PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species

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.

Targeted Proteomics to Assess the Response to Anti-Angiogenic Treatment in Human Glioblastoma (GBM)

“…the selection of the surrogate peptides and the normalization procedure of the data). The selection step of surrogate peptides was expedited and facilitated by the use of PeptideManager , a software developed in our laboratory ( 27 ). PeptideManager provides the peptide sequences and available related information of a given protein in a proteome of interest, as well as the occurrence for each peptide sequence within a host/background proteome (mouse or rat such as in the case of xenografts).…”

“…Thus an automated workflow for species specific peptide selection and the precise quantification of protein content in human tumor versus non-neoplastic host cells has been developed. Our in house developed software PeptideManager, released in open-access, provided an efficient and fast solution in this crucial selection step ( 27 ). We have previously applied iTRAQ analysis in GBM xenograft samples, where the species specificity was established a posteriori in the data analysis step ( 24 , 41 ).…”

“…However, in some cases, when only very few peptides (1–2 peptides) suited these criteria, the selection was partly broadened and signature peptides that were present in either rat or mouse proteome were added. To facilitate and expedite this selection step, an in-house software, named PeptideManager , combining data from two protein databases was developed ( 27 ). This software provides the peptide sequences and available related information of a given protein in a proteome of interest as well as the occurrence for each peptide sequences within a host/background proteome.…”

Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using MS-Based Targeted Proteomics

“…PeptidePicker [10] is a web-based workflow to select peptides by providing, amongst further options, the protein accession number and was designed for human and mouse proteomes. PeptideManager [11] is a tool developed to select peptide candidates as protein surrogates from a defined proteome. It was optimized for the use case of xenografts, i.e., human tumors orthotopically implanted into a different species.…”

Elucidation of protein biomarkers for verification of selected biological warfare agents using tandem mass spectrometry

“…Proteotypic peptides are classically defined as "the peptides that uniquely identify each protein and are consistently observed when a sample mixture is interrogated by a (tandem) mass spectrometer" 38 . There are a few software applications available for the in silico digestion and predictive elucidation of proteotypic peptides for the targeted proteomic analysis [39][40][41][42] . For example, Skyline software aids selection of proteotypic peptides for the MRM assay development for the quantitative analysis of target proteins (https://sciex.…”