Limits...
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.

Show MeSH

Related in: MedlinePlus

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

License
getmorefigures.php?uid=PMC2481425&req=5

Figure 1: 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).

Mentions: The mean peptide length for the 13,779 peptide set was 16, with a range of 6-49 amino acids. There was a bias in the distribution of peptide length, which favored relatively long peptides (Figure 1). A similar finding from human proteome studies was previously reported [12]. The under-representation of short peptides may result from losses due to reduced sequence-specific fragment ions, or difficulty in distinguishing them from noise due to low m/z values. The mean molecular weight of this set was approximately 1,750 Da with a range of 640-4,100 Da. The majority of peptides identified were either neutral or acidic, with an average pI of approximately 6. There were 5958, 8874, 7753, and 5368 distinct peptides identified for the 4 reference sets (Table 1). The number of peptides identified may relate to variability in protein levels between reference sets, particularly for abundant proteins, which affects mass spectrometer peptide sampling and variability in protein recovery with sample processing.


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)

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

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

Figure 1: 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).
Mentions: The mean peptide length for the 13,779 peptide set was 16, with a range of 6-49 amino acids. There was a bias in the distribution of peptide length, which favored relatively long peptides (Figure 1). A similar finding from human proteome studies was previously reported [12]. The under-representation of short peptides may result from losses due to reduced sequence-specific fragment ions, or difficulty in distinguishing them from noise due to low m/z values. The mean molecular weight of this set was approximately 1,750 Da with a range of 640-4,100 Da. The majority of peptides identified were either neutral or acidic, with an average pI of approximately 6. There were 5958, 8874, 7753, and 5368 distinct peptides identified for the 4 reference sets (Table 1). The number of peptides identified may relate to variability in protein levels between reference sets, particularly for abundant proteins, which affects mass spectrometer peptide sampling and variability in protein recovery with sample processing.

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