Figure 1.
A pipeline to identify peptides originating from uncharacterised proteins using LC MS/MS data.
Data are subjected first to identification using ProteinPilot and then filtered according to genome annotation. A subset of predicted novel peptides were then confirmed by addition MS/MS.
Table 1.
Summary of the results obtained from LC-MS/MS analysis of the MCF7 and MCF10A cell lines.
Table 2.
Pipeline predictions.
Figure 2.
Location and nature of novel exon-3′ extending peptide in HNRNPL.
Top: Location of peptide relative to exons. (Blue rectangle: gene; brown rectangles: transcripts; red/white rectangles: exons; red: coding, white: UTR). Bottom: alignment between NP_001128232.1 (hnRNPL isoform a, Rattus norvegicus) and HNRPL_HUMAN , showing location of the candidate peptide, and the retained intron found in the rat, but not the human, sequence.
Table 3.
Pipeline predictions confirmed by comparisons to spectra obtained from synthetic peptides.
Figure 3.
Location and nature of novel integenic peptide relative to Genscan prediction.
Top: the peptide identified by the pipeline is classified as intronic, but is within the Genscan prediction GENSCAN00000020420. Bottom: the predicted protein is similar to hnRNPA1 (RA1L3_HUMAN; BLAST; Expect = 1e−33; 73% Identity).