Search

Lung cancer is a leading cause of death globally, with lung adenocarcinoma being the most common subtype. Despite advancements in targeted therapy, drug resistance remains a major challenge. This study investigated the impact of Bacillus coagulans on drug resistance in lung adenocarcinoma cells. The cells were pretreated with B. coagulans culture filtrate (BCCF), and functional assays were performed, including cell proliferation, cell cycle, apoptosis, and immunofluorescence staining. Results showed that BCCF induced cell cycle arrest at the S phase, reducing cell proliferation and suppressing drug resistance marker P-glycoprotein expression in BCCF-treated resistant cells rather than BCCF-treated control cells. Moreover, drug-resistant cells exhibited the ability for epithelial-mesenchymal transition, which could contribute to their necrosis through the iron-mediated cell death pathway upon BCCF treatment. Proteomic analysis identified downregulation of DNA mismatch repair protein PMS2 after BCCF treatment. These findings suggest that B. coagulans may modulate the DNA repair pathway, influencing drug resistance in lung adenocarcinoma cells. In conclusion, this study highlights the potential impact of B. coagulans on drug-resistant lung adenocarcinoma cells. Further investigation and understanding of the regulatory mechanisms by which B. coagulans modulates drug resistance in lung adenocarcinoma can aid in the development of more effective treatment strategies to improve the prognosis of lung cancer patients., (© 2024 International Union of Biochemistry and Molecular Biology, Inc.)

Stellar chemical compositions can be altered by ingestion of planetary material 1,2 and/or planet formation, which removes refractory material from the protostellar disk 3,4 . These 'planet signatures' appear as correlations between elemental abundance differences and the dust condensation temperature 3,5,6 . Detecting these planet signatures, however, is challenging owing to unknown occurrence rates, small amplitudes and heterogeneous star samples with large differences in stellar ages 7,8 . Therefore, stars born together (that is, co-natal) with identical compositions can facilitate the detection of planet signatures. Although previous spectroscopic studies have been limited to a small number of binary stars 9-13 , the Gaia satellite 14 provides opportunities for detecting stellar chemical signatures of planets among co-moving pairs of stars confirmed to be co-natal 15,16 . Here we report high-precision chemical abundances for a homogeneous sample of ninety-one co-natal pairs of stars with a well defined selection function and identify at least seven instances of planetary ingestion, corresponding to an occurrence rate of eight per cent. An independent Bayesian indicator is deployed, which can effectively disentangle the planet signatures from other factors, such as random abundance variation and atomic diffusion 17 . Our study provides evidence of planet signatures and facilitates a deeper understanding of the star-planet-chemistry connection by providing observational constraints on the mechanisms of planet engulfment, formation and evolution., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Background: Creativity is an important ability for problem-solving in both personal life and academic learning. Few creativity studies have investigated the development of children's creativity in disadvantaged rural areas or compared the rural-urban differences through digital game-based creativity learning. Understanding such differences can help provide resources for promoting learning equality in creativity., Aims: This study aimed to compare the rural-urban difference in elementary school children's creativity performance and their learning effect through digital game-based creativity learning., Sample: Participants were 261 3rd and 4th graders and 194 5th and 6th graders from 6 elementary schools., Method: Two digital game-based creativity learning systems were employed to conduct a five-class experimental instruction. A creativity test and a questionnaire were also used., Results and Conclusions: The results indicate that the urban middle graders, but not the upper graders, outperformed their rural counterparts in the creativity test before game-based learning. Nevertheless, all children got a higher score on the creativity test after the game-based learning, suggesting the employed creativity learning systems could be vehicles for improving elementary school children's creativity. However, the rural children gained less from the learning than the urban children, which may be due to weaker competencies in self-regulated learning. Further studies can employ an inventory to verify this and also consider providing more scaffolding of self-regulated learning to more disadvantaged students during digital game-based creativity learning. Additionally, the results of this study reflect the importance of self-determination and rewards in learning motivation. Appropriate rewards may encourage persistence in taking on challenges., (© 2023 British Psychological Society.)

This study evaluated the effects of sodium alginate, pectin and chitosan addition (0.5-1.5%) on the physicochemical properties including pH, water activity, moisture content, color values, hardness, diameter, thickness, spread ratio, antioxidant activities and sensory scores of biscuits in air frying processing. In addition, the formation of acrylamide and hydroxymethylfurfural (HMF) were discussed. Physicochemical properties of biscuits including water content, water activity, hardness, appearance, shape, color, flavor, texture, overall acceptability, and DPPH radical scavenging activity of biscuits were not influenced significantly by the addition (0.5-1.0%) of three food hydrocolloids. The data showed that the biscuits with hydrocolloids addition had lower acrylamide contents than that of the control biscuit without hydrocolloids addition, and the reducing power of biscuits increased after adding the hydrocolloids. The highest mitigation of acrylamide formation was obtained by the chitosan addition formulation. The formation of acrylamide showed a negative correlation with the content of sodium alginate and chitosan addition, and they were effective ingredients in terms of mitigating the formation of acrylamide in biscuit formulation.

The objectives of this study were to evaluate the effect of 0.5% chitosan incorporation on acrylamide development in a food model solution containing 0.5% fructose and asparagine after heating for 30 min at 180 °C. All the solutions were investigated for the following characteristics: acrylamide, asparagine, reducing sugar content, color, kinematic viscosity, Maillard reaction products (MRPs), and pH every 10 min. After heating for 10 min, the viscosity of chitosan-containing solutions reduced significantly. The investigational data confirmed that chitosan may have decomposed into lower molecular structures, as demonstrated by the reduced viscosity of the solution at pH < 6 and a decrease in the acrylamide content during 30 min of heating in a fructose−asparagine system. This study also confirms that the formation of ultraviolet-absorbing intermediates and browning intensity of MRPs containing acrylamide prepared by fructose−asparagine was more than those of MRPs prepared by glucose−asparagine solution system. MRPs containing acrylamide resulted from the reaction of asparagine with fructose (ketose) rather than glucose (aldose). Acrylamide formation could be significantly mitigated in the fructose−asparagine−chitosan model system as compared to the fructose−asparagine model system for possible beverage and food application.

Introduction: In this study, we described paediatric sports injuries seen in the paediatric emergency department of a large, tertiary paediatric hospital in Singapore and evaluated risk factors for severe sports injuries., Methods: This is a retrospective review of a paediatric trauma surveillance registry from February 2012 to October 2017, including patient demographics, type of sports, circumstances, type of injuries, and clinical management in the hospital. Patients 5 to 17 years old with a sports-related injury were included. We performed logistic regression to identify predictors of severe sports injuries (defined by Injury Severity Score of ≥9), injuries requiring hospitalisation, trauma team activation, resuscitation, or those that resulted in death., Results: Among 10,951 patients analysed, the most common injuries sustained were fractures (4,819, 44.0%), sprains and contusions (3,334, 30.4%). For patients with severe injuries, the median length of hospital stay was 2 days (IQR 1-3 days), and time away from sports was 162 days (IQR 104-182 days). Predictors for severe injuries include transportation by emergency medical service (aOR 6.346, 95% CI 5.147-7.823), involvement in rugby (aOR 2.067, 95% CI 1.446-2.957), neurological injuries (aOR 4.585, 95% CI 2.393-4.365), dislocations (aOR 2.779, 95% CI 1.744-4.427), fractures (aOR 1.438, 95% CI 1.039-1.990), injuries to the head and neck (aOR 2.274, 95% CI 1.184-4.365), and injuries to the abdomen and pelvis (aOR 5.273, 95% CI 3.225-8.623)., Conclusion: Predictors for severe sports injuries identified may aid in risk stratification and resource allocation.

Neoantigens arise from mutations in cancer cells and are important targets of T cell-mediated anti-tumor immunity. Here, we report the first open-label, phase Ib clinical trial of a personalized neoantigen-based vaccine, NEO-PV-01, in combination with PD-1 blockade in patients with advanced melanoma, non-small cell lung cancer, or bladder cancer. This analysis of 82 patients demonstrated that the regimen was safe, with no treatment-related serious adverse events observed. De novo neoantigen-specific CD4 + and CD8 + T cell responses were observed post-vaccination in all of the patients. The vaccine-induced T cells had a cytotoxic phenotype and were capable of trafficking to the tumor and mediating cell killing. In addition, epitope spread to neoantigens not included in the vaccine was detected post-vaccination. These data support the safety and immunogenicity of this regimen in patients with advanced solid tumors (Clinicaltrials.gov: NCT02897765)., Competing Interests: Declaration of Interests P.A.O.: research funding paid to the institution—Bristol-Myers Squibb, Merck, AstraZeneca, Celldex, CytomX, GlaxoSmithKline, ARMO Biosciences, Neon Therapeutics; consultant—Array, Bristol-Myers Squibb, Merck, Genentech, Pfizer, Novartis, Neon Therapeutics, CytomX, Celldex. S.H.-L.: consultant—Amgen, Bristol-Myers Squibb, Genmab, Xencor; research support—Bristol-Myers Squibb, Merck, and Vaccinex. B.C.: member of the speakers’ bureaus for Regeneron and Sanofi. R.G.: advisory board member—Achilles; consultant—Horizon Pharma (spouse), GenePlus. A.N.: research funding from NCI, EMD Serono, MedImmune, Healios Oncology Nutrition, Atterocor, Amplimmune, ARMO BioSciences, Eli Lilly, Karyopharm Therapeutics, Incyte, Novartis, Regeneron, Merck, Bristol-Myers Squibb, Pfizer, CytomX Therapeutics, Neon Therapeutics, Calithera Biosciences, TopAlliance Biosciences, Kymab, PsiOxus, and Immune Deficiency Foundation (spouse); advisory board member—CytomX Therapeutics, Novartis, Kymab, and Genome; travel and accommodation expense—ARMO BioSciences. N.B.: scientific advisory board member—Checkpoint Sciences, Curevac, Primevax, Novartis, Avidea, BI, Rome Therapeutics, Neon Therapeutics, Roche, and Genentech. Extramural member of the Parker Institute for Cancer Immunotherapy K.M.: advisory boards or consultant—Nektar, ImaginAb, Neoleukin, and Akrevia; DSMB—IOvance. M.M.A.: research grants—Genentech, Bristol-Myers Squibb, AstraZeneca, Lilly; consultant—Genentech, Bristol-Myers Squibb, AstraZeneca, Merck, Maverick, Blueprint Medicine, Syndax, Ariad, Nektar, Gritstone, and Neon Therapeutics M.D.H.: research funding—Bristol-Myers Squibb; consultant—Merck, Bristol-Myers Squibb, AstraZeneca, Genentech/Roche, Nektar, Syndax, Mirati, Blueprint, Immunai, and Shattuck Labs; travel support/honoraria—AstraZeneca, Eli Lilly, Merck, and Bristol-Myers Squibb; and a patent has been filed by MSK related to the use of tumor mutation burden to predict the response to immunotherapy (PCT/US2015/062208), which has received licensing fees from PGDx. J.J.L.: honoraria/consultant—Pfizer, C4 Therapeutics, Nuvalent, and Genentech; institutional research funding—Neon, Hengrui Therapeutics, Turning Point Therapeutics, and Novartis; travel fees—Pfizer; CME funding—OncLive. T.F.: research funding—Janssen; research funding to the institute—Seattle Genetics, Incyte, Bristol-Myers Squibb, Neon Therapeutics, and Roche/Genentech. R.B.G.: board of directors—Alkermes plc and Infinity Pharmaceuticals; scientific advisory board—Leap Therapeutics; stockholder and employee—Neon Therapeutics/BioNTech US. Stockholder and either current or past employees of Neon Therapeutics/BioNTech US: M.E.B., K.N.B., T.E.S., V.K., S.J.T., R.B., R.R.C., B.T., J.S., A.P., D.H., D.B., Y.S.T., J.Z.D., Y.W., Y.H., Z.H., A.W., L.D.C., M.A.M., K.M., J.G., Z.S.K., M.S.R., M.D., E.F., and L.S., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Morbidity and mortality of coronavirus disease 2019 (COVID-19) are due in large part to severe cytokine storm and hypercoagulable state brought on by dysregulated host-inflammatory immune response, ultimately leading to multi-organ failure. Exacerbated oxidative stress caused by increased levels of interleukin (IL)-6 and tumor necrosis factor α (TNF-α) along with decreased levels of interferon α and interferon β (IFN-α, IFN-β) are mainly believed to drive the disease process. Based on the evidence attesting to the ability of glutathione (GSH) to inhibit viral replication and decrease levels of IL-6 in human immunodeficiency virus (HIV) and tuberculosis (TB) patients, as well as beneficial effects of GSH on other pulmonary diseases processes, we believe the use of liposomal GSH could be beneficial in COVID-19 patients. This review discusses the epidemiology, transmission, and clinical presentation of COVID-19 with a focus on its pathogenesis and the possible use of liposomal GSH as an adjunctive treatment to the current treatment modalities in COVID-19 patients.

Dendritic cells are the principal antigen-presenting cells (APCs) in the host defense mechanism. An altered dendritic cell response increases the risk of susceptibility of infections, such as Mycobacterium tuberculosis ( M. tb ), and the survival of the human immunodeficiency virus (HIV). The altered response of dendritic cells leads to decreased activity of T-helper-1 (Th1), Th2, Regulatory T cells (Tregs), and Th17 cells in tuberculosis (TB) infections due to a diminishment of cytokine release from these APCs, while HIV infection leads to DC maturation, allowing DCs to migrate to lymph nodes and the sub-mucosa where they then transfer HIV to CD4 T cells, although there is controversy around this topic. Increases in the levels of the antioxidant glutathione (GSH) plays a critical role in maintaining dendritic cell redox homeostasis, leading to an adequate immune response with sufficient cytokine release and a subsequent robust immune response. Thus, an understanding of the intricate pathways involved in the dendritic cell response are needed to prevent co-infections and co-morbidities in individuals with TB and HIV.

Diastolic dysfunction is a prominent feature of cardiac aging in both mice and humans. We show here that 8-week treatment of old mice with the mitochondrial targeted peptide SS-31 (elamipretide) can substantially reverse this deficit. SS-31 normalized the increase in proton leak and reduced mitochondrial ROS in cardiomyocytes from old mice, accompanied by reduced protein oxidation and a shift towards a more reduced protein thiol redox state in old hearts. Improved diastolic function was concordant with increased phosphorylation of cMyBP-C Ser282 but was independent of titin isoform shift. Late-life viral expression of mitochondrial-targeted catalase (mCAT) produced similar functional benefits in old mice and SS-31 did not improve cardiac function of old mCAT mice, implicating normalizing mitochondrial oxidative stress as an overlapping mechanism. These results demonstrate that pre-existing cardiac aging phenotypes can be reversed by targeting mitochondrial dysfunction and implicate mitochondrial energetics and redox signaling as therapeutic targets for cardiac aging., Competing Interests: YC, HZ, MS, JW, YT, NB, LP, EQ, NN, MC, TZ, MG, GM, LW, YY, DD, HG, HS, WQ, DM, MM, PR No competing interests declared, (© 2020, Chiao et al.)

Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here, we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly parallel quantification of the nuclear proteome in human cells. We apply this approach to quantify the response to acute degradation of BET bromodomains, revealing unexpected chromatin regulatory dynamics. The method is simple and enables system-level study of previously inaccessible chromatin and genome regulators., Competing Interests: Declaration of Interests The MacCoss Lab at the University of Washington has a sponsored research agreement with Thermo Fisher Scientific, the manufacturer of the instrumentation used in this research. Additionally, M.J.M. is a paid consultant for Thermo Fisher Scientific. A patent application has been filed on the methods described., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Increasing evidence indicates CD4 + T cells can recognize cancer-specific antigens and control tumor growth. However, it remains difficult to predict the antigens that will be presented by human leukocyte antigen class II molecules (HLA-II), hindering efforts to optimally target them therapeutically. Obstacles include inaccurate peptide-binding prediction and unsolved complexities of the HLA-II pathway. To address these challenges, we developed an improved technology for discovering HLA-II binding motifs and conducted a comprehensive analysis of tumor ligandomes to learn processing rules relevant in the tumor microenvironment. We profiled >40 HLA-II alleles and showed that binding motifs were highly sensitive to HLA-DM, a peptide-loading chaperone. We also revealed that intratumoral HLA-II presentation was dominated by professional antigen-presenting cells (APCs) rather than cancer cells. Integrating these observations, we developed algorithms that accurately predicted APC ligandomes, including peptides from phagocytosed cancer cells. These tools and biological insights will enable improved HLA-II-directed cancer therapies., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment. These coordinates calibrate protein databases or spectrum libraries to a specific mass spectrometer and chromatography setup, facilitating DIA-only pipelines and the reuse of global resource libraries. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect 20-25% more peptides from DIA experiments than with data dependent acquisition-based spectrum libraries alone.

Overexpression of thioredoxin-interacting protein (TXNIP) is associated with reduced insulin sensitivity and β-cell apoptosis. We have previously shown that W2476 inhibited high glucose-induced TXNIP expression at both mRNA and protein levels in INS-1E cells. In this study, we describe structural modification and optimization of W2476 leading to three more active derivatives, 8d, 8g, and 9h, capable of suppressing TXNIP expression in BG73 and INS-1E cells, increasing insulin production, and reducing high glucose-induced apoptosis in INS-1E cells., (© 2018 John Wiley & Sons A/S.)

Introduction: Immunophenotyping by flow cytometry is routinely employed in distinguishing between chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). Inclusion of CD200 has been reported to contribute to more reliable differentiation between CLL and MCL. We investigated the value of CD200 in assessment of atypical CLL cases., Methods: CD200 expression on mature B cell neoplasms was studied by eight-color flow cytometry in combination with a conventional panel of flow cytometry markers. The study included 70 control samples, 63 samples with CLL or atypical CLL phenotype, 6 MCL samples, and 40 samples of other mature B cell neoplasms., Results: All CLL samples were positive for CD200, whereas MCL samples were dim or negative for CD200. Of the CLL samples, 7 were atypical by conventional flow cytometry, with Matutes scores ≤3. These cases were tested for evidence of a t(11;14) translocation, characteristic of MCL, and all were negative, consistent with their classification as atypical CLL. All these atypical CLL samples were strongly positive for CD200., Conclusion: CD200 proved to be a useful marker for differentiation between CLL and MCL by flow cytometry. In particular, CD200 was useful in distinguishing CLL samples with atypical immunophenotypes from MCL., (© 2018 John Wiley & Sons Ltd.)

Assigning links between microbial activity and biogeochemical cycles in the ocean is a primary objective for ecologists and oceanographers. Bacteria represent a small ecosystem component by mass, but act as the nexus for both nutrient transformation and organic matter recycling. There are limited methods to explore the full suite of active bacterial proteins largely responsible for degradation. Mass spectrometry (MS)-based proteomics now has the potential to document bacterial physiology within these complex systems. Global proteome profiling using MS, known as data dependent acquisition (DDA), is limited by the stochastic nature of ion selection, decreasing the detection of low abundance peptides. The suitability of MS-based proteomics methods in revealing bacterial signatures outnumbered by phytoplankton proteins was explored using a dilution series of pure bacteria (Ruegeria pomeroyi) and diatoms (Thalassiosira pseudonana). Two common acquisition strategies were utilized: DDA and selected reaction monitoring (SRM). SRM improved detection of bacterial peptides at low bacterial cellular abundance that were undetectable with DDA from a wide range of physiological processes (e.g. amino acid synthesis, lipid metabolism, and transport). We demonstrate the benefits and drawbacks of two different proteomic approaches for investigating species-specific physiological processes across relative abundances of bacteria that vary by orders of magnitude.

A challenge in developing personalized cancer immunotherapies is the prediction of putative cancer-specific antigens. Currently, predictive algorithms are used to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid in the selection of putative epitope targets. One drawback of current epitope prediction algorithms is that they are trained on datasets containing biochemical HLA-peptide binding data that may not completely capture the rules associated with endogenous processing and presentation. The field of MS has made great improvements in instrumentation speed and sensitivity, chromatographic resolution, and proteogenomic database search strategies to facilitate the identification of HLA-ligands from a variety of cell types and tumor tissues. As such, these advances have enabled MS profiling of HLA-binding peptides to be a tractable, orthogonal approach to lower throughput biochemical assays for generating comprehensive datasets to train epitope prediction algorithms. In this review, we will highlight the progress made in the field of HLA-ligand profiling enabled by MS and its impact on current and future epitope prediction strategies., (© 2018 Neon Therapeutics. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The avian nucleus laminaris (NL) is a brainstem nucleus necessary for binaural processing, analogous in structure and function to the mammalian medial superior olive. In chickens (Gallus gallus), NL is a well-studied model system for activity-dependent neural plasticity. Its neurons have bipolar extension of dendrites, which receive segregated inputs from two ears and display rapid and compartment-specific reorganization in response to unilateral changes in auditory input. More recently, fragile X mental retardation protein (FMRP), an RNA-binding protein that regulates local protein translation, has been shown to be enriched in NL dendrites, suggesting its potential role in the structural dynamics of these dendrites. To explore the molecular role of FMRP in this nucleus, we performed proteomic analysis of NL, using micro laser capture and liquid chromatography tandem mass spectrometry. We identified 657 proteins, greatly represented in pathways involved in mitochondria, translation and metabolism, consistent with high levels of activity of NL neurons. Of these, 94 are potential FMRP targets, by comparative analysis with previously proposed FMRP targets in mammals. These proteins are enriched in pathways involved in cellular growth, cellular trafficking and transmembrane transport. Immunocytochemistry verified the dendritic localization of several proteins in NL. Furthermore, we confirmed the direct interaction of FMRP with one candidate, RhoC, by in vitro RNA binding assays. In summary, we provide a database of highly expressed proteins in NL and in particular a list of potential FMRP targets, with the goal of facilitating molecular characterization of FMRP signaling in future studies., (© 2017 Wiley Periodicals, Inc.)

Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the main method for high-throughput identification and quantification of peptides and inferred proteins. Within this field, data-independent acquisition (DIA) combined with peptide-centric scoring, as exemplified by the technique SWATH-MS, has emerged as a scalable method to achieve deep and consistent proteome coverage across large-scale data sets. We demonstrate that statistical concepts developed for discovery proteomics based on spectrum-centric scoring can be adapted to large-scale DIA experiments that have been analyzed with peptide-centric scoring strategies, and we provide guidance on their application. We show that optimal tradeoffs between sensitivity and specificity require careful considerations of the relationship between proteins in the samples and proteins represented in the spectral library. We propose the application of a global analyte constraint to prevent the accumulation of false positives across large-scale data sets. Furthermore, to increase the quality and reproducibility of published proteomic results, well-established confidence criteria should be reported for the detected peptide queries, peptides and inferred proteins.

Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detection capability of PECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECAN to build a plasma proteome library from DIA data and to query known sequence variants.

In mass spectrometry-based bottom-up proteomics, data-independent acquisition is an emerging technique because of its comprehensive and unbiased sampling of precursor ions. However, current data-independent acquisition methods use wide precursor isolation windows, resulting in cofragmentation and complex mixture spectra. Thus, conventional database searching tools that identify peptides by interpreting individual tandem MS spectra are inherently limited in analyzing data-independent acquisition data. Here we discuss an alternative approach, peptide-centric analysis, which tests directly for the presence and absence of query peptides. We discuss how peptide-centric analysis resolves some limitations of traditional spectrum-centric analysis, and we outline the unique characteristics of peptide-centric analysis in general., (© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.)

In mass spectrometry-based proteomics, data-independent acquisition (DIA) strategies can acquire a single data set useful for both identification and quantification of detectable peptides in a complex mixture. However, DIA data are noisy owing to a typical five- to tenfold reduction in precursor selectivity compared to data obtained with data-dependent acquisition or selected reaction monitoring. We demonstrate a multiplexing strategy, MSX, for DIA analysis that increases precursor selectivity fivefold.

Deciphering the network of signaling pathways in cancer via protein-protein interactions (PPIs) at the cellular level is a promising approach but remains incomplete. We used an in situ proximity ligation assay to identify and quantify 67 endogenous PPIs among 21 interlinked pathways in two hepatocellular carcinoma (HCC) cells, Huh7 (minimally migratory cells) and Mahlavu (highly migratory cells). We then applied a differential network biology analysis and determined that the novel interaction, CRKL-FLT1, has a high centrality ranking, and the expression of this interaction is strongly correlated with the migratory ability of HCC and other cancer cell lines. Knockdown of CRKL and FLT1 in HCC cells leads to a decrease in cell migration via ERK signaling and the epithelial-mesenchymal transition process. Our immunohistochemical analysis shows high expression levels of the CRKL and CRKL-FLT1 pair that strongly correlate with reduced disease-free and overall survival in HCC patient samples, and a multivariate analysis further established CRKL and the CRKL-FLT1 as novel prognosis markers. This study demonstrated that functional exploration of a disease network with interlinked pathways via PPIs can be used to discover novel biomarkers.

Surface acoustic wave nebulization (SAWN) is a novel method to transfer nonvolatile analytes directly from the aqueous phase to the gas phase for mass spectrometric analysis. The lower ion energetics of SAWN and its planar nature make it appealing for analytically challenging lipid samples. This challenge is a result of their amphipathic nature, labile nature, and tendency to form aggregates, which readily precipitate clogging capillaries used for electrospray ionization (ESI). Here, we report the use of SAWN to characterize the complex glycolipid, lipid A, which serves as the membrane anchor component of lipopolysaccharide (LPS) and has a pronounced tendency to clog nano-ESI capillaries. We also show that unlike ESI SAWN is capable of ionizing labile phospholipids without fragmentation. Lastly, we compare the ease of use of SAWN to the more conventional infusion-based ESI methods and demonstrate the ability to generate higher order tandem mass spectral data of lipid A for automated structure assignment using our previously reported hierarchical tandem mass spectrometry (HiTMS) algorithm. The ease of generating SAWN-MS(n) data combined with HiTMS interpretation offers the potential for high throughput lipid A structure analysis.

In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set.