PMC:6599329 / 33935-35137 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/6599329","sourcedb":"PMC","sourceid":"6599329","source_url":"https://www.ncbi.nlm.nih.gov/pmc/6599329","text":"Data analysis\nProteinLynx Global SERVER™ (PLGS) v2.5.3 (Waters, Altrincham, UK) was used to analyze the acquired ion mobility enhanced MSE spectra for protein identification as well as for the label-free relative protein quantification. Data processing and parameter setups were carried out as followed by [44]. The sequence database of the reference strain E. faecalis V583 (NCBI Reference Sequence: NC_004668.1) was used for database search. The false positive rate (FPR) was set to 4% with a randomized database, appended to the original one. The parameters for protein identification were made in such a way that a peptide was required to have at least one fragment ion match, a protein was required to have at least three fragment ion matches, and two peptide matches for identification. The peptides with 50% or more probability to be present in the mixture and detected with a score above 20, as calculated by the software were selected for proteomic analysis [45]. Data sets were normalized using the ‘internal standard-normalization’ function of PLGS and label-free quantitative analysis was performed by comparing the normalized peak area/intensity of identified peptides between the samples.","divisions":[{"label":"title","span":{"begin":0,"end":13}}],"tracks":[{"project":"2_test","denotations":[{"id":"31253082-24856245-12221393","span":{"begin":307,"end":309},"obj":"24856245"},{"id":"31253082-18936059-12221394","span":{"begin":968,"end":970},"obj":"18936059"}],"attributes":[{"subj":"31253082-24856245-12221393","pred":"source","obj":"2_test"},{"subj":"31253082-18936059-12221394","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecd393","default":true}]}]}}