finally, with the target assisted MALDI-MS as biosensor was suitable to analyze practical sample such as bacitracin A in milk. Horse heart myoglobin and, angiotensin III molecules can be quantified without internal standard using α-cyano-4-hydroxycinnamic acid as matrix. This biosensor presented good linearity, high salts tolerance and high signal-to-noise ratio (up to 271.8), even the 1 mol/L salt concentration. This strategy could provide an alternative for improving the performance of MALDI-MS.

Room-temperature synthesis of core–shell structured magnetic covalent organic frameworks for efficient enrichment of peptides and simultaneous exclusion of proteins

Core–shell structured Fe₃O₄@COFs were synthesized and used as a new absorbent for efficient enrichment of peptides and simultaneous exclusion of proteins.

(E)-Propyl α-Cyano-4-Hydroxyl Cinnamylate: A High Sensitive and Salt Tolerant Matrix for Intact Protein Profiling by MALDI Mass Spectrometry

Low-abundance samples and salt interference are always of great challenges for the practical protein profiling by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Herein, a series of carboxyl-esterified derivatives of α-cyano-4-hydroxycinnamic acid (CHCA) were synthesized and evaluated as matrices for MALDI-MS analysis of protein. Among them, (E)-propyl α-cyano-4-hydroxyl cinnamylate (CHCA-C3) was found to exhibit excellent assay performance for intact proteins by improving the detection sensitivity 10 folds compared with the traditional matrices [i.e., super2,5-dihydroxybenzoic acid (superDHB), sinapic acid (SA), and CHCA]. In addition, CHCA-C3 was shown to have high tolerance to salts, the ion signal of myoglobin was readily detected even in the presence of urea (8 M), NH4HCO3 (2 M), and KH2PO4 (500 mM), meanwhile sample washability was robust. These achievements were mainly attributed to improved ablation ability and increased hydrophobicity or affinity of CHCA-C3 to proteins in comparison with hydrophilic matrixes, leading to more efficient ionization of analyte. Furthermore, direct analysis of proteins from crude egg white demonstrated that CHCA-C3 was a highly efficient matrix for the analysis of low-abundance proteins in complex biological samples. These outstanding performances indicate the tremendous potential use of CHCA-C3 in protein profiling by MALDI-MS. Graphical Abstract ᅟ.

Molecularly imprinted polymers coupled to matrix assisted laser desorption ionization mass spectrometry for femtomoles detection of cardiac troponin I peptides

Molecularly imprinted polymers (MIPs) were combined to MALDI-TOF-MS to evaluate a selective enrichment (SE) method for the determination of clinically relevant biomarkers from complex biological samples. The concept was proven with the myocardial injury marker Troponin I (cTnI). In a first part, MIP materials entailed for the recognition of cTnI epitopes (three peptides selected) were prepared and characterized in dimensions (0.7-2μm), dissociation constants (58-817 nM), kinetics of binding (5-60 min), binding capacity (ca. 1.5 µg/mg polymer), imprinting factors (3 > IF > 5) and selectivity for the peptide epitope. Then, the MIPs, incubated with cTnI peptides and spotted on the target with the DHB matrix, were assayed for the desorption of the peptides in MALDI-TOF-MS. The measured detection limit was ca. 300 femtomols. Finally, the MIP-SE MALDI-TOF-MS was tested for its ability to enrich in the cTnI peptides from a complex sample, mimic of serum (i.e. 81 peptides of digested albumin). The MIP-SE MALDI-TOF-MS successfully enriched in cTnI peptides from the complex sample proving the technique could offer a flexible platform to prepare entailed materials suitable for diagnostic purposes.

Facile synthesis of novel magnetic silica nanoparticles functionalized with layer-by-layer detonation nanodiamonds for secretome study

A novel approach for fast and efficient specific enrichment of low abundance peptides and proteins in secretome analysis was developed by using novel magnetic silica nanoparticles functionalized with layer-by-layer detonation nanodiamonds (dNDs).

A combo-pore approach for the programmable extraction of peptides/proteins

A novel combo-pore approach has been designed for the programmable purification, minimisation of sample complexity, enrichment and sensitive detection of peptides in biosamples. This approach has a superior performance to conventional protocols and commercial products.

Polydopamine-coated magnetic nanoparticles for enrichment and direct detection of small molecule pollutants coupled with MALDI-TOF-MS

Polydopamine-coated Fe(3)O(4) nanoparticles (Fe(3)O(4)@PDA NPs) were synthesized and applied as matrix for the detection of pollutants by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The synthesis of Fe(3)O(4)@PDA NPs was accomplished in 30 min by in situ polymerization of dopamine without any toxic reagent. Using Fe(3)O(4)@PDA NPs as matrix of MALDI-TOF, eleven small molecule pollutants (molecular weight from 251.6 to 499.3), including Benzo(a)pyrene (BaP), three perfluorinated compounds (PFCs), and seven antibiotics, were successfully detected in either positive or negative reflection mode without background interference. Furthermore, the Fe(3)O(4)@PDA NPs can also enrich trace amounts of hydrophobic target, such as BaP, from solution to nanoparticles surface. Then the Fe(3)O(4)@PDA-BaP can be isolated through magnetic sedimentation step and directly spotted on the stainless steel plate for MALDI measurement. With Fe(3)O(4)@PDA NPs as adsorbent and matrix, we also realized the analysis of BaP in tap water and lake water samples. Thus, a magnetic solid-phase extraction (MSPE)-MALDI-TOF-MS method was established for the measurement of BaP.

On-plate selective enrichment and self-desalting of peptides/proteins for direct MALDI MS analysis

In this paper, a new technique has been proposed to achieve simultaneous peptides/proteins enrichment and wash-free self-desalting on a novel sample support with a circle hydrophobic-hydrophilic-hydrophobic pattern. Upon deposition, the sample solution is first concentrated in a small area by repulsion of the hydrophobic outer layer, and then, the peptides/proteins and coexisting salt contaminants are selectively captured in different regions of the pattern through strong hydrophobic and hydrophilic attractions, respectively. As a result, the detection sensitivity is improved by 2 orders of magnitude better than the use of the traditional MALDI plate, and high-quality mass spectra are obtained even in the presence of NaCl (1 M), NH(4)HCO(3) (100 mM), or urea (1 M). The practical application of this method is further demonstrated by the successful analysis of myoglobin digests with high sequence coverage, demonstrating the great potential in proteomic research.

Enrichment and detection of peptides from biological systems using designed periodic mesoporous organosilica microspheres

Periodic mesoporous organosilica microspheres (PMOMs) are designed with integrated structural features, including a cubic mesostructure, hydrophobic wall composition, a uniform pore size of ≈3 nm, and a spherical morphology in micrometers, all advantageous for size-selective and highly efficient enrichment of peptides from mixtures. Consequently, PMOMs can be used to capture peptides in a range of complex biological systems.

Pseudomorphic synthesis of monodisperse magnetic mesoporous silica microspheres for selective enrichment of endogenous peptides

In this work, we describe a novel synthetic strategy of magnetic mesoporous silica spheres (Fe3O4@mSiO2) for the selective enrichment of endogenous peptides. Fe3O4 particles were coated with silica shell by a sol-gel method, followed by pseudomorphic synthesis to transform nonporous silica shell into ordered mesoporous silica shell. The core/shell structure and mesostructure were individually fabricated in two steps, which can be expedient to independently optimize the properties of monodispersion, magnetization and mesostructure. Actually, it was confirmed that the produced Fe3O4@mSiO2 particles possess good monodispersion, high magnetization, superparamagnetism, uniform accessible mesopores, and large surface area and pore volume. With these good properties, Fe3O4@mSiO2 spheres were applied to the rapid enrichment of peptides. Based on the size-exclusion mechanism and hydrophobic interaction with siloxane bridge group mainly on the surface of inside pores, Fe3O4@mSiO2 can selectively capture peptides and exclude high-MW proteins and salts. Furthermore, peptides in human plasma were successfully enriched by Fe3O4@mSiO2.

Octyl-functionalized hybrid magnetic mesoporous microspheres for enrichment of low-concentration peptides prior to direct analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Octyl-functionalized hybrid magnetic mesoporous (Fe(3)O(4)·nSiO(2)·meso-hybrid-C8) microspheres were synthesized and applied in the isolation and pre-concentration of low-concentration peptides prior to direct analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Such microspheres possess high surface area (324 m(2)/g), hydrophobic group (C8), relatively large pore volume (0.304 cm(3)/g), uniform pore diameter (~3.7 nm), and magnetic responsivity, which make them a simple and efficient kind of adsorbent for the enrichment of low-concentration peptides. For bovine serum albumin (BSA, 15 fmol μL(-1)) digest, after concentration by Fe(3)O(4)·nSiO(2)·meso-hybrid-C8 microspheres, the enrichment performance was evidently better than those obtained by solvent evaporation and C8-functionalized magnetic particles, and comparable to those obtained by commercial Anchor chip target and ZipTipC18 pipette tip. Such microspheres were further applied in the enrichment of the tryptic digests of rat cerebellum proteins and endogenous peptides of crude human serum, and more peaks with higher signal-to-noise (S/N) ratio were obtained than before pre-concentration. Furthermore, the pre-concentration reproducibility of magnetic microspheres for biological samples was good, and the limit of detection (LOD) for BSA digests by MALDI-TOF MS was decreased by at least one order of magnitude compared with that obtained without pre-concentration. All the above-mentioned results indicate that the synthesized Fe(3)O(4)·nSiO(2)·meso-hybrid-C8 microspheres are promising for the enrichment of low-concentration peptides from complex biosamples.

Metal-organic frameworks for efficient enrichment of peptides with simultaneous exclusion of proteins from complex biological samples

Metal-organic frameworks MIL-53, MIL-100 and MIL-101 demonstrate efficient enrichment of peptides with simultaneous exclusion of proteins from complex biological samples.

Functionalized periodic mesoporous organosilicas for enhanced and selective peptide enrichment

The analysis of peptides by the mass spectrometry (MS) technique is important in modern life science. The enrichment of peptides can increase the detection efficiency and is sometimes indispensable for collecting the information on proteins with low-abundance. Herein, we first report that functionalized periodic mesoporous organosilica (PMO) materials have a superior peptide enrichment property. It is demonstrated that the PMO materials with an organo-bridged (-CH(2)-) hybrid wall composition display a highly enhanced peptide enrichment ability compared to the pure silica material (SBA-15) with similar mesostructured parameters and morphology. More importantly, by surface modification of PMO with amino groups (denoted NH(2)-PMO), PMO and NH(2)-PMO with opposite charged surfaces (-25.2 and +39.0 mV, respectively) show selective affinities for positively and negatively charged peptides, respectively. By directly adding PMO, NH(2)-PMO as well as pure silica materials to the peptides solution with a low concentration (1-2 fmol/microL), 36 and 28 peptides can be detected from the BSA digestion in the presence of PMO and NH(2)-PMO, respectively, while only 6 and 4 are monitored in the case of SBA-15 enrichment and from solution without enrichment, respectively. Moreover, 69.4% (25 of 36) of enriched peptides by PMO have pI > or = 6 and 80% (21 of 28) of enriched peptides by NH(2)-PMO possess pI < or = 6. Combining the results from the NH(2)-PMO and PMO enrichment together, 51 peptides can be identified with a MOWSE score of 333. It is also noted that similar conclusions can also be obtained from the peptides solution originated from other proteins. This might be an important contribution to the understanding of the interaction between peptides and porous hosts, and the proposed method is promising for the development of both material science and biotechnology.

Boronic acid functionalized core-satellite composite nanoparticles for advanced enrichment of glycopeptides and glycoproteins

A core-satellite-structured composite material has been successfully synthesized for capturing glycosylated peptides or proteins. This novel hybrid material is composed of a silica-coated ferrite "core" and numerous "satellites" of gold nanoparticles with lots of "anchors". The anchor, 3-aminophenylboronic acid, designed for capturing target molecules, is highly specific toward glycosylated species. The long organic chains bridging the gold surface and the anchors could reduce the steric hindrance among the bound molecules and suppress nonspecific bindings. Due to the excellent structure of the current material, the trap-and-release enrichment of glycosylated samples is quite simple, specific, and effective. Indeed, the composite nanoparticles could be used for enriching glycosylated peptides and proteins with very low concentrations, and the enriched samples can be easily separated from bulk solution by a magnet. By using this strategy, the recovery of glycopeptides and glycoproteins after enrichment were found to be 85.9 and 71.6% separately, whereas the adsorption capacity of the composite nanoparticles was proven to be more than 79 mg of glycoproteins per gram of the material. Moreover, the new composite nanoparticles were applied to enrich glycosylated proteins from human colorectal cancer tissues for identification of N-glycosylation sites. In all, 194 unique glycosylation sites mapped to 155 different glycoproteins have been identified, of which 165 sites (85.1%) were newly identified.

Rapid and automatic on-plate desalting protocol for MALDI-MS: using imprinted hydrophobic polymer template

A novel protocol of rapid and automatic on-plate desalting (OPD) and peptide concentration for 2-DE-MALDI-MS has been developed by the approach of templating the hydrophobic polymer solution over Kapton-etched mask. For the template technique, small hydrophobic polymer [linear poly(methyl methacrylate) (PMMA), PMMA derivatized with fullerene-C60 (PMMA-C60), linear polystyrene (PSt), or PSt derivatized with fullerene-C60 (PSt-C60)] spots (990 microm od) are patterned at the centers of stainless MALDI plate wells (1400 microm id). Tryptic-peptide solution with no predesalting was dropped onto the central hydrophobic spots, resulting in a concentration of proteolytic peptides on the hydrophobic polymer surface with a reduced spot size. The dried peptide layer was then covered subsequently with over-volume matrix solution, causing the removal of redissolved salts from the spot center to the spot edge by means of a natural "outward flow." The proposed OPD protocol exhibited a dramatic enhancement in S/N up to 850 for 14 fmol BSA digests in the coexistence of 100 mM salts, compared with barely detectable peaks in ordinary way. This analysis has shown that the success rate of identification was increased by two-fold for low abundance proteins in the human liver tissue with no need for the conventional ZipPlate desalting strategy.

On-plate digestion of proteins using novel trypsin-immobilized magnetic nanospheres for MALDI-TOF-MS analysis

In this study, a novel method of on-plate digestion using trypsin-immobilized magnetic nanospheres was developed followed by MALDI-TOF-MS for rapid and effective analysis and identification of proteins. We utilized a facile one-pot method for the direct preparation of amine-functionalized magnetic nanospheres with highly magnetic properties and the amino groups on the outer surface. Through the reaction of the aldehyde groups with amine groups, trypsin was simply and stably immobilized onto the magnetic nanospheres. The obtained trypsin-linked magnetic nanospheres were then applied for on-plate digestion of sample proteins (myoglobin and Cytochrome c). Moreover, after digestion, the trypsin-linked nanospheres could be easily removed from the plate due to their magnetic property, which would avoid causing contamination on the ion source chamber in MS. The effects of the temperature and incubation time on the digestion efficiency were characterized. Within only 5 min, proteins could be efficiently digested with the peptide sequence coverage higher than or equal to that of the traditional in-solution digestion for 12 h. Furthermore, RPLC fractions of rat liver extract were also successfully processed using this novel method. These results suggested that our improved on-plate digestion protocol for MALDI-MS may find further application in automated analysis of large sets of proteins.

Wash-free in-situ self-desalting and peptide enrichment by block copolymer analyzed with MALDI-TOFMS

A novel technique of simultaneous peptide enrichment and wash-free in-situ self-desalting for MALDI analysis is reported, where a newly synthesized block copolymer with a microphase-separated configuration is applied to embed salts with its hydrophilic domain of poly(ethylene oxide) and concentrate peptides with its hydrophobic domain of polysulfone.

Enhancement of proteolysis through the silica-gel-derived microfluidic reactor

An on-chip enzymatic reactor providing rapid protein digestion is presented. Trypsin-embedding stationary phase within the microchannel has been prepared by the sol-gel method. Such a microfluidic reactor has been used for low-level protein digestion at 16 fmol per analysis. The analytical potential of the microreactor combined with the strong cation exchange and RPLC ESI-MS/MS for the identification of real samples from the cytoplasma of the human liver tissue has been demonstrated.

Sub-microlitre dialysis system to enable trace level peptide detection from volume-limited biological samples using MALDI-TOF-MS

The detection of peptides with mass spectrometry from volume-limited biological samples is a challenging task due to low sample volume, a broad range of peptide concentrations down to trace levels, endogenous high proteins and salt levels. Previously, a microspotting method was presented for trace-level peptide detection with MALDI-MS from sub-microlitre samples with biological salt levels. However, in the presence of proteins, peptide signals are significantly reduced. This paper presents a novel dialysis device for removal of proteins from sub-microlitre samples using a semipermeable hollow fiber membrane to enhance peptide detection. A dialysis device was constructed to perform sub-microlitre dialysis to remove proteins from complex samples. Angiotensin I was used as a model peptide in the presence of 350 mg L(-1) BSA prepared in physiological saline to mimic biological samples. In the absence of BSA, clear angiotensin I peaks were seen at 250 pM, yet in the presence of the BSA, 10 nM angiotensin I was barely detected. After dialysis, peak detection was improved to a 500 pM level. Protein removal and peptide recovery (approximately 66%) were determined using CE-LIF. Clinical vitreous samples as low as 200 nL were successfully dialyzed in 30 min and a 3-fold increase in peptide peaks were detected with greatly improved signals. This method is simple and can be a useful technique for trace level peptide detection from volume-limited biological samples.