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Publication for Peppy
Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity
[…] spectrometry (LTQ Orbitrap Velos or XL).Spectra were searched against database of six-frame translated genome, a reverse decoy peptide database and contaminant sequences of keratin and trypsin using Peppy™ (2015) : maximumFDR 0.01; precursorTolerance 2000; fragmentTolerance 300; Digestion rules - cleavageAcid R, cleavageAcid K, numberOfMissedCleavages 1; static mods -modC 57.021464, variable mo […]
FSPP: A Tool for Genome Wide Prediction of smORF Encoded Peptides and Their Functions
[…] ify the proper expressed SEPs. FSPP has integrated RiboTaper () to process Ribo-seq and resulted in the translation production sets including SEPs and other proteins longer than 100. On another hand, Peppy () was used to match the MS spectra to the reference genome and obtained the best genomic location for each spectrum. At last, FSPP intersected the two results from Ribo-seq and mass spectrometr […]
Metaproteomics of complex microbial communities in biogas plants
[…] interaction might not be an ‘one way road’. In particular, ‘proteogenomics’ approaches might be applied to assist the annotation of metagenome data using the recently published proteogenomic software Peppy (Risk et al., ). Another option might be the combination of flow cytometry and metaproteomics (Jehmlich et al., ) as cell sorting enriches microbial subpopulations and therefore reduces complexi […]
Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework
[…] ,,− have emerged recently to support such analyses, offering tools for steps within one or more of the modules defined in Figure . Platforms expressly designed for proteogenomic analysis, such as the Peppy software, are also emerging. Although none of these software tools offer the combined flexibility, accessibility, and completeness of our Galaxy-based workflow, many of these programs are well-d […]
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