script for N-glycan analysis

[NasserMS2]

Hi,

Im working on analyzing small molecules (N-glycnas) in mzML format. I'm trying to deconvolute them and then use my script to annotate them. I want to use deconv function from your script but not sure which one works best for molecules like glycans. I will appreciate if you provide me the code using ms_deisotope functions or modules to deconvolute my mzml containing m/z vs intensity and return the corresponding masses. if we can have output mass range and also input m/z range with input charge rage, would be great. I really need it. I tried several scripts for deconv but those are not good for small molecules.

[mobiusklein]

The best parameters will depend upon the type of data you have. ms_deisotope was written in part to support my own work on released N-glycan LC-MS and N-glycoproteomics.

If you just want to deisotope and charge state deconvolve an entire LC-MS file, you can use the command line tool ms-deisotope with the following options:

ms-deisotope -g 1 -a glycan -an glycan -m 2 -t 10 -tn 0 -b 1 $INPUT_FILE $OUTPUT_FILE

Where -g 1 enables MS1 signal averaging, smoothing noisy data, -a glycan and -an glycan specify that the analytes will follow the glycan isotopic model, -m 2 indicates that up to two missing isotopic peaks will be tolerated for MS1 fits, not uncommon for large molecules, -t 10 specifies a fairly relaxed minimum fit quality for MS1 spectra that discards spurious fits but doesn't throw away everything, and -tn 0 indicates that if there are MS2 spectra that it will tolerate even partial fits. The -b 1 option does some additional background noise reduction, but depending upon your instrument you may want to set this to 0 or raise it to 5 if you have a lot of background noise, e.g. TOF or FTICR data.

This produces a new mzML file with isotopic peaks removed and an associated charge array for each peak. The fitted isotopic patterns are still stored in a separate array that ms_deisotope can unpack for you with ms_deisotope.output.ProcessedMzMLLoader.

If you need to do it programmatically, I can provide an example for that as well.

[NasserMS2]

Hi,

thanks for the quick reply. if you give me an example, it would be great.