Transcriptional states are formed and maintained by the interaction and 
post-translational modification (PTM) of several chromatin proteins, such as 
histones and high mobility group (HMG) proteins. Among these, HMGA1a, a small 
heterochromatin-associated nuclear protein has been shown to be 
post-translationally modified, and some of these PTMs have been linked to 
apoptosis and cancer. In cancerous cells, HMGA1a PTMs differ between metastatic 
and nonmetastatic cells, suggesting the existence of an HMGA1a PTM code 
analogous to the "histone code." In this study, we expand on current knowledge 
by comprehensively characterizing PTMs on HMGA1a purified from human cells using 
both nanoflow liquid chromatography collision activated dissociation mediated 
Bottom Up and electron-transfer dissociation facilitated middle and Top Down 
mass spectrometry (MS). We find HMGA1a to be pervasively modified with many 
types of modifications such as methylation, acetylation, and phosphorylation, 
including finding novel sites. While Bottom Up MS identified lower level 
modification sites, Top and Middle Down MS were utilized to identify the most 
commonly occurring combinatorially modified forms. Remarkably, although we 
identify several individual modification sites through our Bottom Up and Middle 
Down MS analyses, we find relatively few combinatorially modified forms dominate 
the population through Top Down proteomics. The main combinatorial PTMs we find 
through the Top Down approach are N-terminal acetylation, Arg25 methylation 
along with phosphorylation of the three most C-terminal serine residues in 
primarily a diphosphorylated form. This report presents one of the most detailed 
analyses of HMGA1a to date and illustrates the strength of using a combined MS 
effort.