References

Mass Spectrometry-Based Proteomics

10.1038/nature01511 · 2003 · External reference

Detecting Protein Variants by Mass Spectrometry: A Comprehensive Study in Cancer Cell-Lines

10.1186/s13073-017-0454-9 · 2017 · External reference

Basic Local Alignment Search Tool

10.1016/s0022-2836(05)80360-2 · 1990 · External reference

Systematic Investigation of Software Tools and Design of a Tailored Pipeline for Paleoproteomics Research

10.24072/pci.mcb.100309 · 2024 · External reference

The SWISS-PROT Protein Sequence Database and Its Supplement TrEMBL in 2000

10.1093/nar/28.1.45 · 2000 · External reference

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

10.1021/acs.jproteome.8b00175 · 2018 · External reference

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

10.1111/j.2517-6161.1995.tb02031.x · 1995 · External reference

Comprehensive Evaluation of Peptide de Novo Sequencing Tools for Monoclonal Antibody Assembly

10.1093/bib/bbac542 · 2023 · External reference

A Learned Embedding for Efficient Joint Analysis of Millions of Mass Spectra

10.1038/s41592-022-01496-1 · 2022 · External reference

Ancient Proteins Provide Evidence of Dairy Consumption in Eastern Africa

10.1038/s41467-020-20682-3 · 2021 · External reference

Limited Lactosylation of Beta-Lactoglobulin from Cow's Milk Exerts Strong Influence on Antigenicity and Degranulation of Mast Cells

10.3390/nu13062041 · 2021 · External reference

Amyloidogenic Motifs Revealed by N-Gram Analysis

10.1038/s41598-017-13210-9 · 2017 · External reference

Early Pleistocene Enamel Proteome from Dmanisi Resolves Stephanorhinus Phylogeny

10.1038/s41586-019-1555-y · 2019 · External reference

A Cross-Platform Toolkit for Mass Spectrometry and Proteomics

10.1038/nbt.2377 · 2012 · External reference

Crystal-C: A Computational Tool for Refinement of Open Search Results

10.1021/acs.jproteome.0c00119 · 2020 · External reference

New insights into Neolithic milk consumption through proteomic analysis of dental calculus

10.1007/s12520-019-00911-7 · 2019 · External reference

A Late Middle Pleistocene Denisovan Mandible from the Tibetan Plateau

10.1038/s41586-019-1139-x · 2019 · External reference

Comprehensive Identification of Peptides in Tandem Mass Spectra Using an Efficient Open Search Engine

10.1038/nbt.4236 · 2018 · External reference

A Mass-Tolerant Database Search Identifies a Large Proportion of Unassigned Spectra in Shotgun Proteomics as Modified Peptides

10.1038/nbt.3267 · 2015 · External reference

False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics

10.1021/pr700747q · 2008 · External reference

Beyond Target-Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics

10.1021/acs.analchem.0c00328 · 2020 · External reference

MaxQuant Enables High Peptide Identification Rates, Individualized p.p.b.-Range Mass Accuracies and Proteome-Wide Protein Quantification

10.1038/nbt.1511 · 2008 · External reference

Unimod: Protein Modifications for Mass Spectrometry

10.1002/pmic.200300744 · 2004 · External reference

Investigation of the Lactosylation of Whey Proteins by Liquid Chromatography-Mass Spectrometry

10.1021/jf061646z · 2006 · External reference

Protein Sequences Bound to Mineral Surfaces Persist into Deep Time

10.7554/elife.17092 · 2016 · External reference

Bridging the False Discovery Gap

10.1021/acs.jproteome.3c00176 · 2023 · External reference

Target-Decoy Search Strategy for Increased Confidence in Large-Scale Protein Identifications by Mass Spectrometry

10.1038/nmeth1019 · 2007 · External reference

De Novo Peptide Sequencing with InstaNovo: Accurate, Database-Free Peptide Identification for Large Scale Proteomics Experiments

10.1101/2023.08.30.555055 · 2023 · External reference

The Impact of Cooking and Burial on Proteins: A Characterisation of Experimental Foodcrusts and Ceramics

10.1098/rsos.240610 · 2024 · External reference

Detection of Dairy Products from Multiple Taxa in Late Neolithic Pottery from Poland: An Integrated Biomolecular Approach

10.1098/rsos.230124 · 2023 · External reference

Prediction of Peptide and Protein Propensity for Amyloid Formation

10.1371/journal.pone.0134679 · 2015 · External reference

Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record

10.1016/j.chemphys.2022.111602 · 2022 · External reference

The Survival of β-lactoglobulin Peptides in the Archaeological Record: Vulnerability vs. Sequence Variation

10.1101/2024.09.13.612646 · 2024 · External reference

PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling

10.1021/ac048788h · 2005 · External reference

Predicting Intensity Ranks of Peptide Fragment Ions

10.1021/pr800677f · 2009 · External reference

A Ranking-Based Scoring Function for Peptide-Spectrum Matches

10.1021/pr800678b · 2009 · External reference

Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry

10.1021/acs.jproteome.3c00902 · 2024 · External reference

PTM-shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications from Open Search Results

10.1074/mcp.tir120.002216 · 2021 · External reference

Recognizing Millions of Consistently Unidentified Spectra across Hundreds of Shotgun Proteomics Datasets

10.1038/nmeth.3902 · 2016 · External reference

Molecular Simulation of Bovine Beta-Lactoglobulin Adsorbed onto a Positively Charged Solid Surface

10.1021/la8024149 · 2009 · External reference

A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics

10.48550/arxiv.1501.00537 · 2015 · External reference

Ancient Proteins from Ceramic Vessels at Çatalhöyük West Reveal the Hidden Cuisine of Early Farmers

10.1038/s41467-018-06335-6 · 2018 · External reference

Proteomic Evidence of Dietary Sources in Ancient Dental Calculus

10.1098/rspb.2018.0977 · 2018 · External reference

A Guide to Ancient Protein Studies

10.1038/s41559-018-0510-x · 2018 · External reference

Bronze Age Population Dynamics and the Rise of Dairy Pastoralism on the Eastern Eurasian Steppe

10.1073/pnas.1813608115 · 2018 · External reference

False Discovery Rates in Spectral Identification

10.1186/1471-2105-13-s16-s2 · 2012 · External reference

Quantitative Metaproteomics of Medieval Dental Calculus Reveals Individual Oral Health Status

10.1038/s41467-018-07148-3 · 2018 · External reference

The Ever-Increasing Necessity of Mass Spectrometry in Dissecting Protein Post-Translational Modifications Catalyzed by Bacterial Effectors

10.1111/mmi.15071 · 2023 · External reference

A Series of PDB Related Databases for Everyday Needs

10.1093/nar/gkq1105 · 2011 · External reference

Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features

10.1002/bip.360221211 · 1983 · External reference

Empirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search

10.1021/ac025747h · 2002 · External reference

MSFragger: Ultrafast and Comprehensive Peptide Identification in Mass Spectrometry-Based Proteomics

10.1038/nmeth.4256 · 2017 · External reference

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

10.1021/pr700600n · 2008 · External reference

Binary Codes Capable of Correcting Deletions, Insertions, and Reversals

1965 · External reference

Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework

10.1021/acs.jproteome.8b00717 · 2019 · External reference

PH Effects on Electrospray Ionization Efficiency

10.1007/s13361-016-1563-1 · 2017 · External reference

Novor: Real-Time Peptide de Novo Sequencing Software

10.1007/s13361-015-1204-0 · 2015 · External reference

Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

10.1021/acs.jproteome.2c00604 · 2023 · External reference

Lessons in de Novo Peptide Sequencing by Tandem Mass Spectrometry

10.1002/mas.21406 · 2015 · External reference

Qscore: An Algorithm for Evaluating SEQUEST Database Search Results

10.1016/s1044-0305(02)00352-5 · 2002 · External reference

Evaluating de Novo Sequencing in Proteomics: Already an Accurate Alternative to Database-Driven Peptide Identification?

10.1093/bib/bbx033 · 2018 · External reference

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

10.1021/pr4008078 · 2014 · External reference

LC-MS/MS, PSM and BLG Properties Data from "Benchmarking the Identification of a Single Degraded Protein to Explore Optimal Search Strategies for Ancient Proteins" [Data set]

10.5281/zenodo.13785293 · 2024 · External reference

A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins

10.1016/0022-2836(70)90057-4 · 1970 · External reference

Mass Spectrometrists Should Search Only for Peptides They Care About

10.1038/nmeth.3450 · 2015 · External reference

The PRIDE Database Resources in 2022: A Hub for Mass Spectrometry-Based Proteomics Evidences

10.1093/nar/gkab1038 · 2021 · External reference

Probability-Based Protein Identification by Searching Sequence Databases Using Mass Spectrometry Data

10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2 · 1999 · External reference

ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins

10.1016/j.jmb.2020.11.006 · 2021 · External reference

Palaeoproteomics resolves sloth relationships

10.1038/s41559-019-0909-z · 2019 · External reference

Assessing the Degradation of Ancient Milk Proteins through Site-Specific Deamidation Patterns

10.1038/s41598-021-87125-x · 2021 · External reference

DeamiDATE 1.0: Site-specific Deamidation as a Tool to Assess Authenticity of Members of Ancient Proteomes

10.1016/j.jas.2020.105080 · 2020 · External reference

Protocol for Micro-Purification, Enrichment, Pre-Fractionation and Storage of Peptides for Proteomics Using StageTips

10.1038/nprot.2007.261 · 2007 · External reference

ismaRP/PPbenchmark: v2.0.0

10.5281/zenodo.13785336 · 2024 · External reference

Glutamine Deamidation: An Indicator of Antiquity, or Preservational Quality?

10.1002/rcm.7445 · 2016 · External reference

Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE

10.1073/pnas.2014956117 · 2020 · External reference

Statistical Characterization of HCD Fragmentation Patterns of Tryptic Peptides on an LTQ Orbitrap Velos Mass Spectrometer

10.1016/j.jprot.2014.06.012 · 2014 · External reference

Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching

10.1021/ac0013709 · 2001 · External reference

Enhanced Global Post-Translational Modification Discovery with MetaMorpheus

10.1021/acs.jproteome.7b00873 · 2018 · External reference

Utility of B-factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability

10.1021/acs.chemrev.8b00290 · 2019 · External reference

DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring

10.1021/pr800154p · 2008 · External reference

Paleoproteomic Profiling of Organic Residues on Prehistoric Pottery from Malta

10.1007/s00726-021-02946-4 · 2021 · External reference

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

10.1007/s13361-016-1460-7 · 2016 · External reference

Maximum Allowed Solvent Accessibilites of Residues in Proteins

10.1371/journal.pone.0080635 · 2013 · External reference

The MaxQuant Computational Platform for Mass Spectrometry-Based Shotgun Proteomics

10.1038/nprot.2016.136 · 2016 · External reference

PeptideShaker Enables Reanalysis of MS-derived Proteomics Data Sets

10.1038/nbt.3109 · 2015 · External reference

Philosopher: A Versatile Toolkit for Shotgun Proteomics Data Analysis

10.1038/s41592-020-0912-y · 2020 · External reference

FineFDR: Fine-grained Taxonomy-Specific False Discovery Rates Control in Metaproteomics

10.1109/bibm55620.2022.9995401 · 2022 · External reference

Paleoproteomics

10.1021/acs.chemrev.1c00703 · 2022 · External reference

Pathogens and Host Immunity in the Ancient Human Oral Cavity

10.1038/ng.2906 · 2014 · External reference

Ancient Proteins Resolve the Evolutionary History of Darwin's South American Ungulates

10.1038/nature14249 · 2015 · External reference

Enamel Proteome Shows That Gigantopithecus Was an Early Diverging Pongine

10.1038/s41586-019-1728-8 · 2019 · External reference

A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra

10.1021/pr301024c · 2013 · External reference

Dairy Pastoralism Sustained Eastern Eurasian Steppe Populations for 5,000 Years

10.1038/s41559-020-1120-y · 2020 · External reference

Dairying Enabled Early Bronze Age Yamnaya Steppe Expansions

10.1038/s41586-021-03798-4 · 2021 · External reference

Introducing π-HelixNovo for practical large-scale de novo peptide sequencing

10.1101/2023.07.15.549133 · 2023 · External reference

De novo Mass Spectrometry Peptide Sequencing with a Transformer Model

10.1101/2022.02.07.479481 · 2022 · External reference

Identification of Modified Peptides Using Localization-Aware Open Search

10.1038/s41467-020-17921-y · 2020 · External reference

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

10.1074/mcp.m111.010587 · 2012 · External reference