Top-Down Mass Spectrometry for Protein Molecular Diagnostics and Biomarker Discovery - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 307

Identified Correct Gene Family

Protein ID

~20-90% Sequence Coverage

Pepide ID

Peptide Mixture

LC-MS/MS

Digest

PTM

Sample

LC-MS

MS/MS MS/MS

Protein ID

Protein ID

100% Sequence Coverage

Identified Correct Protein Forms

FIGURE 2 Comparison of top-down and bottom-up proteomic strategies. In bottom-up MS, proteins are typically digested
with trypsin prior to peptide

fingerprinting or LC/MS/MS analysis to deduce the peptide amino acid sequence. In many
cases, particularly those for global proteomics studies, limited sequence coverage or incomplete genome databases allows
assignment of the correct gene family but prevents the identi cation of the true protein species present. With top-down MS,

the determination of protein molecular mass and MS/MS on each species serves to differentiate and identify the heteroge-
neous states of closely related proteins.