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

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.

Hydrophobic/hydrophilic patterned surfaces for directed evaporative preconcentration

We present a microfluidic platform that rapidly deposits many samples and preconcentrates them, making it suitable for a wide range of high-throughput detection schemes.

Nanosecond photochemically promoted click chemistry for enhanced neuropeptide visualization and rapid protein labeling

Comprehensive protein identification and concomitant structural probing of proteins are of great biological significance. However, this is challenging to accomplish simultaneously in one confined space. Here, we develop a nanosecond photochemical reaction (nsPCR)-based click chemistry, capable of structural probing of proteins and enhancing their identifications through on-demand removal of surrounding matrices within nanoseconds. The nsPCR is initiated using a photoactive compound, 2-nitrobenzaldehyde (NBA), and is examined by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Benefiting from the on-demand matrix-removal effect, this nsPCR strategy enables enhanced neuropeptide identification and visualization from complex tissue samples such as mouse brain tissue. The design shows great promise for structural probing of proteins up to 155 kDa due to the exclusive accessibility of nsPCR to primary amine groups, as demonstrated by its general applicability using a series of proteins with various lysine residues from multiple sample sources, with accumulated labeling efficiencies greater than 90%.

Mass spectrometry-based quantitative proteomics aim to identify and quantify proteins from complex biological samples. Here, the authors developed a method for simultaneous high-throughput protein labelling and on-demand matrix removal within nanoseconds.

Quantitation of Glutathione by Quinoline-5, 8-Dione-Based Tag Strategy Using MALDI Mass Spectrometry

In the present work, we developed an UV-absorptive and highly reactive tag aromatic molecule, quinoline-5,8-dione (QLD), for robust quantitative analysis of GSH by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The QLD could react with GSH with high efficiency at room temperature, and the resultant QLD-GSH conjugate could be readily detected by MALDI MS without interferences. By using the QLD tag, the detection limit of GSH was lowered to 10 fmol μL^-1, which was four orders of magnitude higher than that detected without using the QLD tag. Furthermore, accurate quantitative measurements of GSH in solution were successfully demonstrated by using glutamic acid-cysteine-alanine (ECA) as an internal standard. By properly adjusting the ECA concentrations, the intensity ratio value of QLD-tagged GSH (QLD-GSH) to QLD-tagged ECA (QLD-ECA) displayed a good linearity with GSH concentrations in a broad range from 4 to 4000 μM. Finally, the GSH level in HeLa cell lysates was also successfully detected, and the results are consistent with that obtained by a colorimetric assay. In summary, the proposed QLD-based tag method should be a rapid, cost-/time-effective, and sensitive new method for quantitative determination of GSH by MALDI MS. Graphical Abstract.

Insulator Nanostructure Desorption Ionization Mass Spectrometry

Surface-assisted laser desorption ionization (SALDI) is an approach for gas-phase ion generation for mass spectrometry using laser excitation on typically conductive or semiconductive nanostructures. Here, we introduce insulator nanostructure desorption ionization mass spectrometry (INDI-MS), a nanostructured polymer substrate for SALDI-MS analysis of small molecules and peptides. INDI-MS surfaces are produced through the self-assembly of a perfluoroalkyl silsesquioxane nanostructures in a single chemical vapor deposition silanization-step. We find that surfaces formed from the perfluorooctyltrichlorosilane monomer assemble semielliptical features with a 10 nm height, diameters between 10 and 50 nm, and have attomole-femtomole sensitivities for selected analytes. Surfaces prepared with silanes that either lack the trichloro or perfluoro groups, lack sensitivity. Further, we demonstrate that hydrophobic INDI regions can be micropatterned onto hydrophilic surfaces to perform on-chip self-desalting in an array format.

Thermoresponsive Arrays Patterned via Photoclick Chemistry: Smart MALDI Plate for Protein Digest Enrichment, Desalting, and Direct MS Analysis

Sample desalting and concentration are crucial steps before matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) analysis. Current sample pretreatment approaches require tedious fabrication and operation procedures, which are unamenable to high-throughput analysis and also result in sample loss. Here, we report the development of a smart MALDI substrate for on-plate desalting, enrichment, and direct MS analysis of protein digests based on thermoresponsive, hydrophilic/hydrophobic transition of surface-grafted poly(N-isopropylacrylamide) (PNIPAM) microarrays. Superhydrophilic 1-thioglycerol microwells are first constructed on alkyne-silane-functionalized rough indium tin oxide substrates based on two sequential thiol-yne photoclick reactions, whereas the surrounding regions are modified with hydrophobic 1H,1H,2H,2H-perfluorodecanethiol. Surface-initiated atom-transfer radical polymerization is then triggered in microwells to form PNIPAM arrays, which facilitate sample loading and enrichment of protein digests by concentrating large-volume samples into small dots and achieving on-plate desalting through PNIPAM configuration change at elevated temperature. The smart MALDI plate shows high performance for mass spectrometric analysis of cytochrome c and neurotensin in the presence of 1 M urea and 100 mM NaHCO₃, as well as improved detection sensitivity and high sequence coverage for α-casein and cytochrome c digests in femtomole range. The work presents a versatile sample pretreatment platform with great potential for proteomic research.

A high sensitive and contaminant tolerant matrix for facile detection of membrane proteins by matrix-assisted laser desorption/ionization mass spectrometry

Despite the significance of membrane proteins (MPs) in biological system is indisputable, their specific natures make them notoriously difficult to be analyzed. Particularly, the widely used Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) prefers analyses of hydrophilic cytosolic proteins and has a limited ionization efficiency towards hydrophobic MPs. Herein, a hydrophobic compound (E)-propyl α-Cyano-4-Hydroxyl Cinnamylate (CHCA-C3), a propyl-esterified derivative of α-cyano-4-hydroxycinnamic acid (CHCA), was applied as a contaminant tolerant matrix for high sensitivity MALDI-MS analyses of MPs. With CHCA-C3, the detection limits of hydrophobic peptides were 10- to 100-fold better than those using CHCA. Furthermore, high quality of spectra could be achieved in the presence of high concentration of chaotropes, salts and detergents, as well as human urinary and serum environment. Also, CHCA-C3 could generate uniform sample distribution even in the presence of contaminants. This high contaminant-resistance was revealed to be ascribed to the enhanced hydrophobicity of CHCA-C3 with a lower affinity towards hydrophilic contaminants. The application of CHCA-C3 is further demonstrated by the analysis of trypsin/CNBr digests of bacteriorhodopsin containing seven transmembrane domains (TMDs), which dramatically increased numbers of identified hydrophobic peptides in TMDs and sequence coverage (∼100%). Besides, a combined method by using CHCA-C3 with fluoride solvent and a patterned paraffin plate was established for analysis of integral MPs. We achieved a low detection limit of 10 fmol for integral bacteriorhodopsin, which could not be detected using traditional matrices such as 3,5-dimethoxy-4-hydroxycinamic acid, 2,5-dihydroxyacetophenone even at sample concentration of 10 pmol.

Preparation of a TiO2-NH2 modified MALDI plate for on-plate simultaneous enrichment of phosphopeptides and glycopeptides

In this work, a TiO₂ film was prepared on a MALDI plate by atomic layer deposition (ALD) technique and then modified with -NH₂. The obtained TiO₂-NH₂ modified plate was applied for on-plate simultaneous enrichment of phosphopeptides and glycopeptides. The ALD TiO₂ film displayed quite uniform morphology, and attached firmly to the MALDI plate with rather stable physical and chemical properties, which resulted in fine stability of the plate in performance. The -NH₂ groups offered the film better hydrophilicity and affinity toward glycopeptides. The on-plate simultaneous enrichment performance of the TiO₂-NH₂ modified plate was investigated by β-casein digests, HRP digests and human serum.

A Surface Pattern on MALDI Steel Plate for One-Step In-Situ Self-Desalting and Enrichment of Peptides/Proteins

We report a novel strategy to achieve simultaneous one-step in-situ self-desalting and enrichment (OISE) of peptides/proteins on a facilely fabricated patterned MALDI steel plate with a circular paraffin-steel-polystyrene structure. The OISE plate could efficiently segregate salts from both analytes and matrices while retaining both analyte and matrix concentrate, and facilitating them to form homogeneous co-crystals on the centrally located polystyrene pattern. With the OISE plate, high quality and reproducible spectra could be obtained for low abundance peptides even in the presence of high salt concentrations (200 mM NH₄HCO₃, 1 M NaCl, or 400 mM urea). Using this strategy, a significant sensitivity enhancement was gained over traditional MALDI plate. The practical utility of this method was further demonstrated by the successful profiling of BSA digests and human serum. Graphical Abstract ᅟ.

(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.

Desalting by crystallization: detection of attomole biomolecules in picoliter buffers by mass spectrometry

Sensitive detection of biomolecules in small-volume samples by mass spectrometry is, in many cases, challenging because of the use of buffers to maintain the biological activities of proteins and cells. Here, we report a highly effective desalting method for picoliter samples. It was based on the spontaneous separation of biomolecules from salts during crystallization of the salts. After desalting, the biomolecules were deposited in the tip of the quartz pipet because of the evaporation of the solvent. Subsequent detection of the separated biomolecules was achieved using solvent assisted electric field induced desorption/ionization (SAEFIDI) coupled with mass spectrometry. It allowed for direct desorption/ionization of the biomolecules in situ from the tip of the pipet. The organic component in the assistant solvent inhibited the desorption/ionization of salts, thus assured successful detection of biomolecules. Proteins and peptides down to 50 amol were successfully detected using our method even if there were 3 × 10(5) folds more amount of salts in the sample. The concentration and ion species of the salts had little influence on the detection results.

Cooperative adsorption behavior of phosphopeptides on TiO2 leads to biased enrichment, detection and quantification

Novel data show that anomalous adsorption behavior and common washing procedures can lead to biased results in TiO₂-based phosphoproteomics.

A Ti4+-immobilized phosphate polymer-patterned silicon substrate for on-plate selective enrichment and self-desalting of phosphopeptides

A circular hydrophobic–hydrophilic-Ti⁴⁺ immobilized phosphate polymer is patterned as the sample support for selective enrichment, wash-free self-desalting and mass spectroscopy (MS) analysis of phosphopeptides.

On-plate self-desalting and matrix-free LDI MS analysis of peptides with a surface patterned sample support

A hydrophobic-hydrophilic-hydrophobic pattern has been produced on the surface of a silicon substrate for selective enrichment, self-desalting, and matrix-free analysis of peptides in a single step. Upon sample application, the sample solution is first confined in a small area by a hydrophobic F-SAM outer area, after which salt contaminants and peptides are selectively enriched in the hydrophilic and hydrophobic areas, respectively. Simultaneously, matrix background noise is significantly reduced or eliminated because of immobilization of matrix molecules. As a result, the detection sensitivity is enhanced 20-fold compared with that obtained using the usual MALDI plate, and interference-free detection is achieved in the low m/z range. In addition, peptide ions can be identified unambiguously in the presence of NH₄HCO₃ (100 mM), urea (1 M), and NaCl (1 M). When the device was applied to the analysis of BSA digests, the peptide recovery and protein identification confidence were greatly improved.

On-plate glycoproteins/glycopeptides selective enrichment and purification based on surface pattern for direct MALDI MS analysis

In this paper, a novel method has been proposed to achieve selective enrichment and purification of glycoproteins/glycopeptides on a surface patterned sample support, which consists of a hydrophobic outer layer (F-SAM) and an internal boronic acid-modified gold microspot (900 μm). Upon deposition, the sample solution is firstly concentrated in a small area by repulsion of the hydrophobic outer layer, and then the glycoproteins/glycopeptides are selectively captured through boronic acid covalently binding in the inner layer. However, the non-glycosylated proteins/peptides or high concentration salts are removed after rinsing with alkaline solution. As a result, the detection sensitivity is improved by an order of magnitude greater than when using a stainless steel MALDI plate. With surface patterned sample support, the glycoproteins/glycopeptides can be detected even under interference from the excessive existing non-glycosylated proteins/peptides (10 times more than glycoproteins/glycopeptides). Simultaneously, high-quality mass spectra can be obtained even in the presence of urea (1 M), NaCl (1 M), or NH4HCO3 (200 mM). Therefore, this novel technique may be applied to high-throughput analysis of low-abundance glycoproteins/glycopeptides in complicated proteome research.

Biomimetic antireflective silicon nanocones array for small molecules analysis

Biomimetic antireflective silicon nanocones array is used for analysis of small molecules by mass spectrometry. The role of the absorbed laser energy and its distribution in the laser desorption/ionization process has been investigated by varying the antireflective features precisely. By optimizing the antireflective silicon array, the absorbed laser energy can be channeled completely into the desorption/ionization of analytes. The optimized silicon array exhibits excellent performance to detect peptide, amino acid, drug molecule, and carbohydrate without any interference in the low-mass region.