Identification of long-lived proteins reveals exceptional stability of essential cellular structures.

Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell's life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process. PAPERCLIP:

Metal-Oxide Heterojunction Optoelectronic Synapse and Multilevel Memory Devices Enabled by Broad Spectral Photocarrier Modulation.

Broad spectral response and high photoelectric conversion efficiency are key milestones for realizing multifunctional, low-power optoelectronic devices such as artificial synapse and reconfigurable memory devices. Nevertheless, the wide bandgap and narrow spectral response of metal-oxide semiconductors are problematic for efficient metal-oxide optoelectronic devices such as photonic synapse and optical memory devices. Here, a simple titania (TiO2 )/indium-gallium-zinc-oxide (IGZO) heterojunction structure is proposed for efficient multifunctional optoelectronic devices, enabling widen spectral response range and high photoresponsivity. By overlaying a TiO2 film on IGZO, the light absorption range extends to red light, along with enhanced photoresponsivity in the full visible light region. By implementing the TiO2 /IGZO heterojunction structure, various synaptic behaviors are successfully emulated such as short-term memory/long-term memory and paired pulse facilitation. Also, the TiO2 /IGZO synaptic transistor exhibits a recognition rate up to 90.3% in recognizing handwritten digit images. Moreover, by regulating the photocarrier dynamics and retention behavior using gate-bias modulation, a reconfigurable multilevel (≥8 states) memory is demonstrated using visible light.

SERS-based dual-mode DNA aptasensors for rapid classification of SARS-CoV-2 and influenza A/H1N1 infection.

We developed a dual-mode surface-enhanced Raman scattering (SERS)-based aptasensor that can accurately diagnose and distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/H1N1 at the same time. Herein, DNA aptamers that selectively bind to SARS-CoV-2 and influenza A/H1N1 were immobilized together on Au nanopopcorn substrate. Raman reporters (Cy3 and RRX), attached to the terminal of DNA aptamers, could generate strong SERS signals in the nanogap of the Au nanopopcorn substrate. Additionally, the internal standard Raman reporter (4-MBA) was immobilized on the Au nanopopcorn substrate along with aptamer DNAs to reduce errors caused by changes in the measurement environment. When SARS-CoV-2 or influenza A virus approaches the Au nanopopcorn substrate, the corresponding DNA aptamer selectively detaches from the substrate due to the significant binding affinity between the corresponding DNA aptamer and the virus. As a result, the related SERS intensity decreases with increasing target virus concentration. Thus, it is possible to determine whether a suspected patient is infected with SARS-CoV-2 or influenza A using this SERS-based DNA aptasensor. Furthermore, this sensor enables a quantitative evaluation of the target virus concentration with high sensitivity without being affected by cross-reactivity. Therefore, this SERS-based diagnostic platform is considered a conceptually new diagnostic tool that rapidly discriminates against these two respiratory diseases to prevent their spread.

Highly Sensitive Textile-Based Capacitive Pressure Sensors Using PVDF-HFP/Ionic Liquid Composite Films.

Textile-based pressure sensors have garnered considerable interest in electronic textiles due to their diverse applications, including human-machine interface and healthcare monitoring systems. We studied a textile-based capacitive pressure sensor array using a poly(vinylidene fluoride)-co-hexafluoropropylene (PVDF-HFP)/ionic liquid (IL) composite film. By constructing a capacitor structure with Ag-plated conductive fiber electrodes that are embedded in fabrics, a capacitive pressure sensor showing high sensitivity, good operation stability, and a wide sensing range could be created. By optimizing the PVDF-HFP:IL ratio (6.5:3.5), the fabricated textile pressure sensors showed sensitivity of 9.51 kPa-1 and 0.69 kPa-1 in the pressure ranges of 0-20 kPa and 20-100 kPa, respectively. The pressure-dependent capacitance variation in our device was explained based on the change in the contact-area formed between the multi-filament fiber electrodes and the PVDF-HFP/IL film. To demonstrate the applicability and scalability of the sensor device, a 3 × 3 pressure sensor array was fabricated. Due to its matrix-type array structure and capacitive sensing mechanism, multi-point detection was possible, and the different positions and the weights of the objects could be identified.

PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies.

A data-independent acquisition (DIA) approach is being increasingly adopted as a promising strategy for identification and quantitation of proteomes. As most DIA data sets are acquired with wide isolation windows, highly complex MS/MS spectra are generated, which negatively impacts obtaining peptide information through classical protein database searches. Therefore, the analysis of DIA data mainly relies on the evidence of the existence of peptides from prebuilt spectral libraries. Consequently, one major weakness of this method is that it does not account for peptides that are not included in the spectral library, precluding the use of DIA for discovery studies. Here, we present a strategy termed Precursor ion And Small Slice-DIA (PASS-DIA) in which MS/MS spectra are acquired with small isolation windows (slices) and MS/MS spectra are interpreted with accurately determined precursor ion masses. This method enables the direct application of conventional spectrum-centric analysis pipelines for peptide identification and precursor ion-based quantitation. The performance of PASS-DIA was observed to be superior to both data-dependent acquisition (DDA) and conventional DIA experiments with 69 and 48% additional protein identifications, respectively. Application of PASS-DIA for the analysis of post-translationally modified peptides again highlighted its superior performance in characterizing phosphopeptides (77% more), N-terminal acetylated peptides (56% more), and N-glycopeptides (83% more) as compared to DDA alone. Finally, the use of PASS-DIA to characterize a rare proteome of human fallopian tube organoids enabled 34% additional protein identifications than DDA alone and revealed biologically relevant pathways including low abundance proteins. Overall, PASS-DIA is a novel DIA approach for use as a discovery tool that outperforms both conventional DDA and DIA experiments to provide additional protein information. We believe that the PASS-DIA method is an important strategy for discovery-type studies when deeper proteome characterization is required.

Flexible Metal Oxide Semiconductor Devices Made by Solution Methods.

For the fabrication of next-generation flexible metal oxide devices, solution-based methods are considered as a promising approach because of their potential advantages, such as high-throughput, large-area scalability, low-cost processing, and easy control over the chemical composition. However, to obtain certain levels of electrical performance, a high process temperature is essential, which can significantly limit its application in flexible electronics. Therefore, this article discusses recent research conducted on developing low-temperature, solution-processed, flexible, metal oxide semiconductor devices, from a single thin-film transistor device to fully integrated circuits and systems. The main challenges of solution-processed metal oxide semiconductors are introduced. Recent advances in materials, processes, and semiconductor structures are then presented, followed by recent advances in electronic circuits and systems based on these semiconductors, including emerging flexible energy-harvesting devices for self-powered systems that integrate displays, sensors, data-storage units, and information processing functions.

Treatment with intravenous busulfan, melphalan, and etoposide followed by autologous stem cell transplantation in patients with non-Hodgkin's lymphoma: a multicenter study from the consortium for improving survival of lymphoma.

Several high-dose therapy (HDT) conditioning regimens have been used to treat non-Hodgkin's lymphoma (NHL), such as bis-chloroethylnitrosourea (BCNU)/etoposide/cytosine arabinoside/melphalan (BEAM), BCNU/etoposide/cytosine arabinoside/cyclophosphamide (BEAC), and cyclophosphamide/BCNU/etoposide (CBV). BCNU is an active drug in HDT of NHL, but the supply is limited in some countries, including Korea. Busulfan has been used in allogeneic and autologous stem cell transplantation (ASCT). This phase II study evaluated the efficacy of busulfan/melphalan/etoposide (BuME) as a conditioning regimen for HDT in relapsed or high-risk NHL. The regimen consisted of intravenous busulfan (3.2 mg/kg/day) on days -8, -7, and -6, etoposide (400 mg/m2 /day) on days -5 and -4, and melphalan (50 mg/m2 /day) on days -3 and -2. A total of 46 patients were included in the study, with 36 (78.3%) achieving a complete response after ASCT. The 2-year progression-free survival (PFS) and overall survival (OS) rates for all patients were 46.7% (95% CI, 31.8-60.4%) and 63.7% (95% CI, 47.7-76.0%), respectively. There was no development of veno-occlusive disease and no treatment-related deaths within 100 days after ASCT. These results indicate that a BuME regimen is well-tolerated and effective for patients with relapsed or high-risk NHL, and may be comparable to some previously used regimens. This regimen may be useful as a substitute for BCNU-containing regimens.

Locally Controlled Sensing Properties of Stretchable Pressure Sensors Enabled by Micro-Patterned Piezoresistive Device Architecture.

For wearable health monitoring systems and soft robotics, stretchable/flexible pressure sensors have continuously drawn attention owing to a wide range of potential applications such as the detection of human physiological and activity signals, and electronic skin (e-skin). Here, we demonstrated a highly stretchable pressure sensor using silver nanowires (AgNWs) and photo-patternable polyurethane acrylate (PUA). In particular, the characteristics of the pressure sensors could be moderately controlled through a micro-patterned hole structure in the PUA spacer and size-designs of the patterned hole area. With the structural-tuning strategies, adequate control of the site-specific sensitivity in the range of 47~83 kPa-1 and in the sensing range from 0.1 to 20 kPa was achieved. Moreover, stacked AgNW/PUA/AgNW (APA) structural designed pressure sensors with mixed hole sizes of 10/200 µm and spacer thickness of 800 µm exhibited high sensitivity (~171.5 kPa-1) in the pressure sensing range of 0~20 kPa, fast response (100~110 ms), and high stretchability (40%). From the results, we envision that the effective structural-tuning strategy capable of controlling the sensing properties of the APA pressure sensor would be employed in a large-area stretchable pressure sensor system, which needs site-specific sensing properties, providing monolithic implementation by simply arranging appropriate micro-patterned hole architectures.

ComPIL 2.0: An Updated Comprehensive Metaproteomics Database.

We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex metasamples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Here, we present a rebuild of the ComPIL libraries comprised of updated publicly disseminated sequence data as well as a modified version of the search engine ProLuCID-ComPIL optimized for querying experimental spectra. ComPIL 2.0 consists of 113 million protein records and roughly 4.8 billion unique tryptic peptide sequences and is 2.3 times the size of our original version. We searched a data set collected on a healthy human gut microbiome proteomic sample and compared the results to demonstrate that ComPIL 2.0 showed a substantial increase in the number of unique identified peptides and proteins compared to the first ComPIL version. The high confidence of protein identification and accuracy demonstrated by the use of ComPIL 2.0 may encourage the method's application for large-scale proteomic annotation of complex protein systems.

Recent Progress of Textile-Based Wearable Electronics: A Comprehensive Review of Materials, Devices, and Applications.

Wearable electronics are emerging as a platform for next-generation, human-friendly, electronic devices. A new class of devices with various functionality and amenability for the human body is essential. These new conceptual devices are likely to be a set of various functional devices such as displays, sensors, batteries, etc., which have quite different working conditions, on or in the human body. In these aspects, electronic textiles seem to be a highly suitable possibility, due to the unique characteristics of textiles such as being light weight and flexible and their inherent warmth and the property to conform. Therefore, e-textiles have evolved into fiber-based electronic apparel or body attachable types in order to foster significant industrialization of the key components with adaptable formats. Although the advances are noteworthy, their electrical performance and device features are still unsatisfactory for consumer level e-textile systems. To solve these issues, innovative structural and material designs, and novel processing technologies have been introduced into e-textile systems. Recently reported and significantly developed functional materials and devices are summarized, including their enhanced optoelectrical and mechanical properties. Furthermore, the remaining challenges are discussed, and effective strategies to facilitate the full realization of e-textile systems are suggested.

Flexible metal-oxide devices made by room-temperature photochemical activation of sol-gel films.

Amorphous metal-oxide semiconductors have emerged as potential replacements for organic and silicon materials in thin-film electronics. The high carrier mobility in the amorphous state, and excellent large-area uniformity, have extended their applications to active-matrix electronics, including displays, sensor arrays and X-ray detectors. Moreover, their solution processability and optical transparency have opened new horizons for low-cost printable and transparent electronics on plastic substrates. But metal-oxide formation by the sol-gel route requires an annealing step at relatively high temperature, which has prevented the incorporation of these materials with the polymer substrates used in high-performance flexible electronics. Here we report a general method for forming high-performance and operationally stable metal-oxide semiconductors at room temperature, by deep-ultraviolet photochemical activation of sol-gel films. Deep-ultraviolet irradiation induces efficient condensation and densification of oxide semiconducting films by photochemical activation at low temperature. This photochemical activation is applicable to numerous metal-oxide semiconductors, and the performance (in terms of transistor mobility and operational stability) of thin-film transistors fabricated by this route compares favourably with that of thin-film transistors based on thermally annealed materials. The field-effect mobilities of the photo-activated metal-oxide semiconductors are as high as 14 and 7 cm(2) V(-1) s(-1) (with an Al(2)O(3) gate insulator) on glass and polymer substrates, respectively; and seven-stage ring oscillators fabricated on polymer substrates operate with an oscillation frequency of more than 340 kHz, corresponding to a propagation delay of less than 210 nanoseconds per stage.

Flavonoid glycosides from leaves and straw of Oryza sativa and their effects of cytotoxicity on a macrophage cell line and allelopathic on weed germination.

Five new flavonoids namely, 5-hydroxy-6-isoprenyl-7,4'-dimethoxyflavonol-3-O-ß-d-arabinofuranoside (1), 5,7-dihydroxy-4'-methoxyflavone-7-O-ß-d-arabinopyranosyl-2''-n-decan-1'''-oate (2), 3-butanoyl-5,6,8-trihydroxy-7,4'-dimethoxyflavonol--5-O-ß-d-glucopyranoside (3), 7, 4'-dimethoxy-5-hydroxyflavone-5-O-α-d-arabinopyranosyl-(2'' → 1''')-O-α-d-arabinopyranoside (4), and 5,6-dihydroxy-7, 4'-dimethoxyflavone-5-O-α-d-glucopyranoside (5), together with two known compounds, were isolated from the methanol extract of Oryza sativa leaves and straw. Their structures of new compounds were elucidated by 1D and 2D NMR spectral methods, viz: COSY, HMBC and HSQC aided by mass techniques and IR spectroscopy. The cytotoxicity of these compounds (1-7) were assessed by using (RAW 264.7) mouse macrophages cell line, and allelopathic effects of compounds (1-7) on the germination characteristics of barnyardgrass (Echinochloa oryzicola) and pigweed (Chenopodium album L.) were also evaluated. The compounds 1, 6 and 7 showed cytotoxicity and compounds 1-7 exhibited significant inhibitory activity on the seed germination of two weed species.

Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases.

Human Proteome Project aims to map all human proteins including missing proteins as well as proteoforms with post translational modifications, alternative splicing variants (ASVs), and single amino acid variants (SAAVs). neXtProt and Ensemble databases are usually used to provide curated information on human coding genes. However, to find these proteoforms, we (Chr #11 team) first introduce a streamlined pipeline using customized and concatenated neXtProt and GENCODE originated from Ensemble, with controlled false discovery rate (FDR). Because of large sized databases used in this pipeline, we found more stringent FDR filtering (0.1% at the peptide level and 1% at the protein level) to claim novel findings, such as GENCODE ASVs and missing proteins, from human hippocampus data set (MSV000081385) and ProteomeXchange (PXD007166). Using our next generation proteomic pipeline (nextPP) with neXtProt and GENCODE databases, two missing proteins such as activity-regulated cytoskeleton-associated protein (ARC, Chr 8) and glutamate receptor ionotropic, kainite 5 (GRIK5, Chr 19) were additionally identified with two or more unique peptides from human brain tissues. Additionally, by applying the pipeline to human brain related data sets such as cortex (PXD000067 and PXD000561), spinal cord, and fetal brain (PXD000561), seven GENCODE ASVs such as ACTN4-012 (Chr.19), DPYSL2-005 (Chr.8), MPRIP-003 (Chr.17), NCAM1-013 (Chr.11), EPB41L1-017 (Chr.20), AGAP1-004 (Chr.2), and CPNE5-005 (Chr.6) were identified from two or more data sets. The identified peptides of GENCODE ASVs were mapped onto novel exon insertions, alternative translations at 5'-untranslated region, or novel protein coding sequence. Applying the pipeline to male reproductive organ related data sets, 52 GENCODE ASVs were identified from two testis (PXD000561 and PXD002179) and a spermatozoa (PXD003947) data sets. Four out of 52 GENCODE ASVs such as RAB11FIP5-008 (Chr. 2), RP13-347D8.7-001 (Chr. X), PRDX4-002 (Chr. X), and RP11-666A8.13-001 (Chr. 17) were identified in all of the three samples.

Photochemical Molecular Tailoring for Efficient Diffusion and Reorganization of Organic Nanocrystals for Ultra-Flexible Organic Semiconductor Arrays.

Solution-processed organic single crystals with high carrier mobility have been actively investigated for diverse applications such as displays, sensors, and next generation electronics on a flexible platform. However, the lack of precise alignment and growth control of organic single crystals impedes the widespread adoption of organic materials in an industrial perspective. Here, a photochemical modification approach is reported tailoring the solubility and molecular diffusivity of polymeric sacrificial layer and sequential batch-type vapor annealing to implement high-performance (average saturation mobility: 8.01 cm2 V-1 s-1 ) organic single-crystal thin film transistors with large channel width including multiple aligned single crystals. Additionally, the mechanical properties of the organic single crystals are systematically investigated with extreme strain conditions such as bending radius of 150 µm.

Salvage therapy for acute chemorefractory leukemia by allogeneic stem cell transplantation: the Korean experience.

Little is known about the characteristics that make patients with acute leukemia suitable for undergoing salvage therapy by allogeneic hematopoietic stem cell transplantation (allo-HSCT). Here, we analyzed the clinical outcomes of 223 patients with acute leukemia who underwent allo-HSCT while not in complete remission (CR). The primary end points were overall survival (OS) and CR rate. CR was achieved in 79.8% of patients after allo-HSCT. Acute graft-versus-host disease (GVHD) was significantly associated with CR (P = 0.045). During a median follow-up of 30.1 months, the median OS was 6.1 months. OS was significantly longer in patients with good or standard risk cytogenetic characteristics than in those with poor risk cytogenetic characteristics (P = 0.029, P = 0.030, respectively). Patients who received allo-HSCT from a matched sibling donor had better survival than those with unrelated donors (P = 0.015). Primary chemorefractoriness was not associated with poor survival (P = 0.071). The number of chemotherapies before allo-HSCT was significantly correlated with outcome (P = 0.006). Chronic GVHD was a strong predictor of a longer OS (P = 0.025). In conclusion, survival of patients with primary chemorefractory acute leukemia is not lower when treated upfront with allo-HSCT. Hence, allo-HSCT should be actively considered in such patients. Acute and chronic GVHD is associated with better outcomes patients with acute leukemia who have undergone allo-HSCT and not achieved CR.

The specification and global reprogramming of histone epigenetic marks during gamete formation and early embryo development in C. elegans.

In addition to the DNA contributed by sperm and oocytes, embryos receive parent-specific epigenetic information that can include histone variants, histone post-translational modifications (PTMs), and DNA methylation. However, a global view of how such marks are erased or retained during gamete formation and reprogrammed after fertilization is lacking. To focus on features conveyed by histones, we conducted a large-scale proteomic identification of histone variants and PTMs in sperm and mixed-stage embryo chromatin from C. elegans, a species that lacks conserved DNA methylation pathways. The fate of these histone marks was then tracked using immunostaining. Proteomic analysis found that sperm harbor ∼2.4 fold lower levels of histone PTMs than embryos and revealed differences in classes of PTMs between sperm and embryos. Sperm chromatin repackaging involves the incorporation of the sperm-specific histone H2A variant HTAS-1, a widespread erasure of histone acetylation, and the retention of histone methylation at sites that mark the transcriptional history of chromatin domains during spermatogenesis. After fertilization, we show HTAS-1 and 6 histone PTM marks distinguish sperm and oocyte chromatin in the new embryo and characterize distinct paternal and maternal histone remodeling events during the oocyte-to-embryo transition. These include the exchange of histone H2A that is marked by ubiquitination, retention of HTAS-1, removal of the H2A variant HTZ-1, and differential reprogramming of histone PTMs. This work identifies novel and conserved features of paternal chromatin that are specified during spermatogenesis and processed in the embryo. Furthermore, our results show that different species, even those with diverged DNA packaging and imprinting strategies, use conserved histone modification and removal mechanisms to reprogram epigenetic information.

Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate.

In the Chromosome-Centric Human Proteome Project (C-HPP), false-positive identification by peptide spectrum matches (PSMs) after database searches is a major issue for proteogenomic studies using liquid-chromatography and mass-spectrometry-based large proteomic profiling. Here we developed a simple strategy for protein identification, with a controlled false discovery rate (FDR) at the protein level, using an integrated proteomic pipeline (IPP) that consists of four engrailed steps as follows. First, using three different search engines, SEQUEST, MASCOT, and MS-GF+, individual proteomic searches were performed against the neXtProt database. Second, the search results from the PSMs were combined using statistical evaluation tools including DTASelect and Percolator. Third, the peptide search scores were converted into E-scores normalized using an in-house program. Last, ProteinInferencer was used to filter the proteins containing two or more peptides with a controlled FDR of 1.0% at the protein level. Finally, we compared the performance of the IPP to a conventional proteomic pipeline (CPP) for protein identification using a controlled FDR of <1% at the protein level. Using the IPP, a total of 5756 proteins (vs 4453 using the CPP) including 477 alternative splicing variants (vs 182 using the CPP) were identified from human hippocampal tissue. In addition, a total of 10 missing proteins (vs 7 using the CPP) were identified with two or more unique peptides, and their tryptic peptides were validated using MS/MS spectral pattern from a repository database or their corresponding synthetic peptides. This study shows that the IPP effectively improved the identification of proteins, including alternative splicing variants and missing proteins, in human hippocampal tissues for the C-HPP. All RAW files used in this study were deposited in ProteomeXchange (PXD000395).

A comprehensive and scalable database search system for metaproteomics.

BACKGROUND: Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. RESULTS: Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. CONCLUSIONS: The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Digestion and depletion of abundant proteins improves proteomic coverage.

Two major challenges in proteomics are the large number of proteins and their broad dynamic range in the cell. We exploited the abundance-dependent Michaelis-Menten kinetics of trypsin digestion to selectively digest and deplete abundant proteins with a method we call DigDeAPr. We validated the depletion mechanism with known yeast protein abundances, and we observed greater than threefold improvement in low-abundance human-protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases and proteomic pipelines.

Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases.

The goal of the Chromosome-Centric Human Proteome Project (C-HPP) is to fully provide proteomic information from each human chromosome, including novel proteoforms, such as novel protein-coding variants expressed from noncoding genomic regions, alternative splicing variants (ASVs), and single amino acid variants (SAAVs). In the 144 LC/MS/MS raw files from human hippocampal tissues of control, epilepsy, and Alzheimer's disease, we identified the novel proteoforms with a workflow including integrated proteomic pipeline using three different search engines, MASCOT, SEQUEST, and MS-GF+. With a <1% false discovery rate (FDR) at the protein level, the 11 detected peptides mapped to four translated long noncoding RNA variants against the customized databases of GENCODE lncRNA, which also mapped to coding-proteins at different chromosomal sites. We also identified four novel ASVs against the customized databases of GENCODE transcript. The target peptides from the variants were validated by tandem MS fragmentation pattern from their corresponding synthetic peptides. Additionally, a total of 128 SAAVs paired with their wild-type peptides were identified with FDR <1% at the peptide level using a customized database from neXtProt including nonsynonymous single nucleotide polymorphism (nsSNP) information. Among these results, several novel variants related in neuro-degenerative disease were identified using the workflow that could be applicable to C-HPP studies. All raw files used in this study were deposited in ProteomeXchange (PXD000395).