AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results

Time-consuming and experience-dependent manual validations of tandem mass spectra are usually applied to SEQUEST results. This inefficient method has become a significant bottleneck for MS/MS data processing. Here we introduce a program AMASS (advanced mass spectrum screener), which can filter the tandem mass spectra of SEQUEST results by measuring the match percentage of high-abundant ions and the continuity of matched fragment ions in b, y series. Compared with Xcorr and DeltaCn filter, AMASS can increase the number of positives and reduce the number of negatives in 22 datasets generated from 18 known protein mixtures. It effectively removed most noisy spectra, false interpretations, and about half of poor fragmentation spectra, and AMASS can work synergistically with Rscore filter. We believe the use of AMASS and Rscore can result in a more accurate identification of peptide MS/MS spectra and reduce the time and energy for manual validation.     

Identification and characterization of cow's milk proteins from the rat intestinal lymph using a proteomic strategy

Food proteins were considered to be absorbed into the body after being digested to amino acids, dipeptides, and tripeptides. However, there are studies indicating that some proteins can pass through the intestinal epithelium under normal physiological conditions, perhaps not in sufficient quantities to be of nutritional importance, but in quantities that may be antigenically or biologically active. In the present study, rat intestinal lymph samples were collected using a modified lymph fistula rat model in fasting and cow's milk postprandial states. Low molecular weight proteins were enriched by ultrafiltration and differential solubilization, separated by 1D‐SDS‐PAGE, digested in‐gel based on molecular weight, and identified using nano‐LC‐MS/MS. In the postprandial rat intestinal lymph, nine bovine‐specific proteins (false discovery rate ≤1%) were identified in different molecular weight regions. Most proteins identified in lymph were highly abundant proteins in the milk, such as β‐lactoglobulin and caseins. Seven of the nine identified bovine‐specific proteins are allergens in milk. This strategy can be used to search for proteins that can enter the intestinal lymph and analyze their common features. Understanding the common features of these proteins might help to develop protein drugs taken orally, so that therapeutic proteins might embody fusion domains for cross‐barrier transport or translocation.     

Screening E3 Substrates Using a Live Phage Display Library

Ubiquitin ligases (E3s) determine specificity of ubiquitination by recognizing target substrates. However, most of their substrates are unknown. Most known substrates have been identified using distinct approaches in different laboratories. We developed a high-throughput strategy using a live phage display library as E3 substrates in in vitro screening. His-ubiquitinated phage, enriched with Ni-beads, could effectively infect E. coli for amplification. Sixteen natural potential substrates and many unnatural potential substrates of E3 MDM2 were identified through 4 independent screenings. Some substrates were identified in different independent experiments. Additionally, 10 of 12 selected candidates were ubiquitinated by MDM2 in vitro, and 3 novel substrates, DDX42, TP53RK and RPL36a were confirmed ex vivo. The whole strategy is rather simple and efficient. Non-degradation substrates can be discovered. This strategy can be extended to any E3s as long as the E3 does not ubiquitinate the empty phage.     

大鼠、豚鼠和金黄地鼠的尿液蛋白质组比较

生物标志物是指与生理或病理变化相关的可监测的变化。尿液作为机体的一种排泄物,不受稳态机制的调节,可以反映机体的多种变化。动物模型可以模拟人类疾病过程,监测疾病的变化,并为早期诊断提供线索。大鼠作为常用的模型动物并非所有疾病的优势模型动物,因此比较大鼠与其他动物的尿液蛋白质组,从而为其他疾病选择优势模型动物提供线索。文中通过膜上酶切切成肽段再通过液相色谱与串联质谱偶联技术(LC-MS/MS)分析肽段信息,比较大鼠、豚鼠和金黄地鼠的尿液蛋白,结果显示3种鼠的尿蛋白数量不同,在机体不同系统中表达情况不同,参与的生物功能也不同。这为不同疾病选择不同的优势模型动物提供了依据。