Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses of the longissimus thoracis of yaks

Quantitative N-Glycoproteomic Analysis of Cattle-Yak and Yak Longissimus Thoracis

“…MS/MS data were retrieved via MaxQuant 1.5.2.8. The database was Bos_mutus_72004 (Bos mutus, Taxon ID: , 18553 sequences), inverse libraries were added to calculate the false discovery rate (FDR) due to random matches, and common contaminating libraries were added to the database . The minimum peptide length was set to 7 amino acid residues and the maximum number of peptide modifications was set to 5.…”

“…After centrifugation at 4 °C for 15 min (4000× g ), the unbound nonglycopeptides were washed using the enrichment buffer three times. Then, the bound glycopeptides were washed from the HILIC column with 10% acetonitrile . Subsequently, the collected and dried glycopeptides were resolved in 50 μL of NH 4 HCO 3 (40 mmol/L) and deglycosylated by adding 2 μL of PNGase F (200 units; Roche, 11365185001, Mannheim, Germany) and incubated overnight at 37 °C.…”

“…Then, the bound glycopeptides were washed from the HILIC column with 10% acetonitrile. 17 Subsequently, the collected and dried glycopeptides were resolved in 50 μL of NH 4 HCO 3 (40 mmol/L) and deglycosylated by adding 2 μL of PNGase F (200 units; Roche, 11365185001, Mannheim, Germany) and incubated overnight at 37 °C. Finally, they were desalted with C18 ZipTips and freeze-dried under a vacuum.…”

“…Recently, the N-glycosites of myofibrillar proteins (tilapia, golden pompano, and skipjack tuna) were identified and compared, and results suggested that N-glycosylation could be related to the solubility and emulsifying activity of fish meat . For livestock meat, we identified 204 N-glycoproteins (285 N-glycosites) from yak longissimus thoracis (YLT), which are mainly related to the remodeling of the extracellular matrix (ECM) and are the main contributors to yak muscle formation . This is only a preliminary understanding of N-glycoproteins in YLT, and there are many important N-glycoproteins whose roles in the differences in meat formation between cattle-yak longissimus thoracis (CYLT) and YLT deserve further investigation, particularly the various glycoproteins located in the extracellular matrix and the protein hydrolases that influence the process of muscle aging.…”

Quantitative Proteomic Analysis of Yorkshire Pig Liver Reveals Its Response to High Altitude

“…To improve the effective utilization of the mass spectrum, the automatic gain control (AGC) was set to 1E5, the signal threshold was set to 8.3E4 ions/s, the maximum injection time was set to 60 ms, and the dynamic exclusion time of the tandem mass spectrometry scan was set to 30 s to avoid repeated scanning of the parent ions. 16,17 Secondary mass spectrometry data were retrieved using Maxquant ( v 1 . 6 .…”