Revolutionizing the exploration and analysis of proteomic data by allowing for real-time query and visualization

Proteomics, the science of studying proteins and their regulation, modifications and functions, generates huge amounts of data. Therefore, software tools for efficient data management, browsing and search are crucial for scientific discovery in this field of biology. Building on an algorithm developed by Facebook, Spectroscape is set to revolutionize the exploration and analysis of proteomic data by allowing for real-time query and visualization of spectral archives and providing researchers with a valuable resource for error correction and novel discoveries. We at Nexco can set up Spectroscape with your private datasets off the web, for you to profit from all its capabilities.

In proteomics, spectral archives house huge volumes of tandem mass spectral data useful for identifying proteins, post-translational modifications, amino acid substitutions, etc. However, the adoption of spectral archives has been hampered by significant challenges. Most importantly, these datasets are usually very large, so spectrum clustering is computationally intensive; besides, the lack of user-friendly interfaces has hindered efficient human intervention on spectrum comparison, limiting the potential for groundbreaking discoveries.

A new tool called Spectroscape emerges as a solution to these challenges. It leverages the inverted file and product quantization encoding (IVF-PQ) algorithm of the Facebook AI Similarity Search package to create a unique indexing system that is blazing fast. This algorithm groups spectra in high-dimensional space based on approximate spectral similarity, facilitating rapid retrieval and clustering of spectral data in real time. Spectroscape’s implementation of the IVF-PQ algorithm thus streamlines spectral data management, making it more efficient and accessible.

Spectroscape is so fast that it enables real-time clustering of spectral data, setting it apart from other tools in the field. By reducing the search space and initially grouping similar spectra, Spectroscape makes spectral data management seamless. After processing the data with the clustering pipeline, a user-friendly web-based interface allows researchers to search spectral repositories by similarity, providing lists of best-matching spectra and detailed insights into clusters within the query spectrum’s neighborhood and enabling graphical navigation of the results.

Spectroscape’s performance is remarkable. It can execute individual queries in just milliseconds on datasets containing millions of spectra, with potential for even faster processing when handling multiple queries in a batch. This efficiency can be achieved even with modest hardware, for example a 32-core CPU. Moreover, Spectroscape can be deployed on graphical processing units (GPUs) resulting in substantial further reductions in search times.

Besides being blazing fast, Spectroscape achieves high recall rates, which is of course crucial in proteomics data analysis. Its use of the IVF-PQ algorithm ensures over 98% overall recall, making it highly reliable despite its high speed.

In the website exemplifying Spectroscape applied to an open dataset, a force-directed graph scheme demonstrates researchers can interactively probe the tightness of spectral clusters, making it easier to detect subtle differences in fragmentation patterns and confirming identifications. This powerful tool can help uncover unexpected post-translational modifications and sequence variants at scale, offering unprecedented potential for proteomic research.

How we at Nexco can leverage Spectroscape for proteomics data analysis

At Nexco we are always up to date with the latest technologies for bioinformatics and computational biology, and as such we recognize the significance of Spectroscape in advancing proteomic research, being one more tool to exploit when working on your problems. In particular, we can setup Spectroscape in our servers and build your own customized spectral archive in a form closed to you, so that you then browse it privately and benefitting from Spectroscape’s capabilities.

We look forward to harnessing the power of Spectroscape to drive your research forward, ultimately deepening our understanding of proteins and their functions.

References

Spectroscape enables real-time query and visualization of a spectral archive in proteomics - Nature Communications