Measurement and utilization of the proteomic reactivity by mass spectrometry

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Measurement and utilization of the proteomic reactivity by mass spectrometry

Abstract

Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.

Clodette Punzalan,
Lei Wang,
Bekim Bajrami,
Xudong Yao
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21837?af=R

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2019–2020

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2019–2020

Abstract

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.

David J. Harvey
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21806?af=R

Mass spectrometry analysis of phosphotyrosine‐containing proteins

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Mass spectrometry analysis of phosphotyrosine‐containing proteins

Abstract

Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.

Jiajia Li,
Xianquan Zhan
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21836?af=R

Inadequate Definition of the Limit of Quantification Applied for the Quantification of Perfluoroalkyl Substances in Food by LC‐MS/MS May Compromise the Reliability of the Data Requested by the European Regulation

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.

Inadequate Definition of the Limit of Quantification Applied for the Quantification of Perfluoroalkyl Substances in Food by LC‐MS/MS May Compromise the Reliability of the Data Requested by the European Regulation

Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a widespread technology used for the quantitative determination of per- and polyfluoroalkyl substances (PFAS) in foodstuffs. Specifically, LC-MS/MS offers attractive performance combining the sensitivity and selectivity required by the European Union for testing perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA) and perfluorohexane sulfonic acid (PFHxS) with maximum limits of quantification (LOQs) in the sub part-per-billion (μg/kg) or the part-per-trillion (ng/kg) domains. In this article we highlight the important diversity in LOQ definitions applied in LC-MS/MS methods described in the literature that raise concerns about the capability of some of those to generate reliable data requested by the European regulation. Here, we point the risk of false response or misquantification if criteria for assessing LOQ suffer from a lack of rigor. We emphasize the need to use PFAS-free samples spiked with the analyte(s) of interest and the application of identification criteria according to official documents for a sound measurement of the LOQ.

Thierry Delatour,
Xanthippe Theurillat,
Bjørn Eriksen,
Claudia Mujahid,
Pascal Mottier
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/rcm.9507?af=R

Rapid on‐site detection of persistent organic pollutants using multi‐walled carbon nanotube‐modified paper spray ionization and a miniature mass spectrometer

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.

Rapid on‐site detection of persistent organic pollutants using multi‐walled carbon nanotube‐modified paper spray ionization and a miniature mass spectrometer

RATIONALE

Rapid on-site detection of persistent organic pollutants (POPs) is highly desirable for environmental protection.

METHODS

Herein, a rapid on-site analytical workflow was developed for the investigation of polycyclic aromatic hydrocarbons (PAHs) and perfluorinated compounds (PFCs) using multi-walled carbon nanotube (MWCNT)-modified paper spray ionization (PSI) coupled with a miniature ion trap mass spectrometer. Critical parameters regarding PSI and miniature mass spectrometry analysis were optimized.

RESULTS

The analytical performance of the developed method was evaluated under optimized conditions, obtaining a short analysis duration of less than 1 min, sufficient linearity with correlation coefficients greater than 0.99, acceptable recovery rates of 93.1–105.8% with relative standard deviations of between 3.5–10.3%, and reasonable sensitivity with limits of detection and quantitation of 2–200 μg/L and 5–500 μg/L, respectively.

CONCLUSIONS

Considering these aspects, the present approach demonstrated a promising solution for rapid on-site detection of emerging POPs.

Xiangyu Guo,
Junfang Li,
Hua Bai,
Qiang Ma
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/rcm.9509?af=R

EI‐MS fragmentation routes of CWC‐related organoarsenic compounds: The electron ionization and DFT studies

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.

EI‐MS fragmentation routes of CWC‐related organoarsenic compounds: The electron ionization and DFT studies

RATIONALE

For unambiguous identification of Chemical Weapons Convention-related chemicals in environmental and biological samples, access to mass spectra and expertise in spectral interpretation is required. As of today, there is no mass spectrum available for dialkyl alkylarsonodithioites in the literature. Therefore, it is essential to obtain spectral information about these compounds.

METHODS

The CWC-related organoarsenic compounds were synthesized and analyzed by GC-MS, and their retention index (RI) was calculated by Van Den Dool’s method. The relationship between RI and DFT-calculated polarizability (⍺) and molecular weight was also studied. Electron ionization (EI) mode was used to investigate the general fragmentation patterns of the synthesized compounds. A DFT analysis of some major fragment ions was performed in order to confirm the fragmentation pathways.

RESULTS

A linear relationship between RI and ⍺ is observed. The mass spectra of compounds 5-7 are affected by alkyl groups on sulfur and arsenic atom. The molecular ion of compounds 5-7 can be observed in their EI-MS with relatively good abundance. EI-MS studies revealed some interesting fragmentation pathways, such as the formation of arsenic analogue of benzilic and tropylium in EI-MS of chemicals 6.

CONCLUSIONS

By analyzing the mass spectra and RI values, it is possible to detect CWC-related chemicals in aqueous, blood, and urine samples during an on-site or off-site inspection.

Masomeh Eskandari,
Sajjad Mousavi Faraz,
Seyed Esmaeil Hosseini,
Shahram Moradi,
Hamid Saeidian
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/rcm.9511?af=R

Examination of Electronically Mismatched Diels–Alder Reaction by Online 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.

Examination of Electronically Mismatched Diels–Alder Reaction by Online Mass Spectrometry

Rationale

Electronically mismatched Diels–Alder reactions have gained much interests as an alternative pathway for C-C bond formation. To faciliate the development of facile organic transformations, mechanistic investigations are required. Spectroscopic methods (NMR, EPR and UV-Vis) are normally adopted for mechainism examinations, but further improvements on direct obtaining of structural information of short-lived intermediates are encouraged. Herein, an electronically mismatched Diels–Alder reaction between indole and 1,3-cyclohexadiene (1,3-CHD) was studied by an in situ electrospray ionization mass spectrometry (in-situ MS). Based on the direct sampling and detection of the in-situ MS without sample pre-treatment, the structures and dynamics of important intermediates were on-line examined.

Methods

A syringe-based photocatalytic reactor and in-situ AMS evaluation system was constructed for mechanism studies. The role of oxygen was confirmed via control reaction employed in the N2-bubbled system. The stepwise cation radical-based pathway and the [2+2] cycloaddition process were determined through a series of experiments, including solvent evaluation, MS/MS experiments and dynamic monitoring.

Results

The dependence of the reaction on solvent polarity demonstrated that the reaction occurs via the formation of cation radicals, which were captured, identified and dynamically monitored via in situ ESI MS. Without pre-separation, the intermediate of [2+2] cycloaddition was identifiedand the cycloaddition process is thereby determined to be the combination of [4+2] cycloaddition and [2+2] cycloaddition. In addition, oxygen was proved to act as an electron mediator for both catalyst Ru (bpz)3(PF6)2 and radical cations.

Conclusions

The mechanism of electronically mismatched Diels–Alder reaction was successfully deduced by in-situ MS associated with a syringe-based photocatalytic reactor. The structures and dynamics of cation radicals, the effect of O2 for the reaction and the detailed process of [2+2] cycloaddition have been well demonstrated. This work could not only promote the understanding and development of facile photocatalytic transformations, but also enlarge the application of AMS in on-line monitoring.

Jianghui Sun,
Mengyu Cao,
Xiyang Ge,
Jin Ouyang,
Na Na
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/rcm.9510?af=R

GC‐MS of some Amaryllidaceae alkaloids of homolycorine type

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.

GC‐MS of some Amaryllidaceae alkaloids of homolycorine type

Rationale

Gas chromatography-mass spectrometry (GC-MS) is the most frequently applied technique for analysis of Amaryllidaceae alkaloids in plant extracts. These compounds, known for their potent bioactivities, are a distinctive chemotaxonomic feature of the Amaryllidoideae subfamily (Amaryllidaceae). The Amaryllidaceae alkaloids of homolycorine type with a C3-C4 double bond generally show molecular and diagnostic ions at the high mass region with low intensity in EIMS mode leading to problematic identification in complex plant extracts.

Methods

Eleven standard homolycorine-type alkaloids (isolated and identified by 1D and 2D nuclear magnetic resonance) were subjected to separation with gas chromatography and studied with electron impact mass spectrometry including single quadropole (GC-EIMS), tandem (GC-EIMS/MS), and high resolution (GC-HR-EIMS) detectors, as well as with chemical ionisation mass spectrometry (GC-CIMS). Alkaloid fractions from two Hippeastrum species and Clivia miniata were subjected to GC-EIMS and GC-CIMS for alkaloid identification.

Results

GC-EIMS in combination with GC-CIMS provided significant structural information for homolycorine-type alkaloids with C3-C4 double bond facilitating their unambiguous identification. Based on the obtained typical fragmentation, other eleven homolycorine-type compounds were identified in extracts from two Hippeastrum species by parallel GC-EIMS, GC-CIMS and LC-ESI/ToF/MS and in extracts from Clivia miniata by GC-EIMS.

Conclusion

GC-MS can be successfully applied for identification of new and known homolycorine-type alkaloids, as well as for chemotaxonomical and chemoecological studies, among others within the Amaryllidoideae subfamily.

Strahil Berkov,
Rumen Denev,
Borjana Sidjimova,
Yancho Zarev,
Alexandar Shkondrov,
Laura Torras‐Claveria,
Francesc Viladomat,
Jaume Bastida
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/rcm.9506?af=R

Discovery of novel glioma serum biomarkers by proximity extension assay

Clinical Proteomics

Most Recent Articles: Clinical Proteomics

Most Recent Articles: Clinical Proteomics

Discovery of novel glioma serum biomarkers by proximity extension assay

Gliomas are among the most malignant tumors, with a very poor prognosis. Early diagnosis is highly desirable since it can help implement more effective treatments for smaller tumors, which have not yet extensi…

Atefeh Ghorbani, Lisa M. Avery, Dorsa Sohaei, Andrea Soosaipillai, Maxime Richer, Craig Horbinski, Katy McCortney, Wei Xu, Eleftherios P. Diamandis and Ioannis Prassas
March 25, 2023
https://clinicalproteomicsjournal.biomedcentral.com/articles/10.1186/s12014-023-09400-5

Editorial from Dominic M. Desiderio

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Editorial from Dominic M. Desiderio

Abstract

I retired as an Editor of Mass Spectrometry Reviews. I signed my contract on November 1, 1993, and published my first editorial (Volume 13, Issue 1, 1994) when I joined Nico M. M. Nibbering as Co-Editor. These two editorials frame my 30-year tenure at the journal.

This article is protected by copyright. All rights reserved.

Dom Desiderio
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/mas.21840?af=R

Innovations in Applications of Mass Spectrometry Impact Many Fields of Science.

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Innovations in Applications of Mass Spectrometry Impact Many Fields of Science.

Abstract

I am pleased and honored that Dan Fabris has organized this special issue of reviews that reflect many of my research interests. I have been a member of the Editorial Advisory Board of Mass Spectrometry Reviews since 1994 and I regard reviews as an important component of the scientific method. Well done, they collect and integrate knowledge in a particular field and construct a factual foundation that directs and supports the next research frontier.

This article is protected by copyright. All rights reserved.

Catherine Fenselau Cotter
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/mas.21839?af=R

Measurement and utilization of the proteomic reactivity by mass spectrometry

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Measurement and utilization of the proteomic reactivity by mass spectrometry

Abstract

Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.

Clodette Punzalan,
Lei Wang,
Bekim Bajrami,
Xudong Yao
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/mas.21837?af=R

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2019–2020

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2019–2020

Abstract

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.

David J. Harvey
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/mas.21806?af=R

Mass spectrometry analysis of phosphotyrosine‐containing proteins

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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

Mass spectrometry analysis of phosphotyrosine‐containing proteins

Abstract

Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.

Jiajia Li,
Xianquan Zhan
March 25, 2023
https://onlinelibrary.wiley.com/doi/10.1002/mas.21836?af=R

DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes

BioRxiv

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

DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes

Most, if not all, proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing the majority of cellular processes in health and disease. Ever-advancing analytical capabilities promise to pinpoint lesions in proteome modularity driving disease phenotypes. Affinity purification of the protein of interest combined with LC-MS/MS (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can however not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. In this study we introduce Deep Interactome Profiling by Mass Spectrometry (DIP-MS) which combines affinity enrichment with BN-PAGE separation, DIA mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organisation of the human prefoldin (PFD) family of complexes, resolving distinct PFD holo- and sub-complex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution and thus represents a critical steppingstone to relate a proteome state to phenotype in both healthy and diseased conditions.
Frommelt, F., Fossati, A., Uliana, F., Wendt, F., Xue, P., Heusel, M., Wollscheid, B., Aebersold, R., Ciuffa, R., Gstaiger, M.
March 25, 2023
http://biorxiv.org/cgi/content/short/2023.03.22.533843v1?rss=1

Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results

BioRxiv

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

Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results

Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights into our understanding of the genetic control of metabolite levels. However, the biological interpretation of these associations remains challenging due to a lack of existing tools to annotate mGWAS gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we computed the shortest reactional distance (SRD) based on the curated knowledge of the KEGG database to explore its utility in enhancing the biological interpretation of results from three independent mGWAS, including a case study on sickle cell disease patients. Results show that, in reported mGWAS pairs, there is an excess of small SRD values and that SRD values and p-values significantly correlate, even beyond the standard conservative thresholds. The added-value of SRD annotation is shown for identification of potential false negative hits, exemplified by the finding of gene-metabolite associations with SRD [≤]1 that did not reach standard genome-wide significance cut-off. The wider use of this statistic as an mGWAS annotation would prevent the exclusion of biologically relevant associations and can also identify errors or gaps in current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs that can be used to integrate statistical evidence to biological networks.

Baron, C., Cherkaoui, S., Therrien-Laperriere, S., Ilboudo, Y., Poujol, R., Mehanna, P., Garrett, M. E., Telen, M. J., Ashley-Koch, A. E., Bartolucci, P., Rioux, J. D., Lettre, G., Des Rosiers, C., Ruiz, M., Hussin, J.
March 25, 2023
http://biorxiv.org/cgi/content/short/2023.03.22.533869v1?rss=1

An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells

BioRxiv

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

An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells

Detecting oscillations in time series datasets remains a challenging problem even after decades of research. Development of improved statistical algorithms, therefore, remains an exciting avenue of research, especially in fields such as chronobiology where gene expression oscillations tend to be low amplitude, noisy and non stationary. Here we introduce a new method, ODeGP (Oscillation Detection using Gaussian Processes), which combines Gaussian Process (GP) regression with Bayesian inference to provide a flexible approach to the problem. Besides naturally incorporating measurement errors and non-uniformly sampled data, ODeGP uses a recently developed kernel to improve the detection of non stationary waveforms. An additional advantage is that it circumvents issues related to p-value based rhythmicity classification by using the Bayes factor instead. Using a variety of synthetic datasets we first demonstrate that ODeGP almost always outperforms eight commonly used methods in detecting stationary as well as nonstationary oscillations. Next, by analyzing existing qPCR datasets with known (non)oscillatory behavior, we find that the ODeGP Bayes factors show a large separation between oscillatory and non-oscillatory datasets, providing a good metric for the classification problem. In qPCR datasets that exhibit low amplitude and noisy oscillations, we demonstrate that our method is more sensitive compared to the existing methods at detecting weak oscillations. Finally, we generate new qPCR time-series datasets on pluripotent mouse embryonic stem cells, which are expected to exhibit no oscillations of the core circadian clock genes. Surprisingly, we discover using ODeGP that increasing cell density can result in the generation of oscillations in the Bmal1 gene, thus highlighting our method’s ability to discover new and unexpected patterns. We make ODeGP available for open-source use as an easy to run R-package.
Sahay, S., Adhikari, S., Hormoz, S., Chakrabarti, S.
March 25, 2023
http://biorxiv.org/cgi/content/short/2023.03.21.533651v1?rss=1

[ASAP] Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

latest articles published in Journal of Proteome Research

[ASAP] Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

TOC Graphic

Journal of Proteome Research
DOI: 10.1021/acs.jproteome.2c00604

Dominik Madej and Henry Lam
March 25, 2023
http://dx.doi.org/10.1021/acs.jproteome.2c00604

[ASAP] Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

latest articles published in Journal of Proteome Research

[ASAP] Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins

TOC Graphic

Journal of Proteome Research
DOI: 10.1021/acs.jproteome.2c00644

Tine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, and Lennart Martens
March 25, 2023
http://dx.doi.org/10.1021/acs.jproteome.2c00644