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SpecpeptidOMS allows fast and without a priori peptide identification in a peptidomics context

AI and Bioinformatics

Abstract #214 Posted on27 March 20259 May 2025 9 May 2025 19h26

Abstract

Peptidomics is an emerging field of the omics sciences, that refers to the identification of the pool of peptides present in a biological fluid or tissue. The field has grown rapidly in the past few years because endogenous and non endogenous peptides have been shown to be of great interest. In practice, most studies in peptidomics use software and workflows derived from bottom-up proteomics. However, the peptidome has specificities that distinguish it from the peptides studied in proteomics: peptides have no predictable end while peptides in proteomics are most often derived from the tryptic hydrolysis of proteins; they can be very small and highly modified. We developed SpecPeptidOMS, a software that was specifically designed for peptidomics. It directly aligns peptide fragmentation spectra to whole and undigested protein sequences. Thus, SpecPeptidOMS can perform alignments starting and ending anywhere in the protein sequence. The underlying computational method, which is based on a dynamic programming approach, is highly optimized. As a result, SpecPeptidOMS can process around 12,000 spectra per hour on an off-to-shelf laptop, with alignment performed against the entire human proteome. The results obtained on two different data sets (synthetic nontryptic spectra and HEK293, a well−known proteomics data set) show the ability of SpecPeptidOMS to identify peptides in a peptidomics context. SpecPeptidOMS is open-source, cross-platform (written in java), and freely available.

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Peptidomics is an emerging field of the omics sciences, that refers to the identification of the pool of peptides present in a biological fluid or tissue. The field has grown rapidly in the past few years because endogenous and non endogenous peptides have been shown to be of great interest. In practice, most studies in peptidomics use software and workflows derived from bottom-up proteomics. However, the peptidome has specificities that distinguish it from the peptides studied in proteomics: peptides have no predictable end while peptides in proteomics are most often derived from the tryptic hydrolysis of proteins; they can be very small and highly modified. We developed SpecPeptidOMS, a software that was specifically designed for peptidomics. It directly aligns peptide fragmentation spectra to whole and undigested protein sequences. Thus, SpecPeptidOMS can perform alignments starting and ending anywhere in the protein sequence. The underlying computational method, which is based on a dynamic programming approach, is highly optimized. As a result, SpecPeptidOMS can process around 12,000 spectra per hour on an off-to-shelf laptop, with alignment performed against the entire human proteome. The results obtained on two different data sets (synthetic nontryptic spectra and HEK293, a well−known proteomics data set) show the ability of SpecPeptidOMS to identify peptides in a peptidomics context. SpecPeptidOMS is open-source, cross-platform (written in java), and freely available.

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