GO-PEI-Au-L-Cys composites were synthesized via loading gold nanoparticles on a GO surface using polyethylenimine as reducing and stabilizing reagents, followed by L-cysteine immobilization through an Au-S bond. The composites were applied as a kind of novel ZIC-HILIC material to achieve highly selective enrichment of glycopeptides from biological samples.

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Discovering differentially expressed proteins in various biological samples requires proteome quantification methods with accuracy, precision, and wide dynamic range. This study describes a mass defect-based pseudo-isobaric dimethyl labeling (pIDL) method based on the subtle mass defect differences between 12 C/ 13 C and 1 H/ 2 H. Lys-C protein digests were labeled with CD 2 O/ 13 CD 2 O and reduced with NaCNBD 3 /NaCNBH 3 as heavy and light isotopologues, respectively. The fragment ion pairs with mass differences of 5.84 mDa were resolved by high-resolution tandem mass spectrometry (MS/MS) and used for quantification. The pIDL method described here resulted in highly accurate and precise quantification results with approximately 100-fold dynamic range. Furthermore, the pIDL method was extended to 4-plex proteome quantification and applied to the quantitative analysis of proteomes from Hca-P and Hca-F, two mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates.M ethods of stable-isotope incorporation with mass spectrometry (MS)-based proteome quantification have advanced rapidly in the past decade. Peptide samples can be differentially tagged with heavy or light isotopes by metabolic labeling 1,2 or chemical labeling. 3,4 The mass differences can be distinguished at either the MS or tandem mass spectrometry (MS/MS) level. Dimethyl labeling, 3 a chemical labeling method, is widely used for proteome quantification at the MS level. Several advantages of this method include quick reaction, high labeling efficiency, low cost, and applicability to different types of samples including tissues, cells, and body fluids. 5 Isobaric tags for relative and absolute quantitation (iTRAQ), 4 an MS/MS-based method, allows the proteome quantification of up to eight samples simultaneously and provides more precise quantification results than the MS level quantification method. 6,7 Although these strategies have been widely used for proteome quantification, their accuracy and dynamic range are limited by the signal-tonoise ratio and the increased MS spectral complexity leads to fewer quantified proteins for MS level-based quantification approaches. 8 In addition, ratio distortion caused by precursor interference is common for MS/MS level-based quantification methods. 9,10 To solve these problems, several innovative methods have been recently developed. Isobaric peptide termini labeling (IPTL) 11−13 is an elegant solution in which the amino groups of the N-termini and C-termini of Lys-C protein digests were crosswise labeled with heavy/light isotope reagents according to the slightly different chemical properties of α-and ε-NH 2 . Fragment ion pairs specific to the labeled peptides were used for peptide/protein quantification. Although IPTL improved the quantification accuracy compared to other reported MS/ MS level methods, the side reactions that are inherent in the multistep labeling can adversely affect quantification accuracy and dynamic range. 12 NeuCode SILAC 14 is another st...

Background: Urinary extracellular vesicles (uEVs) are secreted into urine by cells from the kidneys and urinary tract. Although changes in uEV proteins are used for quantitative assessment of protein levels in the kidney or biomarker discovery, whether they faithfully reflect (patho)physiological changes in the kidney is a matter of debate. Methods: Mass spectrometry was used to compare in an unbiased manner the correlations between protein levels in uEVs and kidney tissue from the same animal. Studies were performed on rats fed a normal or a high K+ diet. Results: Absolute quantification determined a positive correlation (Pearson R=0.46 or 0.45, control or high K+ respectively, p<0.0001) between the ~ 1000 proteins identified in uEVs and corresponding kidney tissue. Transmembrane proteins had greater positive correlations relative to cytoplasmic proteins. Proteins with high correlations (R>0.9), included exosome markers Tsg101 and Alix. Relative quantification highlighted a monotonic relationship between altered transporter/channel abundances in uEVs and the kidney following dietary K+ manipulation. Analysis of genetic mouse models also revealed correlations between uEVs and kidney. Conclusion: This large-scale unbiased analysis identifies uEV proteins that track the abundance of the parent proteins in the kidney. The data form a novel resource for the kidney community and support the reliability of using uEV protein changes to monitor specific physiological responses and disease mechanisms.

ABSTRACT:An integrated sample pretreatment system, composed of a click maltose hydrophilic interaction chromatography (HILIC) column, a strong cation exchange (SCX) precolumn, and a PNGase F immobilized enzymatic reactor (IMER), was established for the simultaneous glycopeptide enrichment, sample buffer exchange, and online deglycosylation, by which the sample pretreatment for glycoproteome could be performed online automatically, beneficial to improve the efficiency and sensitivity of the N-linked glycosylation site identification. With such a system, the deglycosylated glycopeptide from the digests of avidin with the coexistence of 50 times (mass ratio) BSA could be selectively detected, and the detection limit as low as 5 fmol was achieved. Moreover, the sample pretreatment time was significantly shortened to ∼1 h. Such a system was further successfully applied for analyzing the digest of the soluble fraction extracted from rat brain. A total of 120 unique glycoprotein groups and 196 N-linked glycosylation sites were identified by nanoreversed phase liquid chromatographyÀelectrospray ionization-tandem mass spectrometry (nanoRPLC-ESI-MS/MS), with the injected digests amount as 6 μg. All these results demonstrate that the integrated system is of great promise for N-linked glycosylation site profiling and could be further online coupled with nanoHPLC-ESI-MS/MS to achieve high-throughput glycoproteome analysis. N -glycosylation is one of the most common and complex posttranslational modification of proteins and plays an important role in cellÀcell interaction, signal transduction, cancer immunology, and so forth. 1À4 The global mapping of the N-linked glycosylation site, which generally falls into the canonical N-!P-S/T (where !P denotes any amino acid except proline) sequence motif, is a prerequisite for fully understanding the biological functions of N-linked glycoproteins. Mass spectrometry (MS) coupled with chromatography has become an effective tool for analyzing N-linked glycoproteins and glycosylation sites in particular.5À9 However, the low abundance of glycopeptides relative to the large excess of nonglycosylated peptides as well as their low ionization efficiency often result in signal suppression when subjected to MS analysis.10 Therefore, the development of a fast and specific protocol to enrich glycopeptides prior to MS becomes indispensable.

The importance of the kidney distal convoluted tubule (DCT) and cortical collecting duct (CCD) is highlighted by various water and electrolyte disorders that arise when the unique transport properties of these segments are disturbed. Despite this critical role, little is known about which proteins have a regulatory role in these cells and how these cells can be regulated by individual physiologic stimuli. By combining proteomics, bioinformatics, and cell biology approaches, we found that the E3 ubiquitin ligase CHIP is highly expressed throughout the collecting duct; is modulated in abundance by vasopressin; interacts with aquaporin-2 (AQP2), Hsp70, and Hsc70; and can directly ubiquitylate the water channel AQP2 shRNA knockdown of CHIP in CCD cells increased AQP2 protein and reduced AQP2 ubiquitylation, resulting in greater levels of AQP2 and phosphorylated AQP2. CHIP knockdown increased the plasma membrane abundance of AQP2 in these cells. Compared with wild-type controls, CHIP knockout mice or novel CRISPR/Cas9 mice without CHIP E3 ligase activity had greater AQP2 abundance and altered renal water handling, with decreased water intake and urine volume, alongside higher urine osmolality. We did not observe significant changes in other water- or sodium-transporting proteins in the gene-modified mice. In summary, these results suggest that CHIP regulates AQP2 and subsequently, renal water handling.

In normal individuals, the epithelium of the colon absorbs 1.5–2 l of water a day to generate dehydrated feces. However, in the condition of bile acid malabsorption (BAM), an excess of bile acids in the colon results in diarrhea. Several studies have attempted to address the mechanisms contributing to BAM induced by various bile acids. However, none have addressed a potential dysregulation of aquaporin (AQP) water channels, which are responsible for the majority of transcellular water transport in epithelial cells, as a contributing factor to the onset of diarrhea and the pathogenesis of BAM. In this study, we aimed to systematically analyze the expression of AQPs in colonic epithelia from rat, mouse, and human and determine whether their expression is altered in a rat model of BAM. Mass spectrometry-based proteomics, RT-PCR, and western blotting identified various AQPs in isolated colonic epithelial cells from rats (AQP1, 3, 4, 7, 8) and mice (AQP1, 4, 8). Several AQPs were also detected in human colon (AQP1, 3, 4, 7–9). Immunohistochemistry localized AQP1 to the apical plasma membrane of epithelial cells in the bottom of the crypts, whereas AQP3 (rat, human) and AQP4 (mice, human) were localized predominantly in the basolateral plasma membrane. AQP8 was localized intracellularly and at the apical plasma membrane of epithelial cells. Rats fed sodium cholate for 72 h had significantly increased fecal water content, suggesting development of BAM-associated diarrhea. Colonic epithelial cells isolated from this model had significantly altered levels of AQP3, 7, and 8, suggesting that these AQPs may be involved in the pathogenesis of bile acid-induced diarrhea.