Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome

In targeted proteomics it is critical that peptides are not only proteotypic but also accurately represent the level of the protein (quantotypic). Numerous approaches are used to identify proteotypic peptides, but quantotypic properties are rarely assessed. We show that measuring ratios of proteotypic peptides across biological samples can be used to empirically identify peptides with good quantotypic properties. We applied this technique to identify quantotypic peptides for 21% of the human kinome.

[1]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[2]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[3]  Susan E Abbatiello,et al.  Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. , 2010, Analytical chemistry.

[4]  John Chilton,et al.  Using iRT, a normalized retention time for more targeted measurement of peptides , 2012, Proteomics.

[5]  Helge Weissig,et al.  Functional interrogation of the kinome using nucleotide acyl phosphates. , 2007, Biochemistry.

[6]  N. Gray,et al.  In situ kinase profiling reveals functionally relevant properties of native kinases. , 2011, Chemistry & biology.

[7]  Ruedi Aebersold,et al.  Proteomics meets the scientific method , 2013, Nature Methods.

[8]  Brendan MacLean,et al.  Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .

[9]  Craig Lawless,et al.  Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy , 2011, Proteomics.

[10]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[11]  Ruedi Aebersold,et al.  High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , 2010, Nature Methods.

[12]  Ruedi Aebersold,et al.  Options and considerations when selecting a quantitative proteomics strategy , 2010, Nature Biotechnology.

[13]  Daniel B. Martin,et al.  Computational prediction of proteotypic peptides for quantitative proteomics , 2007, Nature Biotechnology.

[14]  Henry H. N. Lam,et al.  A database of mass spectrometric assays for the yeast proteome , 2008, Nature Methods.

[15]  Luis Mendoza,et al.  PASSEL: The PeptideAtlas SRMexperiment library , 2012, Proteomics.

[16]  R. Beavis,et al.  An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC , 2004, Molecular & Cellular Proteomics.

[17]  R. Aebersold,et al.  Selected reaction monitoring for quantitative proteomics: a tutorial , 2008, Molecular systems biology.

[18]  R. Aebersold,et al.  Scoring proteomes with proteotypic peptide probes , 2005, Nature Reviews Molecular Cell Biology.

[19]  William Stafford Noble,et al.  Semi-supervised learning for peptide identification from shotgun proteomics datasets , 2007, Nature Methods.

[20]  S. Carr,et al.  Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry , 2013, Nature Methods.

[21]  Brendan MacLean,et al.  Rapid empirical discovery of optimal peptides for targeted proteomics , 2011, Nature Methods.

[22]  Ruedi Aebersold,et al.  Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry , 2011, Molecular & Cellular Proteomics.

[23]  Henry H. N. Lam,et al.  PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , 2008, EMBO reports.

[24]  Robertson Craig,et al.  Open source system for analyzing, validating, and storing protein identification data. , 2004, Journal of proteome research.

[25]  Johannes Griss,et al.  The Proteomics Identifications (PRIDE) database and associated tools: status in 2013 , 2012, Nucleic Acids Res..

[26]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[27]  B. Garcia,et al.  Proteomics , 2011, Journal of biomedicine & biotechnology.