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References from Critical evaluation of the use of artificial data for machine learning based de novo peptide identification. Local targets link to admitted publications; unresolved targets remain external evidence.
Knowledge-based analysis of proteomics data
2012 · External reference
10.1021/cr3003533
10.1021/cr3003533 · External reference
10.1016/j.jprot.2010.08.009
10.1016/j.jprot.2010.08.009 · External reference
10.1038/nmeth.3902
10.1038/nmeth.3902 · External reference
Statistical model for large-scale peptide identification in databases from tandem mass spectra using sequest
10.1021/ac049305c · 2004 · External reference
Algorithms for de novo peptide sequencing using tandem mass spectrometry
2004 · External reference
Pride: a public repository of protein and peptide identifications for the proteomics community
10.1093/nar/gkj138 · 2006 · External reference
De novo peptide sequencing by deep learning
10.1073/pnas.1705691114 · 2017 · External reference
10.1038/s42256-021-00304-3
10.1038/s42256-021-00304-3 · External reference
Novor: real-time peptide de novo sequencing software
10.1007/s13361-015-1204-0 · 2015 · External reference
False discovery rates in spectral identification
2012 · External reference
10.1002/mas.20024
10.1002/mas.20024 · External reference
Energy dependence of hcd on peptide fragmentation: stepped collisional energy finds the sweet spot
10.1007/s13361-013-0709-7 · 2013 · External reference
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
10.1021/ac0258709 · 2003 · External reference
10.1016/j.csbj.2022.03.008 · Admitted local publication
Synthetic data with neural machine translation for automatic correction in arabic grammar
10.1016/j.eij.2020.12.001 · 2021 · External reference
10.1038/s41551-021-00751-8
10.1038/s41551-021-00751-8 · External reference
10.1109/bigdata.2018.8622525
10.1109/bigdata.2018.8622525 · External reference
Leveraging deep learning algorithms for synthetic data generation to design and analyze biological networks
2022 · External reference
10.1007/978-3-030-01216-8_14
10.1007/978-3-030-01216-8_14 · External reference
10.1016/j.neucom.2019.12.136
10.1016/j.neucom.2019.12.136 · External reference
Unresolved reference
External reference
10.1145/1377966.1377977
10.1145/1377966.1377977 · External reference
10.1109/raise.2019.00012
10.1109/raise.2019.00012 · External reference
10.1109/cvpr.2017.496
10.1109/cvpr.2017.496 · External reference
Intensity-based protein identification by machine learning from a library of tandem mass spectra
10.1038/nbt930 · 2004 · External reference
Unresolved reference
2006 · External reference
Ms2pip: a tool for ms/ms peak intensity prediction
10.1093/bioinformatics/btt544 · 2013 · External reference
10.1038/s41592-019-0426-7
10.1038/s41592-019-0426-7 · External reference
De novo analysis of peptide tandem mass spectra by spectral graph partitioning
10.1089/cmb.2006.13.364 · 2006 · External reference
Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?
10.1093/bib/bbx033 · 2018 · External reference
10.1021/acs.jproteome.6b00211
10.1021/acs.jproteome.6b00211 · External reference
Impact of cystinosin glycosylation on protein stability by differential dynamic stable isotope labeling by amino acids in cell culture (silac)
10.1074/mcp.m116.063867 · 2017 · External reference
Combination of bottom-up 2d-lc-ms and semi-top-down gelfree-lc-ms enhances coverage of proteome and low molecular weight short open reading frame encoded peptides of the archaeon methanosarcina mazei
10.1021/acs.jproteome.6b00569 · 2016 · External reference
10.1101/gr.215293.116
10.1101/gr.215293.116 · External reference
Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation
2016 · External reference
In-depth characterization of the tomato fruit pericarp proteome
10.1002/pmic.201600406 · 2017 · External reference
10.1021/acs.jproteome.6b00647
10.1021/acs.jproteome.6b00647 · External reference
Proteome analysis of the hemolymph, mushroom body, and antenna provides novel insight into honeybee resistance against varroa infestation
10.1021/acs.jproteome.6b00423 · 2016 · External reference
Proteomic and bioinformatic characterization of extracellular vesicles released from human macrophages upon influenza a virus infection
10.1021/acs.jproteome.6b00596 · 2017 · External reference
Peaks db: de novo sequencing assisted database search for sensitive and accurate peptide identification
2012 · External reference
Pyteomics 4.0: five years of development of a python proteomics framework
10.1021/acs.jproteome.8b00717 · 2018 · External reference
Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra
10.1021/pr070479v · 2008 · External reference
Protein sequencing by tandem mass spectrometry
10.1073/pnas.83.17.6233 · 1986 · External reference
10.1002/mas.21406
10.1002/mas.21406 · External reference
Application of a novel hybrid cnn-gnn for peptide ion encoding
2022 · External reference
Unresolved reference
External reference
10.1021/pr3007045
10.1021/pr3007045 · External reference
Peptide sequence analysis
10.1016/s0076-6879(05)02007-0 · 2005 · External reference
Accurate mass measurement: terminology and treatment of data
10.1016/j.jasms.2010.06.006 · 2010 · External reference
Sequence scrambling in shotgun proteomics is negligible
10.1007/s13361-011-0130-z · 2011 · External reference
High-quality ms/ms spectrum prediction for data-dependent and data-independent acquisition data analysis
10.1038/s41592-019-0427-6 · 2019 · External reference
Impact of ion trap tandem mass spectra variability on the identification of peptides
10.1021/ac0348219 · 2004 · External reference
Unresolved reference
2006 · External reference
Tandem mass spectrometry for trace analysis
10.1021/ac00284a718 · 1985 · External reference
Modeling peptide mass fingerprinting data using the atomic composition of peptides
10.1002/(sici)1522-2683(19991201)20:18<3527::aid-elps3527>3.0.co;2-9 · 1999 · External reference
Semi-supervised lc/ms alignment for differential proteomics
10.1093/bioinformatics/btl219 · 2006 · External reference
Unresolved reference
2012 · External reference
10.1093/nar/gkab1062
10.1093/nar/gkab1062 · 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
10.1101/2022.02.07.479481
10.1101/2022.02.07.479481 · External reference
Full-spectrum prediction of peptides tandem mass spectra using deep neural network
10.1021/acs.analchem.9b04867 · 2020 · External reference
High resolution/accurate mass (hrms) detection of anatoxin-a in lake water using ldtd–apci coupled to a q-exactive mass spectrometer
10.1016/j.talanta.2014.10.021 · 2015 · External reference