# DPST: De Novo Peptide Sequencing with Amino-Acid-Aware Transformers

arXiv: https://arxiv.org/abs/2203.13132 · HTML: https://mlsanity.com/paper/2203.13132/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 11 of its 22 references that are in the map.
- First posted on arXiv 23 Mar 2022.

## Builds on (most cited first, 11 of 11)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Dynamic Graph CNN for Learning on Point Clouds](https://mlsanity.com/paper/1801.07829/) (2018)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Point Transformer](https://mlsanity.com/paper/2011.00931/) (2020)
- [PoinTr: Diverse Point Cloud Completion with Geometry-Aware Transformers](https://mlsanity.com/paper/2108.08839/) (2021)
- [Fast Convergence of DETR with Spatially Modulated Co-Attention](https://mlsanity.com/paper/2101.07448/) (2021)
- [SOTR: Segmenting Objects with Transformers](https://mlsanity.com/paper/2108.06747/) (2021)

## Built on by (most cited first, 1 of 1)

- [MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry](https://mlsanity.com/paper/2606.11868/) (2026)

## Abstract (arXiv)

De novo peptide sequencing aims to recover amino acid sequences of a peptide from tandem mass spectrometry (MS) data. Existing approaches for de novo analysis enumerate MS evidence for all amino acid classes during inference. It leads to over-trimming on receptive fields of MS data and restricts MS evidence associated with following undecoded amino acids. Our approach, DPST, circumvents these limitations with two key components: (1) A confidence value aggregation encoder to sketch spectrum representations according to amino-acid-based connectivity among MS; (2) A global-local fusion decoder to progressively assimilate contextualized spectrum representations with a predefined preconception of localized MS evidence and amino acid priors. Our components originate from a closed-form solution and selectively attend to informative amino-acid-aware MS representations. Through extensive empirical studies, we demonstrate the superiority of DPST, showing that it outperforms state-of-the-art approaches by a margin of 12% - 19% peptide accuracy.