Data for ZooMS analysis of avian fauna from Teotihuacan, Mexico, for Codlin et al. 2022

This data is associated with a manuscript on the analysis of avian fauna via Zooarchaeology by Mass Spectrometry (ZooMS) by Codlin et al. (2022)
See publication for more details https://doi.org/10.1016/j.jas.2022.105692. Additional data will be made available on ProteomeXchange

All samples were processed with HCl, gelatinized at 65ºC in AmBic and digested with trypsin.
While some samples underwent purification using a C18 ZipTip, all digested peptide solutions were diluted to various concentrations prior to spotting and analysis on a Bruker Autoflex Speed LRF MALDI-TOF Mass Spectrometer.

# Details of files uploaded

## "Sample_details.csv"
Lists sample IDs and taxonomic information for modern reference specimens and archaeological specimens selected for LC-MS/MS analysis

## "MALDI_arch_samples.zip"
Contains the unprocessed .MZML MALDI spectra for archaeological specimens.

    File names are composed of:
    - MCsample#_MALDIplate#_dilutionAND/ORziptip_platelocation

## "MALDI_modern_samples.zip"
Contains the unprocessed .MZML MALDI spectra for modern reference specimens.
All samples except MC2 are from AMNH collections. See "Sample_details.csv" for sample information

    File names are composed of:
    - MCsample#_dilution_speciesidentification_MALDIplatelocation

## "Curated_avian_collagen_fasta.zip"
Contains two .fasta files with curated avian COL1a1 and COL1a2 sequences from publicly available data.

##"MS2_images.zip"
Contains MS2 images from LC-MS/MS confirmation of biomarker peaks. See "Sample_details.csv" for sample information.

    File names are composed of:
    - COL1A2chain_markerlocation_masspeak_sample#

##"MALDI_spectra_images.zip"
Contains images of representative spectra for modern and archaeological taxa identified in the study. These spectra were processed and averaged in mMass using the "MALDI-TOF Peptides" settings.
Spectra were aligned to more closely fit confirmed biomarker peaks for each sample. See "Sample_details.csv" for sample information.

    File names are composed of:
    - Sample#

## "biomarkers_list.txt"
Contains the list of peaks and deamidated peaks used in clustering MALDI spectra.