Figure 1.

Gene view: display of genomic peptide matches. The figure depicts an example of how genomic matches of peptides from a single experiment are dealt with. Gene ENSG00000171467 (top), which has three possible transcripts/proteins (middle), was matched by several peptides obtained from an experiment. Of all the three transcripts, ENSP00000354964 was the one containing the highest number of peptides, even though none of them was unique for this protein. Therefore, ENSP00000354964 was considered to be part of the minimal list (peptides highlighted in red). However, it may be that the peptide patterns could be explained by the presence of the other two transcripts that are not included in the minimal list (peptides in green). However, even though more information would be needed to confirm either scenario, the raw data are kept for the users to draw their own conclusions. Peptides matching to proteins from other genes are shown at the bottom of the figure. Some of these protein/genes matched additional peptides and therefore they were included in the minimal list (red) whereas others did not (green). The latter assignments could thus be considered spurious.