[SIM-XL] New version 1.4

[Diogo Borges]

Dear all,

We've released a new version of SIM-XL (v.1.4).

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 1.4

August 11th, 2017

• (NEW) Quality Control Filter (Xrea): Xrea is a signal-to-noise score proposed by Na and Paek, that only considers relative and cumulative intensities without taking into account the distribution of intensities along the m/z axis. A high Xrea score usually means a spectrum with some distinctive peaks in relation to other, low-intensity peaks. On the other hand, a low Xrea means a spectrum with many peaks of close intensity all over, that is, a spectrum in which it is difficult to discriminate between signal peaks and noise peaks. So, this filter removes all spectra which contains a Xrea score below than threshold value, set up as default 0.2 (Figure 1).




Figure 1

• (NEW) Mono-link search: All cross-linking searches will be performed in two steps: i) Comet will be used to find out all linear and mono-link peptides. All identified spectra of the linear peptides will not be searched in the cross-linking step. All identified mono-link peptides will be shown in the 2D-map, as well as, all reaction sites will be flagged (dash-line) on the protein representation (Figure 2). ii) SIM-XL search engine will be used to find out the cross-linkings. 
  
  

  
  Figure 2

  • All identified mono-links will also be shown in a specific tab termed Dynamic Result Report - Mono-link (Figure 3), which can be visualized all information about each identification (e.g. scan number, Comet score - Primary Score - etc.) and by double-clicking on a specific mono-link, a new window will be opened showing the spectrum viewer.
  
  

  
  Figure 3

  ⇒ This feature is not able to perform homodimer analysis.

• (NEW) Protein sequence coverage: By double-clicking on the protein representation, a new window will be opened showing the protein sequence coverage, as can be seen in Figure 4.




Figure 4

• Optimized homodimer searches.

You can visit our webpage to visualize other notes.

Should you have any question, please email us.

Best regards,

Developer Team