DOI: 10.5061/dryad.3tv1523
title: Data from: A proteomic method to extract, concentrate, digest, and enrich peptides from fossils with colored (humic) substances for mass spectrometry analyses

description: 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.
description: Raw: Moa NaOH Inject
 1Raw
 MS data file for Moa Fossil Sample, NaOH fraction, Injection
 1ERS_NaOH_MOA1_20Mar2018_18.rawRaw: Moa NaOH Inject 2Raw MS data file for Moa Fossil Sample, NaOH fraction, Injection 2ERS_NaOH_MOA2_20Mar2018_19.rawRaw: Moa NaOH Inject 3Raw MS data file for Moa Fossil Sample, NaOH fraction, Injection 3ERS_NaOH_MOA3_20Mar2018_20.rawRaw: Blank NaOH Inject 1Raw MS data file for Blank Negative Control Sample, NaOH fraction, Injection 1ERS_NaOH_BLANK1_20Mar2018_6.rawRaw: Blank NaOH Inject 2Raw MS data file for Blank Negative Control Sample, NaOH fraction, Injection 2ERS_NaOH_BLANK2_20Mar2018_7.rawRaw: Blank NaOH Inject 3Raw MS data file for Blank Negative Control Sample, NaOH fraction, Injection 3ERS_NaOH_BLANK3_20Mar2018_8.rawRaw: Moa NaOH-400/200/4 Inject 1Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 1ERS_N400_MOA1_20Mar2018_22.rawRaw: Moa NaOH-400/200/4 Inject 2Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 2ERS_N400_MOA2_20Mar2018_23.rawRaw: Moa NaOH-400/200/4 Inject 3Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 3ERS_N400_MOA3_20Mar2018_24.rawRaw: Blank 400/200/4 Inject 1Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 1ERS_N400_BLANK1_20Mar2018_10.rawRaw: Blank 400/200/4 Inject 2Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 2ERS_N400_BLANK2_20Mar2018_11.rawRaw: Blank NaOH-400/200/4 Inject 3Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction AFTER NaOH Pretreatment, Injection 3ERS_N400_BLANK3_20Mar2018_12.rawRaw: Moa 400/200/4 Inject 1Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction, Injection 1ERS_400_MOA1_20Mar2018_26.rawRaw: Moa 400/200/4 Inject 2Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction, Injection 2ERS_400_MOA2_20Mar2018_27.rawRaw: Moa 400/200/4 Inject 3Raw MS data file for Moa Fossil Sample, 400/200/4 Fraction, Injection 3ERS_400_MOA3_20Mar2018_31.rawRaw: Blank 400/200/4 Inject 1Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction, Injection 1ERS_400_BLANK1_20Mar2018_14.rawRaw: Blank 400/200/4 Inject 2Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction, Injection 2ERS_400_BLANK2_20Mar2018_15.rawRaw: Blank 400/200/4 Inject 3Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction, Injection 3ERS_400_BLANK3_20Mar2018_16.rawComplete Scaffold Data FileScaffold project data file containing completed database search dataSchroeter_Moa-NCBI-aves.sf3Scaffold Output FilesScaffold data output files in excel formatSchroeter_Moa-NCBI-aves_Scaffold output excel files.zipREADMESCHROETER_HUMICMS_README.TXT