DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000

Runoff and soil erosion of field plots in a subtropical mountainous region of China

Anthropogenic pressure coupled with strong precipitation events and a mountainous landscape have led to serious soil erosion and associated problems in the subtropical climate zone of China. This study analyzes 1576 rainfall-runoff-soil loss events at 36 experimental plots (a total of 148 plot-years of data) under a wide range of conditions in subtropical mountainous areas of China where slope farming is commonly practiced. The plots, which have standardized dimensions, represent five common types of land use and have four different slopes. Event-based analyses show that almost half of the total rainfall caused soil erosion in the study area. The dominant factor controlling the runoff coefficient is the slope gradient rather than the land use type. The maximum soil lossfor crop plots under steep tillage (35 degrees) is 5004 t km(-2) for a single event. Among the common local crops, the average soil loss values increase in the following order: buckwheat cropland (1179 t km(-2) year(-1)) > terraced cropland (1083 t km(-2) year(-1)) > orchard land (1020 t km(-2) year(-1)) > grassland (762 t km(-2) year (-1)) > terraced orchard land (297 t km(-2) year(-1)) > forest and grassland (281 t km(-2) year-(1)). (C) 2017 Elsevier B.V. All rights reserved

A thermoplastic forming map of a Zr-based bulk metallic glass

A thermoplastic forming (TPF) map of a Zr35Ti30Be26.75Cu8.25 bulk metallic glass was constructed through systematic hot-embossing experiments, spanning a wide range of strain rates and temperatures in the supercooled liquid region. By comparison with the corresponding deformation map, it is found that Newtonian flow, non-Newtonian flow and inhomogeneous flow regions correspond well to fully filled, partially filled and non-filled regions, respectively, in the hot-embossing TPF map. Furthermore, the spatio-temporally homogeneous flow facilitates the thermoplastic formabillity of the Zr-based bulk metallic glass, which is rationalized in terms of free volume theory as well as by finite element simulations. Finally, our results are corroborated by potential application tests