Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses
Data files
Jul 23, 2019 version files 5.97 GB
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ERS_400_BLANK1_20Mar2018_14.raw
476.33 MB
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ERS_400_BLANK2_20Mar2018_15.raw
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ERS_400_BLANK3_20Mar2018_16.raw
431.86 MB
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ERS_400_MOA1_20Mar2018_26.raw
235.14 MB
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ERS_400_MOA2_20Mar2018_27.raw
229.78 MB
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ERS_400_MOA3_20Mar2018_31.raw
232.11 MB
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ERS_N400_BLANK1_20Mar2018_10.raw
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ERS_N400_BLANK2_20Mar2018_11.raw
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ERS_N400_BLANK3_20Mar2018_12.raw
435.24 MB
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ERS_N400_MOA1_20Mar2018_22.raw
239.49 MB
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ERS_N400_MOA2_20Mar2018_23.raw
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ERS_N400_MOA3_20Mar2018_24.raw
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ERS_NaOH_BLANK1_20Mar2018_6.raw
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ERS_NaOH_BLANK2_20Mar2018_7.raw
388.66 MB
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ERS_NaOH_BLANK3_20Mar2018_8.raw
390.52 MB
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ERS_NaOH_MOA1_20Mar2018_18.raw
264.31 MB
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ERS_NaOH_MOA2_20Mar2018_19.raw
261.52 MB
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ERS_NaOH_MOA3_20Mar2018_20.raw
264.12 MB
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SCHROETER_HUMICMS_README.TXT
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Schroeter_Moa-NCBI-aves_Scaffold output excel files.zip
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Schroeter_Moa-NCBI-aves.sf3
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Abstract
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.