Is MS1 necessary in DIA?

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

A COVID-19 paper in retrospect

We submitted a COVID-19-related paper recently, reporting a longitudinal proteomic investigation of diverse serological patterns in COVID-19 (link to the paper: medRxiv). It is not a paper with fancy analysis nor sophisticated modeling per se, yet the journey of shaping up the research work is quite interesting. Briefly, during COVID-19, we found that some patients did not secret serum IgG or IgM (seronegative) whereas others secreted drastically high levels of serum IgM. We thus used clinical i…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