The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L. 2018. A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms. Journal of proteome research. 17(5):1879-1886. doi:10.1021/acs.jproteome.7b00899 (opens in a new tab)
Jarman KH, Heller NC, Jenson SC, Hutchison JR, Payne SH, Wunschel DS, Merkley ED. 2018. Proteomics Goes to Court: A Statistical Foundation for Forensic Toxin/Organism Identification Using Bottom-Up Proteomics. doi:10.1021/acs.jproteome.8b00212 (opens in a new tab)
2017
Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO. 2017. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. 33(11):1744-1746. doi:10.1093/bioinformatics/btx046 (opens in a new tab)
Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. 2017. Methods, Tools and Current Perspectives in Proteogenomics. 16(6):959-981. doi:10.1074/mcp.MR117.000024 (opens in a new tab)
Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, et al. 2017. Informed-Proteomics: open-source software package for top-down proteomics. 14(9):909-914. doi:10.1038/nmeth.4388 (opens in a new tab)
Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ. 2017. PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data. 14(9):903-908. doi:10.1038/nmeth.4390 (opens in a new tab)
Nakayasu ES, Burnet MC, Walukiewicz HE, Wilkins CS, Shukla AK, Brooks S, Plutz MJ, Lee BD, Schilling B, Wolfe AJ, et al. 2017. Ancient Regulatory Role of Lysine Acetylation in Central Metabolism. 8(6). doi:10.1128/mBio.01894-17 (opens in a new tab)
2016
Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, et al. 2016. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. 1(8):16065. doi:10.1038/nmicrobiol.2016.65 (opens in a new tab)
Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, et al. 2016. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. 166(3):755-765. doi:10.1016/j.cell.2016.05.069 (opens in a new tab)
Na S, Payne SH, Bandeira N. 2016. Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks. 15(11):3501-3512. doi:10.1074/mcp.O116.060913 (opens in a new tab)
Tripp HJ, Sutton G, White O, Wortman J, Pati A, Mikhailova N, Ovchinnikova G, Payne SH, Kyrpides NC, Ivanova N. 2015. Toward a standard in structural genome annotation for prokaryotes. 10:45. doi:10.1186/s40793-015-0034-9 (opens in a new tab)
Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, et al. 2015. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. 2:150041. doi:10.1038/sdata.2015.41 (opens in a new tab)
Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH. 2014. Accounting for population variation in targeted proteomics. 13(1):321-3. doi:10.1021/pr4011052 (opens in a new tab)
Amidan BG, Orton DJ, Lamarche BL, Monroe ME, Moore RJ, Venzin AM, Smith RD, Sego LH, Tardiff MF, Payne SH. 2014. Signatures for mass spectrometry data quality. 13(4):2215-22. doi:10.1021/pr401143e (opens in a new tab)
Prost SA, Crowell KL, Baker ES, Ibrahim YM, Clowers BH, Monroe ME, Anderson GA, Smith RD, Payne SH. 2014. Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements. 25(12):2020-2027. doi:10.1007/s13361-014-0895-y (opens in a new tab)
2013
Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, et al. 2013. Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. 20(1):123-33. doi:10.1016/j.chembiol.2012.11.008 (opens in a new tab)
2012
Haft DH, Payne SH, Selengut JD. 2012. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. 194(1):36-48. doi:10.1128/JB.06026-11 (opens in a new tab)
Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolić L, Smith RD, Pevzner PA. 2012. Unexpected diversity of signal peptides in prokaryotes. 3(6). doi:10.1128/mBio.00339-12 (opens in a new tab)
Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. 2008. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. 7(8):3373-81. doi:10.1021/pr800129m (opens in a new tab)
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. 2008. Discovery and revision of Arabidopsis genes by proteogenomics. 105(52):21034-8. doi:10.1073/pnas.0811066106 (opens in a new tab)
