DeepLC can predict retention times for peptides that carry as-yet unseen modifications

R Bouwmeester, R Gabriels, N Hulstaert, L Martens… - Nature …, 2021 - nature.com
The inclusion of peptide retention time prediction promises to remove peptide identification
ambiguity in complex liquid chromatography–mass spectrometry identification workflows …

Toward proteome‐wide exploration of proteins in dried blood spots using liquid chromatography‐coupled mass spectrometry

D Nakajima, O Ohara, Y Kawashima - Proteomics, 2021 - Wiley Online Library
Dried blood spot (DBS) sampling is a method with advantages over conventional blood
sampling in relation to collection, cost, storage, and transportation. Such advantages have …

Identifying individuals using proteomics: are we there yet?

I Fierro-Monti, JC Wright, JS Choudhary… - Frontiers in Molecular …, 2022 - frontiersin.org
Multi-omics approaches including proteomics analyses are becoming an integral
component of precision medicine. As clinical proteomics studies gain momentum and their …

Deep time paleoproteomics: Looking forward

ER Schroeter, TP Cleland… - Journal of Proteome …, 2021 - ACS Publications
The goal of paleoproteomics is to characterize proteins from specimens that have been
subjected to the degrading and obscuring effects of time, thus obtaining biological …

Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides

D Skiadopoulou, J Vašíček… - Journal of Proteome …, 2023 - ACS Publications
Precision medicine focuses on adapting care to the individual profile of patients, for
example, accounting for their unique genetic makeup. Being able to account for the effect of …

A Non-targeted proteomics newborn screening platform for inborn errors of immunity

H Shibata, D Nakajima, R Konno, A Hijikata… - Journal of Clinical …, 2025 - Springer
Purpose Newborn screening using dried blood spot (DBS) samples for the targeted
measurement of metabolites and nucleic acids has made a substantial contribution to public …

Identification of protein Isoforms using reference databases built from Long and Short Read RNA-Sequencing

AP Tay, JJ Hamey, GE Martyn… - Journal of Proteome …, 2022 - ACS Publications
Alternative splicing can lead to distinct protein isoforms. These can have different functions
in specific cells and tissues or in different developmental stages. In this study, we explored …

[HTML][HTML] PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics–catching the (un) usual suspects

A Raj, S Aggarwal, P Singh, AK Yadav… - Computational and …, 2024 - Elsevier
Variant peptides resulting from single nucleotide polymorphisms (SNPs) can lead to
aberrant protein functions and have translational potential for disease diagnosis and …

Quality control of variant peptides identified through proteogenomics-catching the (un) usual suspects

A Raj, S Aggarwal, AK Yadav, D Dash - bioRxiv, 2023 - biorxiv.org
The importance of single nucleotide polymorphisms (SNPs) is well known in diseases but
which ones are translated to form single amino acid variant (SAV or variant) is not studied in …

moPepGen: Rapid and Comprehensive Identification of Non-canonical Peptides

C Zhu, LY Liu, A Ha, TN Yamaguchi, H Zhu… - …, 2024 - pmc.ncbi.nlm.nih.gov
Gene expression is a multi-step transformation of biological information from its storage form
(DNA) into functional forms (protein and some RNAs). Regulatory activities at each step of …