IBench: A ground truth approach for advanced validation of mass spectrometry identification method.

ABSTRACT: The discovery of many noncanonical peptides detectable with sensitive mass spectrometry inside, outside, and on cells shepherded the development of novel methods for their identification, often not supported by a systematic benchmarking with other methods. We here propose iBench, a bioinformatic tool that can construct ground truth proteomics datasets and cognate databases, thereby generating a training court wherein methods, search engines, and proteomics strategies can be tested, and their performances estimated by the same tool. iBench can be coupled to the main database search engines, allows the selection of customized features of mass spectrometry spectra and peptides, provides standard benchmarking outputs, and is open source. The proof-of-concept application to tryptic proteome dig

SUBMITTER: Cormican JA 

PROVIDER: S-EPMC10078205 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature