Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree Ensembles

Fannes, Thomas; Vandermarliere, Elien; Schietgat, Leander; Degroeve, Sven; Martens, Lennart; Ramon, Jan

doi:10.1021/pr4001114

Cited by 44 publications

(75 citation statements)

References 32 publications

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“…These authors identified amino acids flanking cleavage sites and strongly influencing digestion efficiency. These data were further confirmed by subsequent studies using different datasets 28,35 .…”

supporting

confidence: 70%

DIGESTIF: A Universal Quality Standard for the Control of Bottom-Up Proteomics Experiments

Lebert¹,

Louwagie

Goetze

et al. 2014

J. Proteome Res.

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In bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy, and precision of peptide detection and quantification. Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS proteomic data obtained under different experimental conditions. Here, we describe the design, synthesis, and validation of a universal protein standard, called DIGESTIF, that can be added to any biological sample. The DIGESTIF standard consists of a soluble recombinant protein scaffold to which a set of 11 artificial peptides (iRT peptides) with good ionization properties has been incorporated. In the protein scaffold, the amino acids flanking iRT peptide cleavage sites were selected either to favor or hinder protease cleavage. After sample processing, the retention time and relative intensity pattern of the released iRT peptides can be used to assess the quality of sample workup, the extent of digestion, and the performance of the LC-MS system. Thus, DIGESTIF can be used to standardize a broad spectrum of applications, ranging from simple replicate measurements to large-scale biomarker screening in biomedical applications. ABSTRACTIn bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy and precision of peptide detection and quantification.Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS proteomic data obtained in different experimental conditions. Here, we describe the design, synthesis and validation of a universal protein standard, called DIGESTIF, that can be added to any biological sample. The DIGESTIF standard consists of a soluble recombinant protein scaffold to which a set of 11 artificial peptides (iRT peptides) with good ionization properties has been incorporated. In the protein scaffold, the amino acids flanking iRT peptide cleavage sites were selected to either favor or hinder protease cleavage. After sample processing, the retention time and relative intensity pattern of the released iRT peptides can be used to assess the quality of sample workup, the extent of digestion and the performance of the LC-MS system. Thus, DIGESTIF can be used to standardize a broad spectrum of applications, ranging from simple replicate measurements up to large-scale biomarker screenings in biomedical applications.

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supporting

confidence: 70%

DIGESTIF: A Universal Quality Standard for the Control of Bottom-Up Proteomics Experiments

Lebert¹,

Louwagie

Goetze

et al. 2014

J. Proteome Res.

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“…Software predicting cleavage probabilities exists for many proteases [86], with as usage mode the theoretical digestion of a single protein or mixture. For trypsin, for example, Cleaving prediction with decision trees (CP-DT) uses the positional information of amino acid sequences around the tryptic site to estimate whether or not the protein will be cleaved [88]. By ranking the peptides by the probability that they will occur after tryptic proteolysis, a list of peptides which can be potentially detected is generated.…”

Section: Protease Activitymentioning

confidence: 99%

Designing biomedical proteomics experiments: state-of-the-art and future perspectives

Maes

Kelchtermans

Bittremieux

et al. 2016

Expert Review of Proteomics

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With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters.

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“…The way each step in such pipeline transforms the sample depends on the characteristics on the instrument and its parameter settings. Recently, there is a growing interest in modeling more precisely each of these transformations (see [5] for an illustration on the digest step). The more accurate are such models, the more accurately one can reason about what was in the sample at the beginning based on the output of the detection step at the end of the pipeline.…”

Section: A Case Study In Experimentalmentioning

confidence: 99%