Is MS1 utilized in DIA-MS? During a DIA-MS experiment, MS1 scans are usually acquired. For the TOF-based DIA-MS experiments, MS1 scans are usually of moderate resolution. For example, the original SWATH-MS paper (PMID: 22261725) by Gilet et al used 250-ms to finish a DDA-MS1 scan while 100-ms to finish a SWATH-MS1 on a TOF-MS system. Considering that each scan, regardless of MS1 or MS2 in SWATH, takes 0.1 s, SWATH-MS1 takes around 3.3% of the cycle time. The authors did, however, additionally de…read more
标签： software
A review for Prof. Nikolai Slavov’s SCP talk
Note: This is a Chinese review for a recent talk of Prof. Nikolai Slavov, focusing on the recent advances of single cell proteomics developed by his lab. Yingqiu and Jiaqi helped with drafting and revising, respectively. The formatted version (Chinese) could be referenced here. You could use the Language Switch icon at the top right of this page for assisted reading. Original title: YIPA研讨会 | Nikolai Slavov 探讨单细胞蛋白组学前沿技术 Talk Theme: Accessible methods for high-throughput, deep and accurate singl…read more
Two issues in software development for proteomic analyses
Software tools for proteomic data analysis are being fast developed. However, several issues remain and expect future improvements. Numerous reviews have elaborated on this topic. Here I enumerate two issues that are not popularly discussed. User-unfriendnessBuilt by lab scientists, several developmental software is command line-based 1-3. They are user-unfriendliness for biologists, especially with multiple computation steps and tedious parameter settings, thus rendering the interest of experim…read more
Who are the specialists in DIA proteomics?
中文标题：做DIA的蛋白质组牛人有哪些？ Please note that authoship is reserved and you must have my consent before reproducing this article. Many researchers are using proteomics as could be witnessed in each year’s HUPO conference. Within them, a group of experts have specialized knowledge on proteomic technologies. Here, based on personal experiences, I nominate a selected list of specialists that are actively contributing to this field, especially in the development of DIA-MS proteomics. Scholars are included r…read more
追溯SEQUEST：1994年的思维尖刀
English title: SEQUEST: Pioneer of the Year 1994 The original version of this article was published in the HUPO Official Wechat. Dr. Luyao Liu from Dalian Institute of Chemical Physics, CAS helped with the revision. I made several edits in this version. 原文标题：An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database；原文链接：https://pubs.acs.org/doi/10.1016/1044-0305(94)80016-2 一作：Jimmy Eng；通讯：John Yates. SEQUEST是由Jimmy Eng和John Yates领衔、在1994年完成设计的…read more
The road of science is never lonely: A Talking to ECRs interview
One of my volunteer jobs in HUPO is to interview scholars and broadcast their thinkings to the community. This is a recorded 1v1 interview with Dr Brian Searle. The content was originically released by HUPO official Wechat account: HUPO-Wechat. Permission to reproduce the article was granted. Original Title: HUPO ReCONNECT 2021 interview: Brian Searle – Xiao Liang To offer ECRs a better opportunity to have deep communications with established experts in the field of proteomics, HUPO WeChat Offic…read more
