simRank-Network

This module performs simRank similarity calculation for MS2 spectra in provided samples. A spectral network is constructed based on the defined simRank similarity threshold.

1. Please log in and upload files before use.

   Data preparation is described in the MSConvert Usage section.

2. Check the parameter settings.

   We recommend using the default parameters provided on the website for data analysis, though you are free to adjust them based on your specific needs.

   Parameter & Description	Default Setting
   Intensity threshold: Intensity threshold for fragments in MS2 spectra. Fragments from a normalized MS2 spectrum (intensity of the more intense fragment is normalized to 100) with intensity lower than this value are not used for analysis.	1
   RT tolerance for MS2 spectra merging: Delta retention time that is allowed when merging MS2 spectra within a sample. Spectra from the same precursor ion with retention time different within 30 seconds can be merged.	30
   ppm: ppm tolerance used to align precursor ions within a sample, determined mainly by the instrument type.	20
   PM tolerance: MS2 spectra pairs, with precursor ions that have differences larger than this value, will not be compared.	300 Da
   Delta mz: that is allowed to align precursor ions within a sample. If set to 0, only the ppm parameter is used.	0.01
   Min mz number: If the number of fragments in an MS2 spectrum is smaller than this value, this spectrum will not be included in analysis.	5
   Merge MS2 spectra by collision energy.	True
   Remove precursor	Ture
   Hit number: For each merged spectrum, only the Top N (N = Hit num) spectra that are most similar to it will be connected with it.	20
   Score threshold: Only hits with simRank similarity scores higher than this value are included in results.	15

3. Upload the corresponding files under the option.

   For MS2 data files option (Required), please insure that the input file contains valid MS/MS information;

   For Data files for control option (Optional), choose your single or multiple control data files;

   For Peaktable file option (Optional), Choose your single peaktable file (support .csv format, it must contain two columns named “mz” and “rt” (in seconds). If this table is provided, only MS2 spectra corresponding to the targeted precursor ions are included in analysis.)

4. Enter a task name to start your analysis journey.

   Click "Tasks" at any time to check your analysis progress.

   

5. Data output & Data analysis.

   The output is a .graphml file that can be visualized using software such as cytoscape. https://cytoscape.org/.