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A mouse plasma peptide atlas as a resource for disease proteomics.

Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, Omenn GS, States DJ, Hanash SM - Genome Biol. (2008)

Bottom Line: A total of 13,779 distinct peptides have been identified with high confidence.The corresponding approximately 3,000 proteins are estimated to span a 7 logarithmic range of abundance in plasma.A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. qing@fhcrc.org

ABSTRACT
We present an in-depth analysis of mouse plasma leading to the development of a publicly available repository composed of 568 liquid chromatography-tandem mass spectrometry runs. A total of 13,779 distinct peptides have been identified with high confidence. The corresponding approximately 3,000 proteins are estimated to span a 7 logarithmic range of abundance in plasma. A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis.

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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/).
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Figure 4: 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/).

Mentions: When the protein products of alternative splice isoforms differ in structure, we expect that the physical properties of these proteins, in particular their fraction location, may vary. Finding evidence for non-neighboring fractions with distinct peptide content for the same protein supports the identification of multiple products from the same gene. Figure 4 illustrates this analysis for the major histocompatibility complex (MHC) H2 K1 K region antigen. Intact proteins were subjected to anion exchange (AX) and reverse phase (RP) chromatography fractionation in this study. Each fraction was then subjected to tryptic digestion and LC-MS/MS analysis. Figure 4 shows the distribution of peptides derived from this gene among the AX and RP chromatography fractions. The unique peptides identified in the major splice isoform and alternative splice variants were found in separate fractions, consistent with translation of the different splice isoforms yielding distinct protein products with distinct physical properties. The MHC H2 K1 K region gene encodes one of the MHC class 1 antigens, which may be altered in tumors [24].


A mouse plasma peptide atlas as a resource for disease proteomics.

Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, Omenn GS, States DJ, Hanash SM - Genome Biol. (2008)

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/).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2481425&req=5

Figure 4: 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/).
Mentions: When the protein products of alternative splice isoforms differ in structure, we expect that the physical properties of these proteins, in particular their fraction location, may vary. Finding evidence for non-neighboring fractions with distinct peptide content for the same protein supports the identification of multiple products from the same gene. Figure 4 illustrates this analysis for the major histocompatibility complex (MHC) H2 K1 K region antigen. Intact proteins were subjected to anion exchange (AX) and reverse phase (RP) chromatography fractionation in this study. Each fraction was then subjected to tryptic digestion and LC-MS/MS analysis. Figure 4 shows the distribution of peptides derived from this gene among the AX and RP chromatography fractions. The unique peptides identified in the major splice isoform and alternative splice variants were found in separate fractions, consistent with translation of the different splice isoforms yielding distinct protein products with distinct physical properties. The MHC H2 K1 K region gene encodes one of the MHC class 1 antigens, which may be altered in tumors [24].

Bottom Line: A total of 13,779 distinct peptides have been identified with high confidence.The corresponding approximately 3,000 proteins are estimated to span a 7 logarithmic range of abundance in plasma.A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. qing@fhcrc.org

ABSTRACT
We present an in-depth analysis of mouse plasma leading to the development of a publicly available repository composed of 568 liquid chromatography-tandem mass spectrometry runs. A total of 13,779 distinct peptides have been identified with high confidence. The corresponding approximately 3,000 proteins are estimated to span a 7 logarithmic range of abundance in plasma. A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis.

Show MeSH
Related in: MedlinePlus