Interesting. I didn't realize dump/pp would put different hash keys etc on the same long line because it my "real" case it printed like below. I guess it's because all of the contents of the 'cell' hash key didn't fit within the value of $Data::Dump::LINEWIDTH I used which was 640,000. However, I'm not sure why it decided not to put some of the other hash keys/values on the same line. I just tried it with 1,000,000 and it did print the whole structure on a single line like in your example. If you set $Data::Dump::LINEWIDTH = 10 in your example, it prints like your "new dump string". It looks like you can just play around with the LINEWIDTH until you get what you want.

EDIT: Regarding the comment "However, I'm not sure why it decided not to put some of the other hash keys/values on the same line.", it seems that if a particular item at a given level is deserving of its own line then all items at that level are.

{
  active => 0,
  attr   => [],
  cell   => [
              [],
              [undef, "Peptide Groups P>
              [undef, "Checked", "FALSE>
              [undef, "Confidence", "Hi>
              [undef, "Annotated Sequen>
              [undef, "Modifications", >
              [undef, "Qvality PEP", 6.>
              [undef, "Qvality q-value">
              [undef, "# Protein Groups>
              [undef, "# Proteins", 1, >
              [undef, "# PSMs", 3, 6, 1>
              [undef, "Master Protein A>
              [undef, "Positions in Mas>
              [undef, "Modifications in>
              [undef, "# Missed Cleavag>
              [undef, "Theo. MH+ [Da]",>
              [undef, "Abundance: F667:>
              [undef, "Abundance: F668:>
              [undef, "Abundance: F669:>
              [undef, "Abundance: F670:>
              [undef, "Quan Info", unde>
              [undef, "Found in Sample:>
              [undef, "Found in Sample:>
              [undef, "Found in Sample:>
              [undef, "Found in Sample:>
              [undef, "Confidence (by S>
              [undef, "Percolator q-Val>
              [undef, "Percolator PEP (>
              [undef, "XCorr (by Search>
              [undef, "Top Apex RT [min>
            ],
  hidden => 0,
  label  => "combined",
  maxcol => 29,
  maxrow => 3941,
  merged => [],
  mincol => 1,
  minrow => 1,
  parser => 0,
}
[download]