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References from PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics – catching the (un)usual suspects. Local targets link to admitted publications; unresolved targets remain external evidence.
In silico data mining of human body fluids to unravel the immunomes in breast cancer
10.1007/s42485-021-00056-z · 2021 · External reference
Shedding light on the hidden human proteome expands immunopeptidome in cancer
2022 · External reference
Unresolved reference
External reference
10.1038/nature18003
10.1038/nature18003 · External reference
Large-scale deep multi-layer analysis of Alzheimer’s disease brain reveals strong proteomic disease-related changes not observed at the RNA level
10.1038/s41593-021-00999-y · 2022 · External reference
Modern proteomics – sample preparation
2016 · External reference
10.1016/j.cell.2022.01.021
10.1016/j.cell.2022.01.021 · External reference
Computational identification of micro-structural variations and their proteogenomic consequences in cancer
10.1093/bioinformatics/btx807 · 2018 · External reference
Editorial: systems biology and omics approaches for understanding complex disease biology
10.3389/fgene.2022.896818 · 2022 · External reference
Big data
2021 · External reference
Proteogenomics
2016 · External reference
Prospects and challenges of cancer systems medicine: from genes to disease networks
2021 · External reference
TANDEM: Matching proteins with tandem mass spectra
10.1093/bioinformatics/bth092 · 2004 · External reference
Open mass spectrometry search algorithm
10.1021/pr0499491 · 2004 · External reference
MS-GF+ makes progress towards a universal database search tool for proteomics
2014 · External reference
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry
10.1074/mcp.m111.011627 · 2011 · External reference
Discovery of rare protein-coding genes in model methylotroph methylobacterium extorquens AM1
10.1002/pmic.201400153 · 2014 · External reference
Proteogenomic analysis of bradyrhizobium japonicum USDA110 using genosuite, an automated multi-algorithmic pipeline
10.1074/mcp.m112.027169 · 2013 · External reference
10.1074/mcp.m114.047126
10.1074/mcp.m114.047126 · External reference
customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search
10.1093/bioinformatics/btt543 · 2013 · External reference
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
10.1038/nmeth1019 · 2007 · External reference
Posterior error probabilities and false discovery rates: Two sides of the same coin
10.1021/pr700739d · 2008 · External reference
False discovery rate estimation in proteomics
10.1007/978-1-4939-3106-4_7 · 2016 · External reference
Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection
10.1021/acs.jproteome.1c00264 · 2021 · External reference
False discovery rate: the Achilles’ heel of proteogenomics
2022 · External reference
Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data
10.1002/pmic.201400206 · 2014 · External reference
Advanced proteogenomic analysis reveals multiple peptide mutations and complex immunoglobulin peptides in colon cancer
10.1021/acs.jproteome.5b00264 · 2015 · External reference
Mass spectrometrists should search only for peptides they care about
10.1038/nmeth.3450 · 2015 · External reference
10.1002/mas.21483
10.1002/mas.21483 · External reference
10.1101/gr.103119.109
10.1101/gr.103119.109 · External reference
10.1101/gr.127951.111
10.1101/gr.127951.111 · External reference
10.1101/gr.077644.108
10.1101/gr.077644.108 · External reference
10.1038/nmeth.3144
10.1038/nmeth.3144 · External reference
Quality control of single amino acid variations detected by tandem mass spectrometry
10.1016/j.jprot.2018.07.004 · 2018 · External reference
Multiaspect examinations of possible alternative mappings of identified variant peptides: a case study on the HEK293 cell line
2022 · External reference
Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines
10.1186/s13073-017-0454-9 · 2017 · External reference
A bioinformatics workflow for variant peptide detection in shotgun proteomics
2011 · External reference
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
10.1038/s41467-018-03311-y · 2018 · External reference
10.1074/mcp.ra118.000812
10.1074/mcp.ra118.000812 · External reference
10.1021/acs.jproteome.6b00344
10.1021/acs.jproteome.6b00344 · External reference
10.1021/pr200031z
10.1021/pr200031z · External reference
Learning from decoys to improve the sensitivity and specificity of proteomics database search results
10.1371/journal.pone.0050651 · 2012 · External reference
10.1074/mcp.m113.028928
10.1074/mcp.m113.028928 · External reference
Posttranslational modifications in systems biology
10.1016/bs.apcsb.2021.03.005 · 2021 · External reference
The language of posttranslational modifications and deciphering it from proteomics data
2023 · External reference
False discovery rates in spectral identification
10.1186/1471-2105-13-s16-s2 · 2012 · External reference
10.1021/acs.jproteome.9b00542
10.1021/acs.jproteome.9b00542 · External reference
MaSS-simulator: a highly configurable simulator for generating MS/MS datasets for benchmarking of proteomics algorithms
2018 · External reference
Systematic optimization of long gradient chromatography mass spectrometry for deep analysis of brain proteome
10.1021/pr500882h · 2015 · External reference
10.1038/nbt.3267
10.1038/nbt.3267 · External reference
A cross-platform toolkit for mass spectrometry and proteomics
10.1038/nbt.2377 · 2012 · External reference
10.1093/nar/gkaa1087
10.1093/nar/gkaa1087 · External reference
The neXtProt knowledgebase in 2020: Data, tools and usability improvements
2020 · External reference
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
10.1002/pmic.200800473 · 2009 · External reference
pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry
10.1002/rcm.3173 · 2007 · External reference
10.1093/nar/gkac1000
10.1093/nar/gkac1000 · External reference
ProteoStats - A library for estimating false discovery rates in proteomics pipelines
10.1093/bioinformatics/btt490 · 2013 · External reference
