Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses

Humic substances are break-down products of decaying organic matter that
co-extract with proteins from fossils. These substances are difficult to
separate from proteins in solution, and interfere with analyses of fossil
proteomes. We introduce a method combining multiple recent advances in
extraction protocols to both concentrate proteins from fossil specimens
with high humic content, and remove humics, producing clean samples easily
analyzed by mass spectrometry (MS). This method includes: 1) a
non-demineralizing extraction buffer that eliminates protein loss during
the demineralization step in routine methods; 2) filter-aided sample
preparation (FASP) of peptides, which concentrates and digests extracts in
one filter, allowing the separation of large humics after digestion; 3)
centrifugal stage-tipping, which further clarifies and concentrates
samples in a uniform process performed simultaneously on multiple samples.
We apply this method to a moa fossil (~800¬–1000 yr) dark with humic
content, generating colorless samples and enabling the detection of more
proteins with greater sequence coverage than previous MS analyses on this
same specimen. This workflow allows analyses of low-abundance proteins in
fossils containing humics, and thus may widen the range of extinct
organisms and regions of their proteomes we can explore with MS.