Comparison of fractionation strategies for offline two-dimensional liquid chromatography tandem mass spectrometry analysis of proteins from mouse adipose tissue

Optimization of reversed-phase solid-phase extraction for shotgun proteomics analysis

Reversed-phase solid-phase extraction (SPE) is the method of choice for the purification of proteomics samples. Even though the efficacy of SPE methods is sample type-dependent, the manufacturers' protocols are used in most studies. Using an optimized SPE method can lead to a substantial gain in identification and recovery. In this tutorial, we give a brief introduction to the most important parameters influencing SPE performance, and we present a short workflow (16 measurements) for optimizing the SPE procedure. This is complemented by method performance assessment instructions and a short troubleshooting guide to help users further understand and investigate their SPE methods.

Segmented two-dimensional liquid chromatography. Proof of concept study

The separation in liquid chromatography is defined either by the space domain where it proceeds until the least retained analyte reaches the outlet of the column or by the time when individual analytes elute out of the column. These two approaches lead to the four possible combinations of two-dimensional liquid chromatography with online space x time coupling being the least experimentally feasible. Here, we show the development of a novel two-dimensional liquid chromatography method combining separation defined by space and the conventional elution-based separation. First-dimension column consisted of four capillary segments coupled serially via two-position six-port valves allowing an online and comprehensive transfer of analytes from the first to the second dimension. After initial experiments using homemade monolithic capillary columns, we tested commercially available columns in both dimensions. We ended with the combination of packed capillary columns in the first dimension and monolithic capillary column in the second dimension. We used a reversed-phase retention mechanism in the first spatial dimension, while HILIC was in the second, time-based dimension. We also developed a theoretical model to describe the proposed two-dimensional separation that was further confirmed by utilizing both an isocratic and gradient elution in the second dimension. Finally, we applied our experimental setup to separate neurotransmitters contained in human urine.

Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs

Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs’ expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.

Recovery and quantification of a myelin oligodendrocyte glycoprotein peptide from rat plasma after protein precipitation

The recovery of high molecular weight peptides from complex biological samples is a challenging task. Herein, a reliable, cost effective and rapid methodology was developed for the recovery and quantification of a myelin oligodendrocyte glycoprotein epitope namely (LysGly)₅MOG_35-55, from rat plasma. Removal of plasma proteins before quantification of the peptide was achieved after precipitation by an acetonitrile/water/formic acid solution. Using the developed protocol, average recoveries of the peptide from plasma ranged between 83.3 and 90.3%.