Comparison of the analgesic effects of cryoanalgesia vs. parecoxib for lung cancer patients after lobectomy.

This study was designed to compare the analgesic effects of cryoanalgesia and parecoxib in lung cancer patients after lobectomy. A total of 178 lung cancer patients awaiting large-sized lobectomy were enrolled in the study. The patients were randomly divided into Group A (intercostal nerve cryoanalgesia) and Group B (parecoxib). The analgesic and adverse effects were compared between the two groups. The pain score of Group A was significantly lower than that of Group B (P < 0.05). The patients in Group A used significantly less morphine than those in Group B (P < 0.05). There were also significantly fewer complications in Group A than in Group B (P < 0.05). Cryoanalgesia of the intercostal nerves can be considered an economical, safe and simple technique for the long-term management of post-lobectomy pain.

[Study on the membrane proteins of Alkalimonas amylolytica N10 expressed at different pH environment].

The research on the membrane proteins expressed in alkaliphiles at different pH media will be benefit to understand the molecular mechanisms how they survive from such harsh alkaline environment. A preliminary investigation to the differential membrane proteomes from Alkalimonas amylolytica N10 (N10), a novel alkaliphilic bacterium, is reported herein. Upon the growth curves of N10 at different pH environment, three pH media, 8.4, 9.4 and 10.4, respectively, were employed to culture N10 followed by membrane preparation using ultracentrifuge and membrane proteins separation by 8% - 20% gradient SDS-PAGE. With carefully image analysis and statistical calculation, 7 stained bands were confirmed the alterations of relative optimal intensities corresponding with pH environment. Furthermore these bands were digested in-gel by trypsin and delivered to LC-MS/MS for protein identification. Twelve proteins were verified, of which four were reported involvement of the regulation of pH homeostasis in cytoplasm of alkaliphiles, and the others were originally found their protein expression responding to the environment with different pH values.

Reprint of "pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data".

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.This article is part of a Special Issue entitled: Computational Proteomics.

pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data.

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.