Dear all,
We've released a new version of SIM-XL (v.1.5.1.1).
Please update your current version or download at
http://patternlabforproteomics.org/sim-xl.
To update your current version, click on Help menu -> Check for updates.
We are fulfilling suggestions of some users, and we are working to turn SIM-XL more robust and sensitive. Continue giving us your feedback about our search engine.
The release notes are:
Version 1.5.1.1
June 25th, 2018
- Bug-fixed: The fusion method was optimized for files of older versions.
- Bug-fixed: The protein identification and quantitation features were optimized.
- Bug-fixed: The export method for TopoLink was reorganized.
- (NEW) Result Browser: Species Count - The results can be filtered by species count.
- (NEW) Result Browser: Protein Domain - The user can specify a domain for each identified protein according to some parameters: protein region, name, and color. For it, the user needs to go to Utils menu -> Protein Domain (or pressing ALT + D), as shown in Figure 1.
![](https://ci5.googleusercontent.com/proxy/RChbQg1Nvj4R6uqpGka5qAiLVaMu-j88gN-TyI-DM62HzQv8afuVwxPFvtctmFU2keCUW4Bq2DJF-u7ca57HSaVfVLbYaMQNta55CdUrMIC_BL1JyikXjbe7n7O1yLU=s0-d-e1-ft#http://patternlabforproteomics.org/sim-xl/Images/Figure1_release_1_5_1_1.png)
Figure 1
A new window will be opened (Figure 2); a ProteinID, a range of the protein domain, a name, and a color need to be filled.
![](https://ci6.googleusercontent.com/proxy/ku7AJeqEplgwBU4RKmLp7KeG9OGDimJ7Mi3TX5HjUZAMZ27wX1pf1HzYt3vNNxo_SyIbrz_014C28XlRMEmUycJ09SzkmMecnaVhUjBsq1E2PETVuElERBCa3T6A7-g=s0-d-e1-ft#http://patternlabforproteomics.org/sim-xl/Images/Figure2_release_1_5_1_1.png)
Figure 2
After that, a new 2D map will be plotted, as can be shown in Figure 3. When the user mouse over the domain, its name is shown.
![](https://ci5.googleusercontent.com/proxy/cQ7FfLeQB2WSv0KpLRgjdLFetN6L4f_U5RgrQv24X-W4dSGcwX8DR340mtq0L9sRWzpQ61DqZZCtNqLenWBdR9d6ftqb3qjflTtI2XjVE_TR9kzbKiP5oRNNmFz7DcM=s0-d-e1-ft#http://patternlabforproteomics.org/sim-xl/Images/Figure3_release_1_5_1_1.png)
Figure 3
- (NEW) Result Browser: Cross-linker color change - Now, it's possible to change the intralink color for each cross-linker. For it, the user needs to go to Utils menu -> Custom Results Report (or pressing ALT + C) and (Figure 1) changes the Color field (Figure 4).
![](https://ci6.googleusercontent.com/proxy/kmQ0UaYfZEgDWoF3YV8hRgj434Vu7cQ-HEb297LCGzGA-yuXYIuUvNq-eHXxj99171edFkqukG6JXZP1wzU3i7WzgbSl-eN6ad5McP6MmsAsQA0Z3VMJjiWruzZiQzs=s0-d-e1-ft#http://patternlabforproteomics.org/sim-xl/Images/Figure4_release_1_5_1_1.png)
Figure 4
After to choose the color, press the 'OK' button. A new 2D map will be plotted with the new colors (Figure 5).
![](https://ci3.googleusercontent.com/proxy/VGpqCpHhnUDwF-kPFr8jAbekoYs5yfXy5Tda35eE_93ltnCrqZk8fF0p2KMFykdl-A85Z6OlmdwGXM46s-aC3TvM37gywhNvTZjA6U4gZKIIxK7dwjgRdFt7eqmIpCA=s0-d-e1-ft#http://patternlabforproteomics.org/sim-xl/Images/Figure5_release_1_5_1_1.png)
Figure 5
You can visit our
webpage to visualize other notes.
Should you have any question, please email us.
Best regards,