Biology subjects

Acquaye, F. L. N. A.

Publications and source records attributed to Acquaye, F. L. N. A..

4 recordsLinked to original sources

bioRxiv2025

Label-free quantification in the Crux toolkit

Ultimately, most tandem mass spectrometry (MS/MS) proteomics experiments aim to not just detect but also quantify the proteins in a given complex sample. Here, we describe an extension to the Crux MS/MS analysis toolkit to enable label-free quantification of peptides. We demonstrate that Cruxs new quantification command, which is modeled after the algorithms implemented in the widely used FlashLFQ software, is both efficient and accurate. In particular, we achieve a 1.9-fold speedup while reducing the memory usage by 26%. The new crux-lfq command is available in Crux v4.3.

bioinformatics↗

bioRxiv2025

Fast and memory efficient searching of large-scale mass spectrometry data using Tide

Over the past 30 years, software for searching tandem mass spectrometry data against a protein database has improved dramatically in speed and statistical power. However, existing tools can still struggle to analyze truly massive datasets, when either the number of spectra or the number of proteins being analyzed grows too large. Here we describe enhancements to the Tide search engine that allow it to handle datasets containing >10 million spectra and databases containing >7 billion peptides on commodity hardware. We demonstrate that the new Tide architecture is around 2-7 times faster than the previous version and is now comparable to MSFragger and Sage in speed while requiring much less memory. Tide is open source and is publicly available as pre-compiled binaries for Windows, Linux and Mac.

bioinformatics↗

bioRxiv2022

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive summary has not been published since 2014. The goal of this work is to summarize the functionality of Crux, focusing on developments since 2014. We begin with empirical results demonstrating our recently implemented speedups to the Tide search engine. Other new features include a new score function in Tide, two new confidence estimation procedures, as well as three new tools: Param-medic for estimating search parameters directly from mass spectrometry data, Kojak for searching cross-linked mass spectra, and DIAmeter for searching data independent acquisition data against a sequence database.

bioinformatics↗

bioRxiv2022

Efficient indexing of peptides for database search using Tide

The first step in the analysis of protein tandem mass spectrometry data typically involves searching the observed spectra against a protein database. During database search, the search engine must digest the proteins in the database into peptides, subject to digestion rules that are under user control. The choice of these digestion parameters, as well as selection of post-translational modifications (PTMs), can dramatically affect the size of the search space and hence the statistical power of the search. The Tide search engine separates the creation of the peptide index from the database search step, thereby saving time by allowing a peptide index to be reused in multiple searches. Here we describe an improved implementation of the indexing component of Tide that consumes around four times less resources (CPU and RAM) than the previous version and can generate arbitrarily large peptide databases, limited by only the amount of available disk space. We use this improved implementation to explore the relationship between database size and the parameters controlling digestion and PTMs, as well as database size and statistical power. Our results can help guide practitioners in proper selection of these important parameters.

bioinformatics↗