Dear Puja,

We have tried this earlier. The data analysis is based on the profile of the diagnostic immonium ion formed. We have applied this to wide number of PTM in high and low Mw proteins (pls see Article Use of Narrow Mass-Window, High-Resolution Extracted Product...

Article Reporter ion-based mass spectrometry approaches for detectio...

The method is versatile to screen a number of PTM in proteins by taking advantage of the high resolution of QToF analysers. In view of this, it will be difficult to apply the proposed approach if you only have low resolution mass spectrometer available to you (QqQ or ion trap). If that's the case you can use the conventional PIS (precursor ion scanning) and NLS (neutral loss scanning) approaches which will require higher amounts (volume) of sample available.

Hope this helps,

Ana Reis

Yes it is, but phosphopeptides need different fragmentation parameters than other peptides to avoid neutral loss (so use beam type CAD). Also the amount of material strongly depends on your set-up (nano-flow gives highest sensitivity), but generally speaking use 1-10mg of material for enrichment whenever you can.

Dear Puja

In principal, the answer is yes, but, in reality it depends on sample prep, sequencing strategy (bottom-up or top down), mass spectrometry equipment, bioinformatics resources available, and bioinformatic skills of the scientist.

Here is a simple overview of approaches for protein characterization that may come useful in understanding the process and your technical options: DOI: 10.1016/B978-0-12-809324-5.02432-9