Evaluation of Data Analysis Strategies for Improved Mass Spectrometry-Based Phosphoproteomics

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target-decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target-decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The "picked" protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The "picked" target-decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used "classic" protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software.

Molecular changes in Opisthorchis viverrini (Southeast Asian liver fluke) during the transition from the juvenile to the adult stage

Background

The Southeast Asian liver fluke (Opisthorchis viverrini) chronically infects and affects tens of millions of people in regions of Asia, leading to chronic illness and, importantly, inducing malignant cancer ( = cholangiocarcinoma). In spite of this, little is known, at the molecular level, about the parasite itself, its interplay with its hosts or the mechanisms of disease and/or carcinogenesis.

Methodology/Principal Findings

Here, we generated extensive RNA-Seq data (Illumina) representing adult and juvenile stages of O. viverrini, and combined these sequences with previously published transcriptomic data (454 technology) for this species, yielding a combined assembly of significantly increased quality and allowing quantitative assessment of transcription in the juvenile and adult stage.

Conclusions

This enhanced assembly reveals that, despite the substantial biological similarities between the human liver flukes, O. viverinni and Clonorchis sinensis, there are previously unrecognized differences in major aspects of their molecular biology. Most notable are differences among the C13 and cathepsin L-like cysteine peptidases, which play key roles in tissue migration, immune evasion and feeding, and, thus, represent potential drug and/or vaccine targets. Furthermore, these data indicate that major lineages of cysteine peptidases of socioeconomically important trematodes have evolved through a process of gene loss rather than independent radiation, contrasting previous proposals.

Opistorchis viverrini is an important and neglected parasite affecting ∼9 million people in South-east Asia. The parasite has a complex life-cycle which involves an intermediate phase in cyprinoid fishes. Consumption of raw or under-cooked fish infected with the metacercarial (larval) stage of O. viverreni results in infection, with adult worms living primarily in the intra-hepatic bile duct. In addition to the affects of the infection itself, O. viverrini is directly carcinogenic, with up to 70% of infected individuals in endemic regions developing malignant cholangiocarcinomas. Control of the parasite relies exclusively on the use of praziquantel and little is known about the mechanisms through which O. viverrini stimulates carcinogenesis. An improved understanding of the molecular biology of O. viverrini is urgently needed. In our study, we employed RNAseq technology to assess changes in gene transcription during the development of O. viverrini within the definitive host, and significantly improved the characterization of the transcriptome of this parasite. In so doing, we shed new light on the evolution of a major group proteins (i.e., the cysteine peptidases) which, given their important function roles as excreted/secreted molecules, have been proposed as attractive drug/vaccine targets for a wide-range of neglected flukes, including species of Opistorchis, Clonorchis, Schistosoma and Fasciola.

A selective inhibitor reveals PI3Kγ dependence of T(H)17 cell differentiation

We devised a high-throughput chemoproteomics method that enabled multiplexed screening of 16,000 compounds against native protein and lipid kinases in cell extracts. Optimization of one chemical series resulted in CZC24832, which is to our knowledge the first selective inhibitor of phosphoinositide 3-kinase γ (PI3Kγ) with efficacy in in vitro and in vivo models of inflammation. Extensive target- and cell-based profiling of CZC24832 revealed regulation of interleukin-17-producing T helper cell (T(H)17) differentiation by PI3Kγ, thus reinforcing selective inhibition of PI3Kγ as a potential treatment for inflammatory and autoimmune diseases.