Oxygen intrusions sustain aerobic nitrite oxidation in anoxic marine zones

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Oxygen intrusions sustain aerobic nitrite oxidation in anoxic marine zones

Anoxic marine zones (AMZs) are host to anaerobic metabolisms that drive losses of bioavailable nitrogen from the ocean. The discovery of active nitrite-oxidising bacteria (NOB), long thought to be obligately aerobic, in AMZs has altered our perception of how nitrogen cycles in these oxygen-deficient waters. Yet, why NOB succeed in AMZs remains unclear. Here, we show that obligately aerobic NOB can thrive alongside aerobic microheterotrophs in AMZs via infrequent intrusions of oxygen. Ecological theory, biogeochemical modelling and metagenome-based maximum growth rate estimates suggest that NOB are opportunists that take advantage of periodic oxygen intrusions to rapidly accumulate biomass. Rather than harsh, AMZs prone to oxygen intrusions appear optimal for NOB, whose abundance and activity peaks in a goldilocks zone of periodic oxygen and high nitrite supply. Our results recast the intermediate disturbance hypothesis to AMZs and highlight how the nitrogen cycle relies on dynamic coexistence of aerobic and anaerobic metabolisms.
Buchanan, P. J., Sun, X., Weissman, J., Zakem, E.
February 23, 2023
http://biorxiv.org/cgi/content/short/2023.02.22.529547v1?rss=1

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Large omics datasets are nowadays routinely generated to provide insights into cellular processes. Nevertheless, making sense of omics data and determining intracellular metabolic states remains challenging. Kinetic models of metabolism are crucial for integrating and consolidating omics data because they explicitly link metabolite concentrations, metabolic fluxes, and enzyme levels. However, the difficulties in determining kinetic parameters that govern cellular physiology prevent the broader adoption of these models by the research community. We present RENAISSANCE (REconstruction of dyNAmIc models through Stratified Sampling using Artificial Neural networks and Concepts of Evolution strategies), a generative machine learning framework for efficiently parameterizing large-scale kinetic models with dynamic properties matching experimental observations. We showcase RENAISSANCE’s capabilities through three applications: generation of kinetic models of E. coli metabolism, characterization of intracellular metabolic states, and assimilation and reconciliation of experimental kinetic data. We provide the open-access code to facilitate experimentalists and modelers applying this framework to diverse metabolic systems and integrating a broad range of available data. We anticipate that the proposed framework will be invaluable for researchers who seek to analyze metabolic variations involving changes in metabolite and enzyme levels and enzyme activity in health and biotechnological studies.
Choudhury, S., Narayanan, B., Moret, M., Hatzimanikatis, V., Miskovic, L.
February 23, 2023
http://biorxiv.org/cgi/content/short/2023.02.21.529387v1?rss=1

Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

The medium composition was crucial for achieving the best performance of synthetic construction. What and how medium components determined the production of the synthetic construction remained poorly investigated. To address the questions, a comparative survey with two genetically engineered Escherichia coli strains was performed. As a case study, the strains carried the synthetic pathways for producing the aromatic compounds of 4APhe or Tyr, which were common in the upstream but differentiated in the downstream metabolism. Bacterial growth and compound production were examined in hundreds of medium combinations that comprised 48 pure chemicals. The resultant data sets linking the medium composition to bacterial growth and production were subjected to machine learning for improved production. Intriguingly, the primary medium components determining the production of 4PheA and Tyr were differentiated, which were the initial resource (glucose) of the synthetic pathway and the inducer (IPTG) of the synthetic construction, respectively. Fine-tuning of the primary component significantly increased the yields of 4APhe and Tyr, indicating that a single component could be crucial for the performance of synthetic construction. Transcriptome analysis observed the local and global changes in gene expression for improved production of 4APhe and Tyr, respectively, revealing divergent metabolic strategies for producing the foreign and native metabolites. The study demonstrated that ML-assisted medium optimization could provide a novel point of view on how to make the synthetic construction meet the original design.
Aida, H., Uchida, K., Nagai, M., Hashizume, T., Masuo, S., Takaya, N., YING, B.-W.
February 23, 2023
http://biorxiv.org/cgi/content/short/2023.02.20.529197v1?rss=1

[ASAP] UHPLC-MS/MS-Based Identity Confirmation of Amino Acids Involved in Response to and Side Effects from Antiseizure Medications

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

latest articles published in Journal of Proteome Research

[ASAP] UHPLC-MS/MS-Based Identity Confirmation of Amino Acids Involved in Response to and Side Effects from Antiseizure Medications

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Journal of Proteome Research
DOI: 10.1021/acs.jproteome.2c00835

Mo Awchi, Pablo Sinues, Alexandre N. Datta, Diego García-Gómez, and Kapil Dev Singh
February 22, 2023
http://dx.doi.org/10.1021/acs.jproteome.2c00835

[ASAP] PyC2MC: An Open-Source Software Solution for Visualization and Treatment of High-Resolution Mass Spectrometry Data

Journal of The American Society for Mass Spectrometry

Journal of the American Society for Mass Spectrometry: Latest Articles (ACS Publications)

latest articles published in Journal of the American Society for Mass Spectrometry

[ASAP] PyC2MC: An Open-Source Software Solution for Visualization and Treatment of High-Resolution Mass Spectrometry Data

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Journal of the American Society for Mass Spectrometry
DOI: 10.1021/jasms.2c00323

Maxime Sueur13, Julien F. Maillard13, Oscar Lacroix-Andrivet134, Christopher P. Rüger356, Pierre Giusti123, Hélène Lavanant1, and Carlos Afonso13
February 22, 2023
http://dx.doi.org/10.1021/jasms.2c00323

Integrating ultra‐high‐performance liquid chromatography tandem mass spectrometry and imaged capillary isoelectric focusing for in‐depth characterization of complex fusion proteins

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Integrating ultra‐high‐performance liquid chromatography tandem mass spectrometry and imaged capillary isoelectric focusing for in‐depth characterization of complex fusion proteins

Rationale

Fc-fusion proteins represent a successful class of biopharmaceutical products, which combine the tailored pharmacological properties of biological ligands with the multiple functions of the fragment crystallizable domain of immunoglobulins. There is great diversity in terms of possible biological ligands creating highly diverse structures, therefore the analytical characterization of fusion proteins is far more complex than that of monoclonal antibodies and requires the use and development of additional product-specific methods over conventional generic/platform methods.

Methods

Employing etanercept analogues as studied fusion proteins, the Orbitrap mass analyzer with ultra-high performance liquid chromatography (UHPLC–MS) and imaged capillary isoelectric focusing (icIEF) were utilized for the in-depth fusion protein characterization.

Results

The amino acid sequence coverage, peptide mapping, and post-translational modifications of etanercept analogues were analyzed by UHPLC–MS. The post-translational modification results were complemented by imaged capillary isoelectric focusing to produce quality research on etanercept analogues.

Conclusions

The developed workflow integrating UHPLC–MS and icIEF provided an innovative strategy for characterizing complex fusion proteins in the process of quality control and manufacturing.

Wenhong Fan,
Xiang Li,
Zhen Long,
Dening Pei,
Xinchang Shi,
Guangyu Wang,
Ying Guo,
Tao Bo,
Yong Zhou,
Tong Chen
February 22, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9484?af=R

Structural confirmation of synthetic cannabinoids in seized electronic cigarette oil: A combined mass spectrometric and computational study

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Structural confirmation of synthetic cannabinoids in seized electronic cigarette oil: A combined mass spectrometric and computational study

Rationale

Synthetic cannabinoids are some of the most used and abused new psychoactive substances, because they can produce a stronger intense pleasure than natural cannabis. Most of the new synthetic cannabinoids are structurally similar to existing synthetic cannabinoids and can be obtained by modifying partial structures of the latter without changing their effects. Therefore, the derivatization rules and common fragmentation patterns of synthetic cannabinoids could be used for rapid screening and structural identification of them.

Methods

The derivatization rules of synthetic cannabinoids are summarized, and the common fragmentation pattern of synthetic cannabinoids including three typical cleavage pathways was explored and extended in this work based on combined mass spectrometry (MS) and density functional theory studies. Five synthetic cannabinoids in electronic cigarette oil from a drug case were separated and characterized using gas chromatography with MS and liquid chromatography coupled to high-resolution quadrupole Orbitrap MS.

Results

The structures of five synthetic cannabinoids in seized electronic cigarette oil were deduced from electron impact ion source (EI) MS and high-resolution electrospray ionization (ESI) MSn
data, along with the derivatization rules and common fragmentation pattern of synthetic cannabinoids. The proposed structures of these synthetic cannabinoids were further verified via reference substances. Computational study showed that selective cleavage of these compounds was mainly controlled by spin population in EI-MS, but a tunneling effect arose from proton transfer in ESI-MSn
detection, which has been rarely reported in previous works.

Conclusions

Our results showed that EI-MS was suitable for identifying synthetic cannabinoids with aromatic ketone structure, which could also be extended to adamantane linked group. Nevertheless, synthetic cannabinoids with carbamoyl linked group were better characterized by high-resolution ESI-MSn
compared to EI-MS. This study demonstrated a method with promising potential for rapid and reliable screening of synthetic cannabinoids in mixtures with enhanced detection throughput and operation simplicity.

Yu Xu,
Jiawei Xu,
Xianxin Chen,
Yi Lei Fan,
Hao Wu
February 22, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9485?af=R

Development of nanomaterial enabling highly sensitive surface‐assisted laser desorption/ionization mass spectrometry peptide analysis

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Development of nanomaterial enabling highly sensitive surface‐assisted laser desorption/ionization mass spectrometry peptide analysis

Rationale

Surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) is an approach derived from matrix-assisted laser desorption/ionization (MALDI)-MS which overcomes the drawbacks associated with the use of organic matrices required to co-crystallize with the analytes. Indeed, nanomaterials commonly used in SALDI-MS as inert surfaces to promote desorption/ionization (D/I) ensure straightforward direct deposition of samples while providing mass spectra with ions only related to the compound of interest. The objective of this study was to develop a novel SALDI-MS approach based on steel plates that are surfaces very rapidly and easily tuned to perform the most efficient peptide detection as possible. To compare the SALDI efficacy of such metal substrates, D/I efficiency and deposit homogeneity were evaluated according to steel plate fabrication processes.

Methods

The studied surfaces were nanostructured steel plates that were chemically modified by perfluorosilane and textured according to different frequencies and laser writing powers. The capacity of each tested 100 surfaces was demonstrated by comparative analyses of a mixture of standard peptides (m/z 600–3000) performed with a MALDI-TOF instrument enabling MALDI, SALDI and imaging experiments.

Results

A peptide mix was used to screen the different surfaces depending on their D/I efficiency and their ability to ensure homogeneous deposit of the samples. For that purpose, deposition homogeneity was visualized owing to reconstructed ionic images from all protonated or sodiated ions of the 10 peptides constituting the standard mix.

Conclusions

Seven surfaces were then selected satisfying the required D/I efficiency and deposit homogeneity criteria. Results obtained with these optimal surfaces were then compared with those recorded by MALDI-MS analyses used as references.

Aline Cournut,
Ioana Silvia Hosu,
Flavie Braud,
Paul Moustiez,
Yannick Coffinier,
Christine Enjalbal,
Claudia Bich
February 22, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9476?af=R

Development and validation of an analytical method for trace‐level quantification of genotoxic nitrosamine impurities in losartan and hydrochlorothiazide fixed‐dose combination tablets using ultra performance liquid chromatography triple quadrupole mass spectrometry

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Development and validation of an analytical method for trace‐level quantification of genotoxic nitrosamine impurities in losartan and hydrochlorothiazide fixed‐dose combination tablets using ultra performance liquid chromatography triple quadrupole mass spectrometry

Abstract

Rationale

Since June 2018, globally large numbers of pharmaceuticals have been recalled due to the unexpected presence of nitrosamines. Beginning with the class of pharmaceuticals known as sartans, subsequent lines of inquiry included antidiabetic medicines, antihistamines, and antibiotics. A critical review of the U.S. Food and Drug Administration database reveals that the highest number of products recall due to the presence of unacceptable levels of nitrosamines were losartan potassium drug products and their coformulations with other drug substances. The problem can be mainly attributed to naively adopted approval revisions and the lack of sufficient current analytical technologies to detect those contaminants in time. In this work, we developed a specific, selective, accurate, precise, and robust ultra-performance liquid chromatography-triple quadrupole-mass spectrometry (UPLC-TQ-MS/MS) method for the estimation of eight genotoxic nitrosamine impurities in losartan and hydrochlorothiazide (HCTZ) tablets, which is the only fixed-dosage combination approved by the USFDA to treat hypertension.

Methods

All the nitrosamine impurities along with the drug substances were separated using an Agilent Pursuit XRs Ultra diphenyl column (150 × 2.0 mm, 2.8 μm) with mobile phase A (0.1% formic acid in water) and mobile phase B (0.1% formic acid in methanol) at a flow rate of 0.4 ml/min using the gradient elution program. The proposed method was validated per ICH (International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use) Q2 (R1) guidelines to ensure the method is suitable for its intended purpose.

Results

Limit of detection and limit of quantification were obtained in the range of 0.25–0.5 ng/mL, which was very low compared to levels specified by the USFDA, European Medicines Agency (EMA), and other regulatory authorities that ensure the sensitivity of the method in its entire life cycle.

Conclusions

The developed method can be incorporated into an official monograph and applied for routine quality control analysis of losartan and HCTZ fixed-dose combination tablets.

Ravi Patel,
Sanjay Purohit,
Ravisinh Solanki,
Dignesh Khunt,
Chhaganbhai Patel,
Rucha Patel,
Shalin Parikh
February 22, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9488?af=R

Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging

Rationale

Proteins extracted from archaeological bone and teeth are utilised for investigating the phylogeny of extinct and extant species, the biological sex and age of past individuals, as well as ancient health and physiology. However, variable preservation of proteins in archaeological materials represents a major challenge.

Methods

To better understand the spatial distribution of ancient proteins preserved within teeth, we applied matrix assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for the first time to bioarchaeological samples to visualise the intensity of proteins in archaeological teeth thin sections. We specifically explored the spatial distribution of four proteins (collagen type I, of which the chains alpha-1 and alpha-2, alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6).

Results

We successfully identified ancient proteins in archaeological teeth thin sections using mass spectrometry imaging. The data are available via ProteomeXchange with identifier PXD038114. However, we observed that peptides did not always follow our hypotheses for their spatial distribution, with distinct differences observed in the spatial distribution of several proteins, and occasionally between peptides of the same protein.

Conclusions

While it remains unclear what causes these differences in protein intensity distribution within teeth, as revealed by MALDI-MSI in this study, we have demonstrated that MALDI-MSI can be successfully applied to mineralised bioarchaeological tissues to detect ancient peptides. In future applications, this technique could be particularly fruitful not just for understanding the preservation of proteins in a range of archaeological materials, but making informed decisions on sampling strategies and the targeting of key proteins of archaeological and biological interest.

Joannes Dekker,
Tony Larson,
Jordan Tzvetkov,
Virginia L. Harvey,
Adam Dowle,
Richard Hagan,
Paul Genever,
Sarah Schrader,
Marie Soressi,
Jessica Hendy
February 22, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9486?af=R

Changes of serum IgG glycosylation patterns in rheumatoid arthritis

Clinical Proteomics

Most Recent Articles: Clinical Proteomics

Most Recent Articles: Clinical Proteomics

Changes of serum IgG glycosylation patterns in rheumatoid arthritis

RA is a common chronic and systemic autoimmune disease, and the diagnosis is based significantly on autoantibody detection. This study aims to investigate the glycosylation profile of serum IgG in RA patients …

Xiaoyue Deng, Xiaomin Liu, Yan Zhang, Dan Ke, Rui Yan, Qian Wang, Xinping Tian, Mengtao Li, Xiaofeng Zeng and Chaojun Hu
February 22, 2023
https://clinicalproteomicsjournal.biomedcentral.com/articles/10.1186/s12014-023-09395-z

Quantitative proteomics reveals reduction in central carbon and energy metabolisms contributes to gentamicin resistance in Staphylococcus aureus

Journal of Proteomics

ScienceDirect Publication: Journal of Proteomics

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Quantitative proteomics reveals reduction in central carbon and energy metabolisms contributes to gentamicin resistance in Staphylococcus aureus

Publication date: 15 April 2023

Source: Journal of Proteomics, Volume 277

Author(s): Zhiyu Pan, Lvyuan Fan, Yilin Zhong, Juan Guo, Xuesa Dong, Xiao Xu, Chao Wang, Yubin Su

February 22, 2023
https://www.sciencedirect.com/science/article/pii/S1874391923000386?dgcid=rss_sd_all

FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes

Motivation: Biological tissues are dynamic and highly organized. Multi-scale models are helpful tools to analyze and understand the processes determining tissue dynamics. These models usually depend on parameters that need to be inferred from experimental data to achieve a quantitative understanding, to predict the response to perturbations, and to evaluate competing hypotheses. However, even advanced inference approaches such as Approximate Bayesian Computation (ABC) are difficult to apply due to the computational complexity of the simulation of multi-scale models. Thus, there is a need for a scalable pipeline for modeling, simulating, and parameterizing multi-scale models of multi-cellular processes. Results: Here, we present FitMultiCell, a computationally efficient and user-friendly open-source pipeline that can handle the full workflow of modeling, simulating, and parameterizing for multi-scale models of multi-cellular processes. The pipeline is modular and integrates the modeling and simulation tool Morpheus and the statistical inference tool pyABC. The easy integration of high-performance infrastructure allows to scale to computationally expensive problems. The introduction of a novel standard for the formulation of parameter inference problems for multi-scale models additionally ensures reproducibility and reusability. By applying the pipeline to multiple biological problems, we demonstrate its broad applicability, which will benefit in particular image-based systems biology. Availability: FitMultiCell is available open-source at https://gitlab.com/fitmulticell/fit. Contact: jan.hasenauer@uni-bonn.de
Alamoudi, E., Schalte, Y., Muller, R., Starruss, J., Bundgaard, N., Graw, F., Brusch, L., Hasenauer, J.
February 22, 2023
http://biorxiv.org/cgi/content/short/2023.02.21.528946v1?rss=1

Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate.

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate.

Lymph nodes (LNs) may serve as a sanctuary site for HIV viruses due to the heterogeneous distribution of the antiretrovirals (ARVs) inside the LNs. There is an ongoing debate whether this represents ongoing cycles of viral replication in the LNs or merely residual virus production by latently infected cells. Previous work has claimed that the measured levels of genetic variation in proviruses sampled from the blood were inconsistent with ongoing replication. However, it is not clear what rate of variation is consistent with ongoing replication in small sanctuary sites. In this study, we used a spherically symmetric compartmental ODE model to track the HIV viral dynamics in the LN and predict the contribution of ongoing replication within the LN to the whole-body proviral pool in an ARV-suppressed patient. This model tracks the reaction-diffusion dynamics of uninfected, actively infected, and latently infected T-cells as well as free virus within the LN parenchyma and the blood, and distinguishes between latently infected cells created before ARV therapy and during ARV therapy. We simulated suppressive therapy beginning in year 5 post-infection. Each LN sanctuary site had a volume of 1 ml, and we considered cases of 1ml, 30ml, and 250ml total volume, which represent a single active sanctuary site, moderate systemic involvement, and involvement of the total lymphoid tissue. Viral load in the blood rapidly dropped and remained below the limit of detection in all cases but remained high in the LN sanctuary sites. Novel latent cells increased systemically over time but very slowly, taking between 25 and 50 years to reach 5% of the total latent pool, depending on the volume of lymphoid tissue involvement. Putative sanctuary sites in LNs are limited in volume and produce novel latent cells slowly. Assays to detect genetic drift due to such sites would require very deep sequencing if sampling only from the blood. Previous studies showing a lack of genetic drift are consistent with the expected contribution of ongoing replication in lymph node sanctuary sites.
Paryad-Zanjani, S., Jagarapu, A., Piovoso, M. J., Zurakowski, R.
February 22, 2023
http://biorxiv.org/cgi/content/short/2023.02.18.529086v1?rss=1

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

Natural communities are incredibly diverse, and explaining how this biodiversity is even possible remains a central question in ecology. Resource competition is thought to play an important role in community interactions, but understanding diverse communities using resource competition is limited by the competitive exclusion principle: the prediction that only as many species as resources should coexist. Here, we demonstrate that sequential resource utilization, also known as diauxie, under periodic growth and death cycles allows for many more coexisting species than resources, violating the competitive exclusion principle. These violations become possible when fluctuations produce variations in the resource depletion order on each growth cycle. The depletion order varying allows the community to experience different sequences of temporal niches on each growth cycle, with temporal niches being the increasingly depleted environments produced by sequential resource depletions. While community-driven fluctuations and competitive-exclusion violations are rare under constant environmental conditions, we find that with even small environmental fluctuations most communities violate competitive exclusion, with several times as many survivors as resources in some simulations. We explore the competitive interactions within these communities and show that survivors are accurately predicted by temporal niches. We thus demonstrate highly diverse communities as a likely outcome of resource competition with a competitive structure based on ordered resource preferences.
Bloxham, B., Lee, H., Gore, J.
February 22, 2023
http://biorxiv.org/cgi/content/short/2023.02.17.529002v1?rss=1

Gas-phase dopant flow to modify nanoLC-MS and nanoESI protein charge

International Journal of Mass Spectrometry

ScienceDirect Publication: International Journal of Mass Spectrometry

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Gas-phase dopant flow to modify nanoLC-MS and nanoESI protein charge

Publication date: May 2023

Source: International Journal of Mass Spectrometry, Volume 487

Author(s): G. Asher Newsome, Timothy P. Cleland

February 21, 2023
https://www.sciencedirect.com/science/article/pii/S1387380623000179?dgcid=rss_sd_all

[ASAP] GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

latest articles published in Journal of Proteome Research

[ASAP] GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching

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Journal of Proteome Research
DOI: 10.1021/acs.jproteome.3c00066

Sujun Li, Jianhui Zhu, David M. Lubman, He Zhou, and Haixu Tang
February 21, 2023
http://dx.doi.org/10.1021/acs.jproteome.3c00066

[ASAP] Assessment and Comparison of Database Search Engines for Peptidomic Applications

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

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[ASAP] Assessment and Comparison of Database Search Engines for Peptidomic Applications

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Journal of Proteome Research
DOI: 10.1021/acs.jproteome.2c00307

Eduardo A. De La Toba, Krishna D. B. Anapindi, and Jonathan V. Sweedler
February 21, 2023
http://dx.doi.org/10.1021/acs.jproteome.2c00307

[ASAP] A Robust Purity Method for Biotherapeutics Using New Peak Detection in an LC–MS-Based Multi-Attribute Method

Journal of The American Society for Mass Spectrometry

Journal of the American Society for Mass Spectrometry: Latest Articles (ACS Publications)

latest articles published in Journal of the American Society for Mass Spectrometry

[ASAP] A Robust Purity Method for Biotherapeutics Using New Peak Detection in an LC–MS-Based Multi-Attribute Method

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Journal of the American Society for Mass Spectrometry
DOI: 10.1021/jasms.2c00355

Monica Sadek, Benjamin Nathan Moore, Christopher Yu, Nicholas Ruppe, Austin Abdun-Nabi, Zhiqi Hao, Melissa Alvarez, Sanket Dahotre, and Galahad Deperalta
February 21, 2023
http://dx.doi.org/10.1021/jasms.2c00355

Integrated Tandem Affinity Protein Purification Using the Polyhistidine Plus Extra 4 Amino Acids (HiP4) Tag System

Proteomics (Wiley)

Wiley: PROTEOMICS: Table of Contents

Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues.

Integrated Tandem Affinity Protein Purification Using the Polyhistidine Plus Extra 4 Amino Acids (HiP4) Tag System

Abstract

Peptide tag systems are a robust biophysical and biochemical method that is widely used for protein detection and purification. Here, we developed a novel tag system termed “HiP4” (histidine plus four amino acids) whose epitope sequence comprises only seven amino acids (HHHDYDI) that partially overlap with the conventional 6x histidine tag. We produced a monoclonal antibody against the HiP4 tag that can be used in multiple immunoassays with high specificity and affinity. Using this system, we developed a tandem affinity purification and mass spectrometry (TAP-MS) system for comprehensive protein interactome analysis. The integrated use of nickel bead purification followed by HiP4 tag immunoprecipitation made it possible to reduce nonspecific binding and improve selectivity, leading to the recovery of previously unrecognized proteins that interact with hepatitis B virus X protein or TAR DNA–binding protein 43. Our results indicate that this system may be viable as a simple and powerful tool for TAP-MS that can achieve low background and high selectivity in comprehensive protein–protein interaction analyses.

This article is protected by copyright. All rights reserved

Yoko Ino,
Yutaro Yamaoka,
Kiho Tanaka,
Kei Miyakawa,
Mayuko Nishi,
Yasuyoshi Hatayama,
Hirokazu Kimura,
Yayoi Kimura,
Akihide Ryo
February 21, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200334?af=R