Abstract
The search for clinically useful protein biomarkers using advanced mass spectrometry approaches represents a major focus in cancer research. However, the direct analysis of human samples may be challenging due to limited availability, the absence of appropriate control samples, or the large background variability observed in patient material. As an alternative approach, human tumors orthotopically implanted into a different species (xenografts) are clinically relevant models that have proven their utility in pre-clinical research. Patient derived xenografts for glioblastoma have been extensively characterized in our laboratory and have been shown to retain the characteristics of the parental tumor at the phenotypic and genetic level. Such models were also found to adequately mimic the behavior and treatment response of human tumors. The reproducibility of such xenograft models, the possibility to identify their host background and perform tumor-host interaction studies, are major advantages over the direct analysis of human samples. At the proteome level, the analysis of xenograft samples is challenged by the presence of proteins from two different species which, depending on tumor size, type or location, often appear at variable ratios. Any proteomics approach aimed at quantifying proteins within such samples must consider the identification of species specific peptides in order to avoid biases introduced by the host proteome. Here, we present an in-house methodology and tool developed to select peptides used as surrogates for protein candidates from a defined proteome (e.g., human) in a host proteome background (e.g., mouse, rat) suited for a mass spectrometry analysis. The tools presented here are applicable to any species specific proteome, provided a protein database is available. By linking the information from both proteomes, PeptideManager significantly facilitates and expedites the selection of peptides used as surrogates to analyze proteins of interest.
Highlights
INTRODUCTIONMass spectrometry(MS)-based proteomics provides various approaches (i.e., shotgun, supervised and targeted approaches) (Domon and Aebersold, 2010) in the field of cancer research (Smith, 2012; Deracinois et al, 2013; Marx, 2013) and is nowadays widely used in pre-clinical and clinical investigations (Lee et al, 2011), and for biomarker studies (Li et al, 2011; Meng and Veenstra, 2011; Pan et al, 2012; Waldemarson et al, 2012)
Animal models consisting in the orthotopical implantation of human tumors into animals have proven their utility as relevant models in many studies (Whiteaker et al, 2007; Huszthy et al, 2012; Tang et al, 2012; Klink et al, 2013)
The tool PeptideManager was designed to: (1) build and store peptide databases from public repositories, (2) link available information (e.g., post-translational modifications (PTMs) sites, single-nucleotide polymorphisms (SNPs), signal peptide) from public databases at the peptide level, (3) allow queries and peptide pre-selection within those databases, and most importantly (4) perform peptide pre-selection within a given proteome of interest while taking into account the presence of another species proteome within the sample (Figure 2)
Summary
Mass spectrometry(MS)-based proteomics provides various approaches (i.e., shotgun, supervised and targeted approaches) (Domon and Aebersold, 2010) in the field of cancer research (Smith, 2012; Deracinois et al, 2013; Marx, 2013) and is nowadays widely used in pre-clinical and clinical investigations (Lee et al, 2011), and for biomarker studies (Li et al, 2011; Meng and Veenstra, 2011; Pan et al, 2012; Waldemarson et al, 2012). Various tools are currently available for the theoretical or semiempirical estimation of the proteotypic properties of a peptide sequence including the digestion efficacy according to the cleavage site (Kuster et al, 2005; Mallick et al, 2007; Fusaro et al, 2009; Eyers et al, 2011; Lawless and Hubbard, 2012; Mohammed et al, 2014; Qeli et al, 2014) These tools do not handle samples containing proteins from multiple species that require a very time-consuming manual selection of surrogate peptide candidates. The tool PeptideManager was designed to: (1) build and store peptide databases from public repositories, (2) link available information (e.g., PTM sites, SNPs, signal peptide) from public databases at the peptide level, (3) allow queries and peptide pre-selection within those databases, and most importantly (4) perform peptide pre-selection within a given proteome of interest while taking into account the presence of another species proteome within the sample (Figure 2)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
