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Communication Dans Un Congrès Année : 2021

SpecOMS, an open modification search approach challenging high-throughput single amino acid variations identification

Résumé

Proteomics studies are based on the identification of proteins. Although biochemistry assays and bioinformatics strategies have made significant advances in this field, they are still unaware of a comprehensive solution. Generally, the protein identification methodology consists of spectrum similarity search by comparing an experimentally acquired fragmentation spectrum against a theoretical spectrum derived from a protein sequence database. Additionally, to process a large universe of pairwise comparisons, most search engines start by selecting theoretical peptides based on their mass. Since the mass modifications must be declared in advance, it represents a challenge to identify unknown post-translation modifications (PTMs) and single nucleotide variants (SAVs). The Open Modification Search algorithms (OMS) use fast calculation methods to identify proteins without holding the mass precursor. Also, the expected mass changes do not need to be declared in advance. In this approach, the first step is to identify all peptides, then the second step is to interpret the mass delta between the precursor ion and the theoretical peptide in terms of PTM or SAV. In this work, we used the OMS algorithm called SpecOMS with the aim to evaluate its performance for SAVs identification. We compare our results with those obtained from X!Tandem, which uses a classic approach to identify peptides. A gold standard dataset was used: four corn lineages (Zea mays - B73, F2, EA1192, and MBS847), each one already sequenced. In order to evaluate the ability of SpecOMS in identifying SAVs, we performed self and cross-interrogations over the databases. The false discovery rate (FDR) estimation was implemented to qualify the peptide spectrum match (PSM). Finally, we will present our results in terms of the FDR implementation, refinement parameters and the performance of SpecOMS to identify SAVs.
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Dates et versions

hal-03879763 , version 1 (30-11-2022)

Identifiants

  • HAL Id : hal-03879763 , version 1

Citer

Luciana de Oliveira, Olivier Langella, Thierry Balliau, Dominique Tessier, Melisande Blein-Nicolas, et al.. SpecOMS, an open modification search approach challenging high-throughput single amino acid variations identification. 4th INPPO Conference, Mar 2021, Visioconférence, France. ⟨hal-03879763⟩
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