Genome-wide CRISPR screenings identified SMCHD1 as a host-restricting factor for AAV transduction.

AAV-mediated gene therapy typically requires a high dose of viral transduction, risking acute immune responses and patient safety, part of which is due to limited understanding of the host-viral interactions, especially post-transduction viral genome processing. Here, through a genome-wide CRISPR screen, we identified SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain 1), an epigenetic modifier, as a critical broad-spectrum restricting host factor for post-entry AAV transgene expression. SMCHD1 knock-down by RNAi and CRISPRi or knock-out by CRISPR all resulted in significantly enhanced transgene expression across multiple viral serotypes, as well as for both single-strand and self-complementary AAV genome types. Mechanistically, upon viral transduction, SMCHD1 effectively repressed AAV transcription by the formation of an LRIF1-HP1-containing protein complex and directly binding with the AAV genome to maintain a heterochromatin-like state. SMCHD1-KO or LRIF1-KD could disrupt such a complex and thus result in AAV transcriptional activation. Together, our results highlight the host factor-induced chromatin remodeling as a critical inhibitory mechanism for AAV transduction and may shed light on further improvement in AAV-based gene therapy.

Design and synthesis of a small molecular NIR-II chemiluminescence probe for in vivo-activated H2S imaging.

Chemiluminescence (CL) with the elimination of excitation light and minimal autofluorescence interference has been wieldy applied in biosensing and bioimaging. However, the traditional emission of CL probes was mainly in the range of 400 to 650 nm, leading to undesired resolution and penetration in a biological object. Therefore, it was urgent to develop CL molecules in the near-infrared window [NIR, including NIR-I (650 to 900 nm) and near-infrared-II (900 to 1,700 nm)], coupled with unique advantages of long-time imaging, sensitive response, and high resolution at depths of millimeters. However, no NIR-II CL unimolecular probe has been reported until now. Herein, we developed an H2S-activated NIR-II CL probe [chemiluminiscence donor 950, (CD-950)] by covalently connecting two Schaap's dioxetane donors with high chemical energy to a NIR-II fluorophore acceptor candidate via intramolecular CL resonance energy transfer strategy, thereby achieving high efficiency of 95%. CD-950 exhibited superior capacity including long-duration imaging (~60 min), deeper tissue penetration (~10 mm), and specific H2S response under physiological conditions. More importantly, CD-950 showed detection capability for metformin-induced hepatotoxicity with 2.5-fold higher signal-to-background ratios than that of NIR-II fluorescence mode. The unimolecular NIR-II CL probe holds great potential for the evaluation of drug-induced side effects by tracking its metabolites in vivo, further facilitating the rational design of novel NIR-II CL-based detection platforms.

Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions.

One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.

Electron ionization mass spectrometry feature peak relationships combined with deep classification model to assist similarity algorithm for fast and accurate identification of compounds.

RATIONALE: Gas chromatography-mass spectrometry (GC-MS) combines chromatography and MS, providing full play to the advantages of high separation efficiency of GC, strong qualitative ability of MS, and high sensitivity of detector. In GC-MS data processing, determining the experimental compounds is one of the most important analytical steps, which is usually realized by one-to-one similarity calculations between the experimental mass spectrum and the standard mass spectrum library. Although the accuracy of the algorithm has been improved in recent years, it is still difficult to distinguish structurally similar mass spectra, especially isomers. At the same time, the library capacity is very large and increasing every year, and the algorithm needs to perform large numbers of calculations with irrelevant compounds in the library to recognize unknown compounds, which leads to a significant reduction in efficiency. METHODS: This work proposed to exclude a large number of irrelevant mass spectra by presearching, perform preliminary similarity calculations using similarity algorithms, and finally improve the accuracy of similarity calculations using deep classification models. The replica library of NIST17 is used as the query data, and the master library is used as the reference database. RESULTS: Compared with the traditional recognition algorithm, the preprocessing algorithm has reduced the time by 4.2 h, and by adding the deep learning models 1 and 2 as the final determination, the recognition accuracy has been improved by 1.9% and 6.5%, respectively, based on the original algorithm. CONCLUSIONS: This method improves the recognition efficiency compared to conventional algorithms and at the same time has better recognition accuracy for structurally similar mass spectra and isomers.

Two-step particle swarm optimization algorithm for effective deconvolution and resolution enhancement of various overlapping peaks.

RATIONALE: The existing particle swarm optimization (PSO) algorithms are only effective in deconvoluting the overlapping peaks in ion mobility spectra with fewer than four component peaks, which limits the applicability of these algorithms. METHODS: A high-performance two-step particle swarm optimization (TSPSO) algorithm was developed. Compared to the existing PSO algorithms, TSPSO can narrow the search ranges of all coefficients for the overlapping peaks through Gaussian model calculation, and thus can deconvolute various overlapping peaks with high accuracy, even for 30-component overlapping peaks. In addition, the TSPSO could be further applied to enhance the resolution of the spectra by narrowing the peak widths after the peak deconvolution. RESULTS: Simulated overlapping peaks were first used to evaluate the performance of TSPSO as compared to the dynamic inertia weight particle swarm optimization (DIWPSO) algorithm. The results showed that the profiles of the peaks deconvoluted by using TSPSO were more consistent with the original ones. The fitness values and the standard deviations of the fitness values from TSPSO were also at least an order of magnitude less than those from DIWPSO. By applying TSPSO, the overlapping peaks from both mass spectrometry (MS) and field asymmetric waveform ion mobility spectrometry (FAIMS) spectra can also be well deconvoluted. In addition, the resolutions of the MS and FAIMS spectra can be effectively enhanced after peak deconvolution. The enhanced spectra matched excellently with the experimental ones acquired at high-resolution modes. CONCLUSIONS: The experiment results convincingly demonstrate that the TSPSO algorithm is capable of both deconvoluting complex overlapping peaks and enhancing the spectrum resolution with high accuracy.

Overlapping peak separation algorithm for ion mobility spectra based on multistrategy JAYA.

RATIONALE: In the field of separation science, ion mobility spectrometry (IMS) plays an important role as an analytical tool. However, the lack of sufficient structural resolution is a common problem in qualitative and quantitative analysis using IMS. A method is needed to solve the problem of overlapping peaks caused by insufficient resolution. METHODS: The method uses multiple strategies to more effectively use population information to balance exploration and exploitation capabilities, prevent local optimization, accurately resolve overlapping peaks, quickly obtain optimal spectral peak model coefficients, and accurately identify compounds. RESULTS: Multistrategy JAYA algorithm's (MSJAYA) performance is compared with improved particle swarm optimization (IPSO), dynamic inertia weight particle swarm optimization (DIWPSO), and multiobjective dynamic teaching-learning-based optimization (MDTLBO). The analysis shows that MSJAYA's maximum separation error is within 0.6%, a level of accuracy not guaranteed by the other algorithms. In addition, the separation error fluctuates within a much smaller range, demonstrating MSJAYA's superior robustness. CONCLUSIONS: Compared with other overlapping peak separation algorithms, MSJAYA is more applicable because no special parameters are used. The method allows fast deconvolution analysis of strong overlapping peaks with multiple components, which greatly improves the resolution of IMS.

BRD2 interconnects with BRD3 to facilitate Pol II transcription initiation and elongation to prime promoters for cell differentiation.

The bromodomain and extraterminal motif (BET) proteins are critical drug targets for diseases. The precise functions and relationship of BRD2 with other BET proteins remain elusive mechanistically. Here, we used acute protein degradation and quantitative genomic and proteomic approaches to investigate the primary functions of BRD2 in transcription. We report that BRD2 is required for TAF3-mediated Pol II initiation at promoters with low levels of H3K4me3 and for R-loop suppression during Pol II elongation. Single and double depletion revealed that BRD2 and BRD3 function additively, independently, or perhaps antagonistically in Pol II transcription at different promoters. Furthermore, we found that BRD2 regulates the expression of different genes during embryonic body differentiation processes by promoter priming in embryonic stem cells. Therefore, our results suggest complex interconnections between BRD2 and BRD3 at promoters to fine-tune Pol II initiation and elongation for control of cell state.

Tunable Optical Vortex from a Nanogroove-Structured Optofluidic Microlaser.

Optical vortices with tunable properties in multiple dimensions are highly desirable in modern photonics, particularly for broadly tunable wavelengths and topological charges at the micrometer scale. Compared to solid-state approaches, here we demonstrate tunable optical vortices through the fusion of optofluidics and vortex beams in which the handedness, topological charges, and lasing wavelengths could be fully adjusted and dynamically controlled. Nanogroove structures inscribed in Fabry-Pérot optofluidic microcavities were proposed to generate optical vortices by converting Hermite-Gaussian laser modes. Topological charges could be controlled by tuning the lengths of the nanogroove structures. Vortex laser beams spanning a wide spectral band (430-630 nm) were achieved by alternating different liquid gain materials. Finally, dynamic switching of vortex laser wavelengths in real-time was realized through an optofluidic vortex microlaser device. The findings provide a robust yet flexible approach for generating on-chip vortex sources with multiple dimensions, high tunability, and reconfigurability.

Structure Regulation of MOF Nanosheet Membrane for Accurate H2 /CO2 Separation.

High-purity H2 production accompanied with a precise decarbonization opens an avenue to approach a carbon-neutral society. Metal-organic framework nanosheet membranes provide great opportunities for an accurate and fast H2 /CO2 separation, CO2 leakage through the membrane interlayer galleries decided the ultimate separation accuracy. Here we introduce low dose amino side groups into the Zn2 (benzimidazolate)4 conformation. Physisorbed CO2 served as interlayer linkers, gently regulated and stabilized the interlayer spacing. These evoked a synergistic effect of CO2 adsorption-assisted molecular sieving and steric hinderance, whilst exquisitely preserving apertures for high-speed H2 transport. The optimized amino membranes set a new record for ultrathin nanosheet membranes in H2 /CO2 separation (mixture separation factor: 1158, H2 permeance: 1417 gas permeation unit). This strategy provides an effective way to customize ultrathin nanosheet membranes with desirable molecular sieving ability.

Near-Infrared II Gold Nanocluster Assemblies with Improved Luminescence and Biofate for In Vivo Ratiometric Imaging of H2S.

Ultrasmall gold nanoclusters (AuNCs) are emerging as promising luminescent nanoprobes for bioimaging due to their fantastic photoluminescence (PL) and renal-clearable ability. However, it remains a great challenge to design them for in vivo sensitive molecular imaging in desired tissues. Herein, we have developed a strategy to tailor the PL and biofate of near-infrared II (NIR-II)-emitting AuNCs via ligand anchoring for improved bioimaging. By optimizing the ligand types in AuNCs and using Er3+-doped lanthanide (Ln) nanoparticles as models, core-satellite Ln@AuNCs assemblies were rationally constructed, which enabled 2.5-fold PL enhancement of AuNCs at 1100 nm and prolonged blood circulation compared to AuNCs. Significantly, Ln@AuNCs with dual intense NIR-II PL (from AuNCs and Er3+) can effectively accumulate in the liver for ratiometric NIR-II imaging of H2S, facilitated by H2S-mediated selective PL quenching of AuNCs. We have then demonstrated the real-time imaging evaluation of liver delivery efficacy and dynamics of two H2S prodrugs. This shows a paradigm to visualize liver H2S delivery and its prodrug screening in vivo. Note that Ln@AuNCs are body-clearable via the hepatobiliary excretion pathway, thus reducing potential long-term toxicity. Such findings may propel the engineering of AuNC nanoprobes for advancing in vivo bioimaging analysis.

Combination of continuous wavelet transform and genetic algorithm-based Otsu for efficient mass spectrometry peak detection.

Mass spectrometry (MS) data is susceptible to random noises and alternating baseline, posing great challenges to spectral peak detection, especially for weak peaks and overlapping peaks. Herein, an efficient peak detection algorithm combining continuous wavelet transform (CWT) and genetic algorithm-based threshold segmentation (denoted as WSTGA) for mass spectrometry was proposed. Firstly, Mexican Hat wavelet was selected as the mother wavelet by comparing the matching degree between the difference of Gaussian (DOG) and different wavelets. Subsequently, the ridges and valleys were identified from 2D wavelet coefficient matrix. Afterward, an improved threshold segmentation method, Otsu method based on genetic algorithm, was introduced to find optimal segmentation threshold and achieve better image segmentation, overcoming the deficiency of traditional Otsu method that cannot handle long-tailed unimodal histograms. Finally, the characteristic peaks were successfully identified by utilizing the ridge-valley lines in wavelet space and original spectrum. Receiver operating characteristic (ROC) curve, area under curve (AUC) and F1 measure are used as criterions to evaluate performance of peak detection algorithms. Compared with multi-scale peak detection (MSPD) and CWT and image segmentation (CWT-IS) methods, all the results showed that WSTGA can achieve better peak detection. More importantly, the experimental results from MALDI-TOF spectra demonstrated that WSTGA can effectively detect more weak peaks and overlapping peaks while maintaining a lower false peak detection rate than MSPD and CWT-IS methods, indicating its great advantages in characteristic peak identification.

A novel graphene oxide/chitosan foam incorporated with metal-organic framework stationary phase for simultaneous enrichment of glycopeptide and phosphopeptide with high efficiency.

A novel hydrophilic porous biocomposite was fabricated by incorporating graphene oxide (GO) @chitosan (CS) foam substrate (GO@CS@ZIF-8 foam) with ZIF-8 crystals in situ via a facile stirring method for simultaneous enrichment of glycopeptides and phosphopeptides from complex biological samples. The experimental results demonstrated that GO@CS@ZIF-8 foam exhibited favorable specificity for simultaneous enrichment of N-glycopeptides and phosphopeptides under the same condition for HRP and ß-casein tryptic digest mixtures. The novel material was further applied to enriching both glycopeptides and phosphopeptides simultaneously from 4 µL complex human serum, and 423 N-glycopeptides and 40 phosphopeptides corresponding to 133 glycoproteins and 29 phosphoproteins were identified, respectively.

Effective Chiral Discrimination of Amino Acids through Oligosaccharide Incorporation by Trapped Ion Mobility Spectrometry.

Chiral analysis is critical to many research fields due to different biological functions of enantiomers in living systems. Although the use of ion mobility spectrometry (IMS) has become an alternative technology in the area of chiral measurements, there is still a lack of a general chiral selector for IMS-based chiral recognition, especially for small chiral molecules. Here, a new method using oligosaccharides as the chiral selector has been developed to discriminate chiral amino acids (AAs) by trapped ion mobility spectrometry-mass spectrometry (TIMS-MS). We analyzed 21 chiral amino acids, including small molecules (e.g., alanine and cysteine). Our data showed that the use of nonreducing tetrasaccharides was effective for the separation of chiral AAs, which differentiated 21 chiral AAs without using metal ions. By further incorporating a copper ion, the separation resolution could be improved to 1.64 on average, which accounts for an additional 52% improvement on top of the already achieved separation in metal-free analysis. These results indicate that the use of tetrasaccharides is an effective strategy for the separation of AA enantiomers by TIMS. The method developed in this study may open up a new strategy for effective IMS-based chiral analysis.

In Situ Activatable Ratiometric NIR-II Fluorescence Nanoprobe for Quantitative Detection of H2S in Colon Cancer.

As key characteristic molecules, several H2S-activated probes have been explored for colon cancer studies. However, a few ratiometric fluorescence (FL) probes with NIR-II emissions have been reported for the quantitative detection of H2S in colon cancer in vivo. Here, we developed an in situ H2S-activatable ratiometric nanoprobe with two NIR-II emission signals for the detection of H2S and intelligently lighting up colon cancer. The nanoprobe comprised a down conversion nanoparticle (DCNP), which emitted NIR-II FL at 1550 nm on irradiation with a 980 nm laser (F1550Em, 980Ex). Further, human serum albumin (HSA) was combined with Ag+ on the surface of DCNP to form a DCNP@HSA-Ag+ nanoprobe. In the presence of H2S, Ag2S quantum dots (QDs) were formed in coated HSA, which emitted FL at approximately 1050 nm on irradiation with an 808 nm laser (F1050Em, 808Ex) through an H2S-induced chemical reaction between H2S and Ag+; however, the FL signal of DCNP was stable at 1550 nm (F1550Em, 980Ex), generating a H2S concentration-dependent ratiometric F1050Em, 808Ex/F1550Em, 980Ex signal. The NIR-II ratiometric nanoprobe was successfully used for the accurate quantitative detection of H2S and the detection of the precise location of colon cancer through an endogenous H2S-induced in situ reduction reaction to form Ag2S QDs. Thus, these findings provide a new strategy for the specific detection of targeted molecules and diagnosis of disease based on the in situ-activatable NIR-II ratiometric FL nanoprobe.

Dilated convolutional neural networks for fiber Bragg grating signal demodulation.

In quasi-distributed fiber Bragg grating (FBG) sensor networks, challenges are known to arise when signals are highly overlapped and thus hard to separate, giving rise to substantial error in signal demodulation. We propose a multi-peak detection deep learning model based on a dilated convolutional neural network (CNN) that overcomes this problem, achieving extremely low error in signal demodulation even for highly overlapped signals. We show that our FBG demodulation scheme enhances the network multiplexing capability, detection accuracy and detection time of the FBG sensor network, achieving a root-mean-square (RMS) error in peak wavelength determination of < 0.05 pm, with a demodulation time of 15 ms for two signals. Our demodulation scheme is also robust against noise, achieving an RMS error of < 0.47 pm even with a signal-to-noise ratio as low as 15 dB. A comparison on our high-performance computer with existing signal demodulation methods shows the superiority in RMS error of our dilated CNN implementation. Our findings pave the way to faster and more accurate signal demodulation methods, and testify to the substantial promise of neural network algorithms in signal demodulation problems.

Hollow electrode capillary plasma ionization source for rapid online detection of gaseous samples.

RATIONALE: Gas chromatography mass spectrometry (GC-MS) with electron ionization (EI) is the most widely used analysis technique of gaseous samples, but it may be time-consuming for online monitoring of mixtures whose concentrations relatively change rapidly. On the contrary, current ionization methods, such as chemical ionization (CI) and proton transfer reaction (PTR), also have some disadvantages such as selectivity. Therefore, appropriate soft ionization sources are searched for rapid online detection. METHODS: Hollow electrode capillary plasma ionization (HECPI) is based on single electrode plasma. A hollow capillary was placed as both the electrode and the inlet of the gaseous samples. The ionization source is coupled with a mass spectrometer for performance evaluation. RESULTS: Several typical compounds have been tested with HECPI-mass spectrometer. In this process, the dominant ion peaks of all compounds can be indexed as molecular ion peaks, and the product ions of HECPI are less than that of dielectric barrier discharge ionization (DBDI). Three gaseous samples (linalool, triethylamine, and styrene) with various concentrations have been used to further confirm the performance of this source, and the detection limit of linalool is as low as 10 ppb. CONCLUSIONS: HECPI is simple in structure and shows good performance. The results also show that HECPI has the potential to be an effective tool for detecting online gaseous samples rapidly.

A TIMS-TOF mass spectrometry study of disaccharides from in situ ESI derivatization with 3-pyridinylboronate.

3-Pyridinylboronate, a zwitterionic boronic acid, displayed effective in situ ESI for reversible covalent tagging of saccharides in both cation and anion modes. The ion mobilities of thus-generated ions were examined with the Bruker timsTOF fleX instrument. Nine disaccharides were examined using this method. They have identical mass-to-charge ratios, differing only in monomer compositions, regio-linkages, and anomeric configurations (α or ß). The IMS separations of the disaccharides from this method were compared with those from sodium adducts reported in the literature. The differentiation effects of this method on the disaccharide isomers were increased on average by an order of magnitude. Using this method, all the pairs of disaccharides selected from nine isomers were completely identified by comparing the mobility spectra of single-tagged and double-tagged ions.

On a separation voltage polarity switching transient capillary isotachophoresis method for higher sample loading capacity and better separation performance.

Limited sample loading capacity is one of the major reasons that prevents the utility of capillary electrophoresis (CE) as a routine separation method as compared to liquid chromatography (LC). In our previous study, separation voltage polarity switching transient capillary isotachophoresis (PS-tCITP) was proposed. Both sample loading capacity and separation resolution could be improved using a single PS-tCITP instead of routine transient capillary isotachophoresis (tCITP). In this study, a detailed investigation on the optimization strategy of the PS-tCITP method was performed systematically. A possible mechanism of sample preconcentration in multiple PS-tCITP was first proposed to better understand the multiple PS-tCITP process. Several optimization experiments were then performed, including single PS-tCITP, paused PS-tCITP and multiple PS-tCITP, sequentially using a mixture of five peptides. By selecting an optimum polarity switching time, sample loading capacity of 100% capillary volume could be achieved in a single PS-tCITP. Introducing an additional pause between each polarity switching in a single PS-tCITP further improved the separation resolution. Experimental results showed a baseline separation of five selected peptide standards at 100% sample loading volume using a 100 min pause in a single PS-tCITP. To further improve separation efficiency while still maintaining 100% sample loading volume, a multiple PS-tCITP technique was developed through this study. Compared to the separation performance of the optimal single PS-tCITP at 100% sample loading volume with a 10 min pause, the separation window was improved by 54% and the peak capacity was improved by 48% in the optimal four PS-tCITP with the same sample loading volume and pause.

NIR-II emissive AIEgen photosensitizers enable ultrasensitive imaging-guided surgery and phototherapy to fully inhibit orthotopic hepatic tumors.

Accurate diagnosis and effective treatment of primary liver tumors are of great significance, and optical imaging has been widely employed in clinical imaging-guided surgery for liver tumors. The second near-infrared window (NIR-II) emissive AIEgen photosensitizers have attracted a lot of attention with higher-resolution bioimaging and deeper penetration. NIR-II aggregation-induced emission-based luminogen (AIEgen) photosensitizers have better phototherapeutic effects and accuracy of the image-guided surgery/phototherapy. Herein, an NIR-II AIEgen phototheranostic dot was proposed for NIR-II imaging-guided resection surgery and phototherapy for orthotopic hepatic tumors. Compared with indocyanine green (ICG), the AIEgen dots showed bright and sharp NIR-II emission at 1250 nm, which extended to 1600 nm with high photostability. Moreover, the AIEgen dots efficiently generated reactive oxygen species (ROS) for photodynamic therapy. Investigations of orthotopic liver tumors in vitro and in vivo demonstrated that AIEgen dots could be employed both for imaging-guided tumor surgery of early-stage tumors and for 'downstaging' intention to reduce the size. Moreover, the therapeutic strategy induced complete inhibition of orthotopic tumors without recurrence and with few side effects.

Boosting the hole transport of conductive polymers by regulating the ion ratio in ionic liquid additives.

Poly(3,4-ethylenedioxythiophene) (PEDOT) has aroused great interest in organic electrics because of its high electrical conductivity and mechanical flexibility. To improve the charge transport, it can act as an ionic liquid (IL) additive due to its ion characteristics and high electrical conductivity. Herein, we investigated the hole-transport performance of PEDOT treated by ILs featuring specific ion ratios (4 : 1, 3 : 1, 2 : 1, 1 : 1, 1 : 2, 1 : 3, and 1 : 4) of the cation and anion through classical dynamics simulations and quantum mechanics computations. The hole mobility of the amorphous PEDOT, constituting nine EDOT monomers, could be improved to 16.81, 18.03, and 10.14 cm2 V-1 s-1 when synergistically regulating the ion ratio to 2 : 1, 3 : 1, and 4 : 1. Consequently, these ratios potentially achieved nearly a 100-fold improvement in the electrical conductivity with respect to the pristine system. The improvements mainly stemmed from the fact that decreasing the amount of anions in ILs and prolonging the chain length of PEDOT yielded an ordered face-to-face π-π stacking. The electronic coupling and charge excitation further confirmed that the anions play an active role in tunneling the hole transport in ILs/heterogeneous PEDOT, and the highest occupied molecular orbital (HOMO) energy level of PEDOT was up-shifted significantly after treatment by the ratios of 2 : 1, 3 : 1, and 4 : 1, which favored the electron-donating ability and was in line with the extraordinary enhancement of the hole mobility. Our results imply that regulating the ion ratio in ILs is a novel strategy for modulating the electronic properties and π-stacked morphology of PEDOT.