Biology subjects

Nair, B. A. B.

Publications and source records attributed to Nair, B. A. B..

3 recordsLinked to original sources

bioRxiv2025

MALDI Deamidation Score (MDS): A Fast and Flexible Method for Assessing Deamidation in ZooMS Data and Its Application to the Denisova Cave Bone Assemblage

Estimating deamidation from MALDI-TOF MS spectra of bones has most frequently been achieved using the q2e method due to its high-throughput capacity and ease of use. Despite this accessibility, q2e is only capable of estimating deamidation at the peptide level on a fixed peptide list and does not generate a sample-wide summary. The introduction of the Parchment Glutamine Index (PQI) presented an alternative method for deamidation estimation. Initially designed for a large ZooMS dataset of parchment, it utilises weighted least squares and a linear mixed-effects model (LME) to generate deamidation estimation on both the peptide and sample level. To address the limitations of q2e and expand the applicability of PQI to a wider range of archaeological tissues and MALDI-derived data (such as ZooMS data on bone collagen), we developed the MALDI Deamidation Score (MDS), an iteration of the PQI method optimized for handling large-scale datasets. Compared to PQI, MDS is more streamlined for the analysis of multi-species data with customisable peptide lists, offering a dramatically decreased processing time while being able to normalise the peak intensity for higher accuracy. Through a case study on the published Denisova Cave ZooMS assemblage, we demonstrate that different peptides exhibit varying deamidation patterns over time, making the use of a single peptide to represent overall deamidation potentially biased. Such information is invaluable for investigating key questions such as protein preservation and site formation processes, especially when contextualized with other lines of archaeological evidence.

bioinformatics↗

bioRxiv2024

Anubis: a multi-level authentication scale for ancient proteins using random forest classification

Deamidation is a time-dependent, post-translational modification with wide applications in clinical proteomics and palaeoproteomics as ageing indicators and authentication markers. Despite its significance, the use of deamidation for authenticating ancient proteins remains controversial, primarily due to variability in deamidation kinetics and context-specific protein preservation. We propose Anubis, an open-source, Python-based pipeline to evaluate relative deamidation patterns and authenticate ancient proteins. Anubis leverages random forest classification based on a range of tandem mass spectrometry-based features and physico-chemical characteristics. We use a combination of ancient and experimentally degraded beta-lactoglobulin to demonstrate that Anubis can authenticate a putative ancient dairy protein using position-specific deamidation patterns, relative deamidation (asparagine vs. glutamine), and overall modification patterns using trypsin processed in the same batch as a baseline. This multi-level approach addresses the complexities of ancient protein deamidation and paves the way for automated, reliable authentication across different archaeological substrates.

bioinformatics↗

bioRxiv2023

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses and interpretations of complex, degraded protein mixtures. The community has also established standards of good practice to interrogate our data. However, there is a lack of a systematic exploration of how these affect the identification of peptides, post-translational modifications (PTMs), proteins and their significance (through the False Discovery Rate) and correctness. We systematically investigated the performance of a wide range of sequencing tools and search engines in a controlled system: the experimental degradation of the single purified bovine {beta}-lactoglobulin (BLG), heated at 95 {degrees}C and pH 7 for 0, 4 and 128 days. We target BLG since it is one of the most robust and ubiquitous proteins in the archaeological record. We tested different reference database choices, a targeted dairy protein one, and the whole bovine proteome and the three digestion options (tryptic-, semi-tryptic- and non-specific searches), in order to evaluate the effects of search space and the identification of peptides. We also explored alternative strategies, including open search that allows for the global identification of PTMs based upon wide precursor mass tolerance and de novo sequencing to boost sequence coverage. We analysed the samples using Mascot, MaxQuant, Metamorpheus, pFind, Fragpipe and DeNovoGUI (pepNovo+, DirecTag, Novor), benchmarked these tools and discuss the optimal strategy for the characterisation of ancient proteins. We also studied physicochemical properties of the BLG that correlate with bias in the identification coverage.

bioinformatics↗