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Selected Publications

For a full list see Google Scholar


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

Lee JY, Fujimoto GM, Wilson R, Wiley HS, Payne SH. 2018. Blazing Signature Filter: a library for fast pairwise similarity comparisons. 19(1):221. doi:10.1186/s12859-018-2210-6

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


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

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

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

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

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


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

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

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


Payne SH. 2015. The utility of protein and mRNA correlation. 40(1):1-3. doi:10.1016/j.tibs.2014.10.010

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

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

Gibbons BC, Chambers MC, Monroe ME, Tabb DL, Payne SH. 2015. Correcting systematic bias and instrument measurement drift with mzRefinery. 31(23):3838-40. doi:10.1093/bioinformatics/btv437


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

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

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


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


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

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


Venter E, Smith RD, Payne SH. 2011. Proteogenomic analysis of bacteria and archaea: a 46 organism case study. 6(11):e27587. doi:10.1371/journal.pone.0027587


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

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