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.
Raw: Moa NaOH Inject 1
Raw MS data file for Moa Fossil Sample, NaOH fraction, Injection 1
ERS_NaOH_MOA1_20Mar2018_18.raw
Raw: Moa NaOH Inject 2
Raw MS data file for Moa Fossil Sample, NaOH fraction, Injection 2
ERS_NaOH_MOA2_20Mar2018_19.raw
Raw: Moa NaOH Inject 3
Raw MS data file for Moa Fossil Sample, NaOH fraction, Injection 3
ERS_NaOH_MOA3_20Mar2018_20.raw
Raw: Blank NaOH Inject 1
Raw MS data file for Blank Negative Control Sample, NaOH fraction, Injection 1
ERS_NaOH_BLANK1_20Mar2018_6.raw
Raw: Blank NaOH Inject 2
Raw MS data file for Blank Negative Control Sample, NaOH fraction, Injection 2
ERS_NaOH_BLANK2_20Mar2018_7.raw
Raw: Blank NaOH Inject 3
Raw MS data file for Blank Negative Control Sample, NaOH fraction, Injection 3
ERS_NaOH_BLANK3_20Mar2018_8.raw
Raw: Moa NaOH-400/200/4 Inject 1
Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 1
ERS_N400_MOA1_20Mar2018_22.raw
Raw: Moa NaOH-400/200/4 Inject 2
Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 2
ERS_N400_MOA2_20Mar2018_23.raw
Raw: Moa NaOH-400/200/4 Inject 3
Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 3
ERS_N400_MOA3_20Mar2018_24.raw
Raw: Blank 400/200/4 Inject 1
Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 1
ERS_N400_BLANK1_20Mar2018_10.raw
Raw: Blank 400/200/4 Inject 2
Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 2
ERS_N400_BLANK2_20Mar2018_11.raw
Raw: Blank NaOH-400/200/4 Inject 3
Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 3
ERS_N400_BLANK3_20Mar2018_12.raw
Raw: Moa 400/200/4 Inject 1
Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction, Injection 1
ERS_400_MOA1_20Mar2018_26.raw
Raw: Moa 400/200/4 Inject 2
Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction, Injection 2
ERS_400_MOA2_20Mar2018_27.raw
Raw: Moa 400/200/4 Inject 3
Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction, Injection 3
ERS_400_MOA3_20Mar2018_31.raw
Raw: Blank 400/200/4 Inject 1
Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction, Injection 1
ERS_400_BLANK1_20Mar2018_14.raw
Raw: Blank 400/200/4 Inject 2
Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction, Injection 2
ERS_400_BLANK2_20Mar2018_15.raw
Raw: Blank 400/200/4 Inject 3
Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction, Injection 3
ERS_400_BLANK3_20Mar2018_16.raw
Complete Scaffold Data File
Scaffold project data file containing completed database search data
Schroeter_Moa-NCBI-aves.sf3
Scaffold Output Files
Scaffold data output files in excel format
Schroeter_Moa-NCBI-aves_Scaffold output excel files.zip
README
SCHROETER_HUMICMS_README.TXT