Journal: Journal of Proteome Research
Article Title: Comprehensive Protein Inference Analysis with PyProteinInference Elucidates Biological Understanding of Tandem Mass Spectrometry Data
doi: 10.1021/acs.jproteome.4c00734
Figure Lengend Snippet: Upset plot showing the overlap of identified proteins at a 1% protein false discovery rate (FDR) from the K562 whole cell lysate data set. The X axis indicates the individual method or overlapping methods examined, while the Y axis indicates the intersection size between methods on the X axis. Peptide-centric protein groups are expanded out to individual proteins to facilitate comparisons to other methods that only output protein group leads; individual methods show total counts for comparison purposes (not only counts unique to the method).
Article Snippet: For algorithm validation of pyProteinInference, 0.5 μg of K562 whole cell lysate (Promega, Madison WI; Catalog #V6951 was loaded into a 25 cm × 75 μm ID, 1.6 μm C18 IonOpticks Aurora Series column (IonOpticks, AUR2-25075C18A) on a Thermo UltiMate 3000 high-performance liquid chromatography (HPLC) system (Thermo Fisher Scientific) at a flow rate of 400 nl min –1 .
Techniques: Comparison