Biology subjects

Pino, L.

Publications and source records attributed to Pino, L..

5 recordsLinked to original sources

bioRxiv2026

MSstatsBioNet: Integrating Statistical Analyses with Prior Knowledge Biomolecular Networks for Quantitative Proteomics and Phosphoproteomics

A common outcome of quantitative mass spectrometry-based proteomic and phosphoproteomic experiments is a list of proteins that are differentially abundant between conditions. However, biological interpretation requires evaluation in the context of prior knowledge of biological mechanisms and protein function. One approach to facilitate mechanistic biological interpretation is to integrate such lists with biological network databases, built from manually curated resources and text mining systems. This manuscript automates this process with MSstatsBioNet, a Bioconductor package that integrates MSstats, a family of open-source packages for detecting differentially abundant proteins, and INDRA, a system that extracts biomolecular networks from biomedical literature using text mining and merges those networks with the content of curated knowledge bases. Taking as input a list of differentially abundant proteins from MSstats, MSstatsBioNet retrieves a protein subnetwork from INDRA and overlays experimental fold changes onto the underlying subnetwork. Users can then interact with the network and overlaid data, interrogating primary literature evidence to construct granular mechanistic narratives for iterative hypothesis generation. We demonstrate the utility of this approach with three case studies, two measuring changes in protein abundance and one measuring changes in phosphorylation.

bioinformatics↗

bioRxiv2026

Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics

Data-independent acquisition (DIA) proteomics enables reproducible and systematic peptide detection and quantification, and trapped ion mobility spectrometry (TIMS) on the timsTOF platform further improves DIA by synchronizing ion mobility separation with quadrupole precursor sampling. Analyzing the highly multiplexed spectra generated by DIA typically relies on spectral libraries, and fully leveraging the additional ion mobility dimension requires these libraries to include accurate retention time, fragment ion intensity, and ion mobility annotations. Existing in silico spectral library generation tools either lack ion mobility support entirely or rely on models trained on data-dependent acquisition (DDA) data, that can introduce a mismatch that may not capture unique experiment-specific biases when applied to each respective timsTOF dataset. Carafe is a software tool that uses deep learning models to generate high-quality, experiment-specific in silico libraries by training directly on DIA data. In this study, we extend Carafe to generate libraries for timsTOF DIA data, which involves fine-tuning retention time (RT), fragment ion intensity, and ion mobility prediction models using timsTOF DIA data. Carafe2 operates directly on native timsTOF raw data (Bruker .d directories) without the need for data conversion. We demonstrate the performance of Carafe2 across a wide range of DIA applications, including global proteome, phosphoproteome, and plasma proteome datasets. Comparing Carafe2 fine-tuned RT, fragment ion intensity, and ion mobility prediction models with pretrained DDA models, we find that Carafe2 models outperform pretrained models on a variety of DIA datasets. We then demonstrate the utility of in silico libraries generated by Carafe2 for peptide detection on several different types of timsTOF DIA datasets by comparing with the libraries generated with DDA-trained AlphaPeptDeep models, DIA-NN built-in models, and empirical spectral libraries generated from DDA experiments.

bioinformatics↗

bioRxiv2022

Expanding the epitranscriptomic RNA sequencing and modification mapping mass spectrometry toolbox with field asymmetric waveform ion mobility and electrochemical elution liquid chromatography

Post-transcriptional modifications of RNA strongly influence RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before mass-spectrometry identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA-MS increases both coverage and throughput, while the EMLC LC-MS orthogonally separates RNA of different length and charge. The combination of the two methods offers a broadly applicable platform to improve length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.

biochemistry↗

bioRxiv2020

Late-life restoration of mitochondrial function reverses cardiac dysfunction in old mice

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.

physiology↗

bioRxiv2018

Quantification of nuclear protein dynamics reveals chromatin remodeling during acute protein degradation

Sequencing-based technologies cannot measure post-transcriptional dynamics of the nuclear proteome, but unbiased mass-spectrometry measurements of chromatin-associated proteins remain difficult. In this work, we have combined facile nuclear sub-fractionation approaches with data-independent acquisition mass spectrometry to improve detection and quantification of nuclear proteins in human cells and tissues. Nuclei are isolated and subjected to a series of extraction conditions that enrich for nucleoplasm, euchromatin, heterochromatin and nuclear-membrane associated proteins. Using this approach, we can measure peptides from over 70% of the expressed nuclear proteome. As we are physically separating chromatin compartments prior to analysis, proteins can be assigned into functional chromatin environments to illuminate systems-wide nuclear protein dynamics. The integrity of nuclear sub-compartments were validated with immunofluorescence, which confirms the presence of key markers during chromatin extraction. We then apply this method to study the nuclear proteome-wide response to pharmacological degradation of the BET bromodomain proteins. BET degradation leads to widespread changes in chromatin composition, and we discover global HDAC1/2-mediated remodeling of chromatin previously bound by BET bromodomains. In summary, we have developed a technology for reproducible, comprehensive characterization of the nuclear proteome to observe the systems-wide nuclear protein dynamics.

systems biology↗