Article

On the impact of the pangenome and annotation discrepancies while building protein sequence databases for bacteria proteogenomics

2018-07-26

Abstract excerpt

In proteomics, peptide information within mass spectrometry data from a specific organism sample is routinely challenged against a protein sequence database that best represent such organism. However, if the species/strain in the sample is unknown or poorly genetically characterized, it becomes challenging to determine a database which can represent such sample. Building customized protein sequence databases mergi...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 34fc6b92-1124-5a1b-a9c0-72b3891df839
DOI: 10.1101/378117

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

On the impact of the pangenome and annotation discrepancies while building protein sequence databases for bacteria proteogenomicsDOI 10.1101/378117Read

Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database.Semantic proximity Read

Large scale analysis of amino acid substitutions in bacterial proteomics.Semantic proximity Read

Stringent proteogenomic discovery of novel small proteins in <i>Mycobacterium tuberculosis</i> clinical reference strainsSemantic proximity Read

Proteogenomic Analysis of Mycobacterium tuberculosis By High Resolution Mass Spectrometry*Semantic proximity Read

Rapid identification and classification of Mycobacterium spp. using whole-cell protein barcodes with matrix assisted laser desorption ionization time of flight mass spectrometry in comparison with multigene phylogenetic analysis.Semantic proximity Read

Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates.Semantic proximity Read

Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomicsSemantic proximity Read

Rise of Clinical Microbial Proteogenomics: A Multiomics Approach to Nontuberculous Mycobacterium-The Case of Mycobacterium abscessus UC22.Semantic proximity Read

Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains.Semantic proximity Read

Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis.Semantic proximity Read

Comparative genomics: the bacterial pan-genome.Semantic proximity Read

Hortense: Horizontal gene transfer detection directly from proteomic MS/MS dataSemantic proximity Read