{"id":"W4417133026","doi":"10.1021/acs.analchem.5c04338","title":"<i>xcms</i> in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem","year":2025,"lang":"en","type":"article","venue":"Analytical Chemistry","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"The Metabolomics Innovation Centre","funders":"German Network for Bioinformatics Infrastructure; European Commission; H2020 Marie Skłodowska-Curie Actions; Simons Foundation","keywords":"Interoperability; Workflow; Software; Preprocessor; Bioconductor; Data pre-processing; Visualization; Modular design; Component (thermodynamics); Data processing","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004273077,0.002938433,0.001457206,0.003208512,0.001171147,0.005269761,0.004389328,0.001903549,0.1172057],"category_scores_gemma":[0.009947044,0.00122486,0.001214575,0.003644233,0.001329934,0.005980563,0.004667563,0.004075271,0.1165753],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001702697,"about_ca_system_score_gemma":0.00321839,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001997568,"about_ca_topic_score_gemma":0.003991108,"domain_scores_codex":[0.9972768,0.0002957085,0.0002216754,0.0005665545,0.001441047,0.0001981699],"domain_scores_gemma":[0.9932566,0.001074703,0.0006070607,0.001376702,0.002993862,0.0006911142],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.000269474,0.00003332849,0.0007491631,0.0006237093,0.00006168518,0.0002000969,0.00007991248,0.0003454796,0.01848529,0.007130674,0.8771918,0.09482947],"study_design_scores_gemma":[0.00004093916,0.00003424649,0.000863881,0.0001207264,0.0000307007,0.0003406137,0.00002691352,0.002333056,0.03493781,0.006740799,0.9544604,0.00006983686],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.004218352,0.003544895,0.4034374,0.01311904,0.00783136,0.0004491522,0.08503335,0.4082558,0.07411066],"genre_scores_gemma":[0.02025158,0.005091117,0.5215924,0.0143255,0.004256408,0.001132798,0.1934875,0.1525428,0.08731992],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.1172057,"threshold_uncertainty_score":0.3920922,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02046208330843912,"score_gpt":0.2836557628464021,"score_spread":0.263193679537963,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}