{"entity": "journal", "iuid": "4bf7ff976eb847af9eea9a1b3e926ec3", "timestamp": "2026-07-15T10:41:51.459Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/J%20Comput%20Biol.json"}, "display": {"href": "https://publications.scilifelab.se/journal/J%20Comput%20Biol"}}, "title": "J Comput Biol", "issn": "1557-8666", "issn-l": null, "publications_count": 1, "publications": [{"entity": "publication", "iuid": "3a682dc8e40e4ab78ca0dedf3279a820", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a682dc8e40e4ab78ca0dedf3279a820.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a682dc8e40e4ab78ca0dedf3279a820"}}, "title": "MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall.", "authors": [{"family": "Ogurtsov", "given": "Aleksey", "initials": "A"}, {"family": "Alves", "given": "Gelio", "initials": "G", "orcid": "0000-0002-1595-1445", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2f7c73d0e0041c0a80dcc6d144a06ac.json"}}, {"family": "Rubio", "given": "Alex", "initials": "A"}, {"family": "Joyce", "given": "Brendan", "initials": "B"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB"}, {"family": "Yu", "given": "Yi-Kuo", "initials": "YK"}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "J Comput Biol", "issn": "1557-8666", "volume": "31", "issue": "2", "pages": "175-178", "issn-l": null}, "abstract": "Although many user-friendly workflows exist for identifications of peptides and proteins in mass-spectrometry-based proteomics, there is a need of easy to use, fast, and accurate workflows for identifications of microorganisms, antimicrobial resistant proteins, and biomass estimation. Identification of microorganisms is a computationally demanding task that requires querying thousands of MS/MS spectra in a database containing thousands to tens of thousands of microorganisms. Existing software can't handle such a task in a time efficient manner, taking hours to process a single MS/MS experiment. Another paramount factor to consider is the necessity of accurate statistical significance to properly control the proportion of false discoveries among the identified microorganisms, and antimicrobial-resistant proteins, and to provide robust biomass estimation. Recently, we have developed Microorganism Classification and Identification (MiCId) workflow that assigns accurate statistical significance to identified microorganisms, antimicrobial-resistant proteins, and biomass estimation. MiCId's workflow is also computationally efficient, taking about 6-17 minutes to process a tandem mass-spectrometry (MS/MS) experiment using computer resources that are available in most laptop and desktop computers, making it a portable workflow. To make data analysis accessible to a broader range of users, beyond users familiar with the Linux environment, we have developed a graphical user interface (GUI) for MiCId's workflow. The GUI brings to users all the functionality of MiCId's workflow in a friendly interface along with tools for data analysis, visualization, and to export results.", "doi": "10.1089/cmb.2023.0149", "pmid": "38301204", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Glycoproteomics and MS Proteomics": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10874827"}], "notes": [], "created": "2024-11-01T08:25:10.031Z", "modified": "2024-11-27T16:31:43.763Z"}], "created": "2024-11-01T08:25:10.112Z", "modified": "2024-11-01T08:25:10.112Z"}