Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing

Data-Independent Acquisition (DIA) was introduced to improve sensitivity to cover all peptides in a range rather than only sampling high-intensity peaks as in Data-Dependent Acquisition (DDA) mass spectrometry. However, it is not very clear how useful DIA data is for de novo peptide sequencing as the DIA data are marred with coeluted peptides, high noises, and varying data quality. We present a new deep learning method DIANovo, and address each of these difficulties, and improves the previous established system DeepNovo-DIA by from 25% to 81%, averaging 48%, for amino acid recall, and by from 27% to 89%, averaging 57%, for peptide recall, by equipping the model with a deeper understanding of coeluted DIA spectra. This paper also provides criteria about when DIA data could be used for de novo peptide sequencing and when not to by providing a comparison between DDA and DIA, in both de novo and database search mode. We find that while DIA excels with narrow isolation windows on older-generation instruments, it loses its advantage with wider windows. However, with Orbitrap Astral, DIA consistently outperforms DDA due to narrow window mode enabled. We also provide a theoretical explanation of this phenomenon, emphasizing the critical role of the signal-to-noise profile in the successful application of de novo sequencing.

Rapid Adaptation of BERT for Information Extraction on Domain-Specific Business Documents

Techniques for automatically extracting important content elements from business documents such as contracts, statements, and filings have the potential to make business operations more efficient. This problem can be formulated as a sequence labeling task, and we demonstrate the adaption of BERT to two types of business documents: regulatory filings and property lease agreements. There are aspects of this problem that make it easier than "standard" information extraction tasks and other aspects that make it more difficult, but on balance we find that modest amounts of annotated data (less than 100 documents) are sufficient to achieve reasonable accuracy. We integrate our models into an end-to-end cloud platform that provides both an easy-to-use annotation interface as well as an inference interface that allows users to upload documents and inspect model outputs.