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. Author manuscript; available in PMC: 2014 Oct 12.

Published in final edited form as: Circ Res. 2013 Aug 21;113(9):1043–1053. doi: 10.1161/CIRCRESAHA.113.301151

The test dataset of the murine mitochondrial proteome containing 111 raw data files was downloaded from the Peptide Atlas Repository¹⁶(PAe000353)¹⁷. A. Compared to a database search workflow (SEQUEST), the COPaKB web service covered 144 shared proteins (78.7%) and an additional 117 identifications (63.9%). The 117 proteins uniquely identified by the COPaKB workflow were categorized according to their Gene Ontology annotations. Among them, 92 proteins had a subcellular location annotation of the mitochondrion with functional implications in metabolism (74), apoptosis (4), transport (3) and unknown (11). Among the 39 proteins identified uniquely with the sequence database search engine, only 7 proteins had a subcellular location annotation of the mitochondrion. B. Mass spectrum corresponding to peptide LFQADNDLPVHLK was identified as belonging to cytochrome c oxidase 7a1 of the mitochondrial electron transport chain complex IV, which was identified by the COPaKB web service. C. The expression profile of cytochrome b-c1 complex subunit 1 (Q9CZ13) in human myocardium was probed by its specific antibody (ID: HPA002815). This image was automatically retrieved by the COPaKB web service from the Human Protein Atlas after its identification. D. Immunofluorescence image of this protein with the same antibody provided organellar resolution of protein expression. With the reference of organellar markers, Q9CZ13 was probed to express in mitochondria.

The test dataset of the murine mitochondrial proteome containing 111 raw data files was downloaded from the Peptide Atlas Repository¹⁶(PAe000353)¹⁷. A. Compared to a database search workflow (SEQUEST), the COPaKB web service covered 144 shared proteins (78.7%) and an additional 117 identifications (63.9%). The 117 proteins uniquely identified by the COPaKB workflow were categorized according to their Gene Ontology annotations. Among them, 92 proteins had a subcellular location annotation of the mitochondrion with functional implications in metabolism (74), apoptosis (4), transport (3) and unknown (11). Among the 39 proteins identified uniquely with the sequence database search engine, only 7 proteins had a subcellular location annotation of the mitochondrion. B. Mass spectrum corresponding to peptide LFQADNDLPVHLK was identified as belonging to cytochrome c oxidase 7a1 of the mitochondrial electron transport chain complex IV, which was identified by the COPaKB web service. C. The expression profile of cytochrome b-c1 complex subunit 1 (Q9CZ13) in human myocardium was probed by its specific antibody (ID: HPA002815). This image was automatically retrieved by the COPaKB web service from the Human Protein Atlas after its identification. D. Immunofluorescence image of this protein with the same antibody provided organellar resolution of protein expression. With the reference of organellar markers, Q9CZ13 was probed to express in mitochondria.