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I am trying to generate simulated MS data (Top-down and Bottom-up) for phosphorylated protein such as platelet-derived growth factor receptor (PDGFR-B). There are 10 tyrosine sites which are phosphorylated. Could you kindly tell me if there is any good software application to help me do that?

Also, how can I include in the input file (FASTA) that there are 10 modification sites on the protein sequence?

What are the parameters required to be set for top-down and bottom-up MS separately?

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I know this is a two years old question... but I recently developed a web application which could be useful for you: Prot pi

The Protein tool lets you simulate the mass spectrum of the intact protein, while the Peptide tool gives you the fragment ions of peptides. Modifications can easily attached to every site you want. enter image description here

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For peptides (bottom up) mMass accepts a sequence of interest and phosphorylated tyrosine can be specified as a modification after that. The program also performs in silico enzyme digests and in silico MS/MS fragmentation.

There are other tools that attempt to accurately mimic the intensities of the various fragments that could be generated.

The meaning of the final question is unclear. If you want to know which parameters to set for the in silico analyses you need to use those that match the sample processing and analyses that would take place in the real world. Sample processing and instrument setup are highly context dependent, there's insufficient information to help with those.

Obtaining good quality intact measurements from a protein the size of PDGFR-B would be a significant challenge.

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Have a look at PeptideMass, you can choose to use the "post-translational modifications" option that will output the masses of phosphorylated (among other modifications) peptides.

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