Characterization of distinct peptides identified from mouse plasma reference sets. The histogram of peptide length of unique sequences in mouse PeptideAtlas (blue) is overlaid on an in silico tryptic digest of the IPI mouse database (black).

Peptide identification and distribution of mouse EGFR. A total of 34 distinct peptides were identified from approximately 4,000 MS2 events. All peptides are from the extracellular domain.

Genomic mapping of mouse peptide LLEAQIATGGIIDPK using UCSC Blast program. Mouse splice variant M13C2563_1_s386_e8960_1_rf2_c1_n0 was identified with 13 distinct peptides. Twelve peptides matched a predicted mouse protein similar to desmoplakin using a homolog search against the NCBI NR database. However, all 13 peptides were homologous to the human desmoplakin sequence. Of note, mouse peptide LLEAQIATGGIIDPK aligns to the coding sequence of human desmoplakin, but not to the annotated mouse desmoplakin gene.

IPAS mapping of splice isoform variants for the MHC H2 K1 K gene. Intact proteins were subjected to anion exchange (AX) and reverse phase (RP) chromatography fractionation. Each fraction was then subjected to tryptic digestion and LC-MS/MS analysis. Peptides derived from novel exons falling within the MHC 2 K1 K gene were identified. Spectral counts for matching peptides derived from this gene are plotted as a function of AX and RP fractionation. The color of each cell indicates the number of matching spectra: black = high; gray = medium; light gray = low; white = zero. (a) The distribution of spectra matching the major annotated splice isoform (ENSMUST00000025181). (b) The distribution of spectra matching the novel splice isoform (M17C4317_13_s2_e917_1_rf2_c1_n0|). (c) The distribution of spectra matching peptides found in both the major annotated splice isoform for this gene (ENSMUST00000025181) and the novel splice isoform (M17C4317_13_s2_e917_1_rf2_c1_n0|).