Top Down Search Task

Since version 0.0.291, MetaMorpheus can search top-down proteomics data. Currently, the top-down search in MetaMorpheus doesn't search for truncated proteoforms.

Recommended search settings:

• Change "Protease" to "top-down"
• Uncheck "Use Provided Precursor"
• Set "Deconvolution Max Assumed Charge State" to a high value, like 60
• Turn off "Trim MS2 peaks"
• Change the "Mass-Difference Acceptor Criterion" to "1, 2, or 3 Missed Monoisotopic Peaks"
• Use "No quantification" - quantification doesn't work for top-down yet
• It is recommended to uncheck all variable modifications. It is best to use an XML protein database (e.g., UniProt) to search for likely mods. Use G-PTM-D to find common unannotated mods, like oxidation, acetylation, etc.

Top-Down Vignette

Some example top-down files and a protein database can be found here. The data is two injection replicates of a GelFree fraction of yeast lysate.

To-do list:

• Biomarker search (searches for truncated proteoforms)
• Top-down mass calibration
• Improved monoisotopic mass determination
• Top-down quantification