An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

Arabi, 2012, Proteomic screen reveals Fbw7 as a modulator of the NF-kappa B pathway, Nat. Commun., 3, 976, 10.1038/ncomms1975

Batth, 2014, Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics, J. Proteome Res., 13, 6176, 10.1021/pr500893m

Beck, 2011, The quantitative proteome of a human cell line, Mol. Syst. Biol., 7, 549, 10.1038/msb.2011.82

Boisvert, 2012, A quantitative spatial proteomics analysis of proteome turnover in human cells, Mol. Cell. Proteomics, 11, M111, 10.1074/mcp.M111.011429

Branca, 2014, HiRIEF LC-MSMS enables deep proteome coverage and unbiased proteogenomics, Nat. Methods, 11, 59, 10.1038/nmeth.2732

Colaert, 2009, Improved visualization of protein consensus sequences by iceLogo, Nat. Methods, 6, 786, 10.1038/nmeth1109-786

de Godoy, 2008, Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast, Nature, 455, 1251, 10.1038/nature07341

Eriksson, 2007, Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs, Nat. Biotechnol., 25, 651, 10.1038/nbt1315

Ezkurdia, 2014, Analyzing the first drafts of the human proteome, J. Proteome Res., 13, 3854, 10.1021/pr500572z

Francavilla, 2016, Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking, Nat. Struct. Mol. Biol., 23, 608, 10.1038/nsmb.3218

Geiger, 2012, Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins, Mol. Cell. Proteomics, 11, M111, 10.1074/mcp.M111.014050

Giansanti, 2015, An augmented multiple-protease-based human phosphopeptide atlas, Cell Rep., 11, 1834, 10.1016/j.celrep.2015.05.029

Giansanti, 2016, Six alternative proteases for mass spectrometry-based proteomics beyond trypsin, Nat. Protoc., 11, 993, 10.1038/nprot.2016.057

Guillaume, 2010, Two abundant proteasome subtypes that uniquely process some antigens presented by HLA class I molecules, Proc. Natl. Acad. Sci. USA, 107, 18599, 10.1073/pnas.1009778107

Guo, 2014, Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics, Mol. Cell. Proteomics, 13, 1573, 10.1074/mcp.M113.035170

Hanke, 2008, Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level, J. Proteome Res., 7, 1118, 10.1021/pr7007175

Hebert, 2014, The one hour yeast proteome, Mol. Cell. Proteomics, 13, 339, 10.1074/mcp.M113.034769

Hornbeck, 2004, PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation, Proteomics, 4, 1551, 10.1002/pmic.200300772

Hunter, 2007, The age of crosstalk: phosphorylation, ubiquitination, and beyond, Mol. Cell, 28, 730, 10.1016/j.molcel.2007.11.019

Huttlin, 2010, A tissue-specific atlas of mouse protein phosphorylation and expression, Cell, 143, 1174, 10.1016/j.cell.2010.12.001

Iwasaki, 2014, Challenges facing complete human proteome analysis, Chromatography, 35, 73, 10.15583/jpchrom.2014.013

Iwasaki, 2012, Human proteome analysis by using reversed phase monolithic silica capillary columns with enhanced sensitivity, J. Chromatogr. A, 1228, 292, 10.1016/j.chroma.2011.10.059

Kelstrup, 2012, Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer, J. Proteome Res., 11, 3487, 10.1021/pr3000249

Kelstrup, 2014, Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer, J. Proteome Res., 13, 6187, 10.1021/pr500985w

Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36

Kim, 2014, A draft map of the human proteome, Nature, 509, 575, 10.1038/nature13302

Kleifeld, 2010, Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products, Nature, 28, 281

Kusebauch, 2016, Human SRMAtlas: a resource of targeted assays to quantify the complete human proteome, Cell, 166, 766, 10.1016/j.cell.2016.06.041

Kutmon, 2015, PathVisio 3: an extendable pathway analysis toolbox, PLoS Comput. Biol., 11, e1004085, 10.1371/journal.pcbi.1004085

Lawrence, 2015, The proteomic landscape of triple-negative breast cancer, Cell Rep., 11, 630, 10.1016/j.celrep.2015.03.050

Low, 2013, Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis, Cell Rep., 5, 1469, 10.1016/j.celrep.2013.10.041

Lundby, 2012, Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues, Nat. Commun., 3, 876, 10.1038/ncomms1871

Masters, 2002, HeLa cells 50 years on: the good, the bad and the ugly, Nat. Rev. Cancer, 2, 315, 10.1038/nrc775

Meggio, 2003, One-thousand-and-one substrates of protein kinase CK2?, FASEB J., 17, 349, 10.1096/fj.02-0473rev

Mertins, 2013, Integrated proteomic analysis of post-translational modifications by serial enrichment, Nat. Methods, 10, 634, 10.1038/nmeth.2518

Mertins, 2016, Proteogenomics connects somatic mutations to signalling in breast cancer, Nature, 534, 55, 10.1038/nature18003

Nagaraj, 2011, Deep proteome and transcriptome mapping of a human cancer cell line, Mol. Syst. Biol., 7, 548, 10.1038/msb.2011.81

Nagaraj, 2012, System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap, Mol. Cell. Proteomics, 11, 10.1074/mcp.M111.013722

Olsen, 2013, Status of large-scale analysis of post-translational modifications by mass spectrometry, Mol. Cell. Proteomics, 12, 3444, 10.1074/mcp.O113.034181

Olsen, 2004, Trypsin cleaves exclusively C-terminal to arginine and lysine residues, Mol. Cell. Proteomics, 3, 608, 10.1074/mcp.T400003-MCP200

Olsen, 2007, Higher-energy C-trap dissociation for peptide modification analysis, Nat. Methods, 4, 709, 10.1038/nmeth1060

Olsen, 2010, Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis, Sci. Signal., 3, ra3, 10.1126/scisignal.2000475

Ongen, 2014, Putative cis-regulatory drivers in colorectal cancer, Nature, 512, 87, 10.1038/nature13602

Puntervoll, 2003, ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins, Nucleic Acids Res., 31, 3625, 10.1093/nar/gkg545

Ruepp, 2008, CORUM: the comprehensive resource of mammalian protein complexes, Nucleic Acids Res., 36, D646, 10.1093/nar/gkm936

Ruepp, 2010, CORUM: the comprehensive resource of mammalian protein complexes – 2009, Nucleic Acids Res., 38, D497, 10.1093/nar/gkp914

Savitski, 2015, A scalable approach for protein false discovery rate estimation in large proteomic data sets, Mol. Cell. Proteomics, 14, 2394, 10.1074/mcp.M114.046995

Schwanhausser, 2011, Global quantification of mammalian gene expression control, Nature, 473, 337, 10.1038/nature10098

Sharma, 2014, Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling, Cell Rep., 8, 1583, 10.1016/j.celrep.2014.07.036

Shaw, 2002, Preferential transformation of human neuronal cells by human adenoviruses and the origin of HEK 293 cells, FASEB J., 16, 869, 10.1096/fj.01-0995fje

Shishkova, 2016, Now, more than ever, proteomics needs better chromatography, Cell Syst., 3, 321, 10.1016/j.cels.2016.10.007

Spicer, 2016, 3D HPLC-MS with reversed-phase separation functionality in all three dimensions for large-scale bottom-up proteomics and peptide retention data collection, Anal. Chem., 88, 2847, 10.1021/acs.analchem.5b04567

Swaney, 2010, Value of using multiple proteases for large-scale mass spectrometry-based proteomics, J. Proteome Res., 9, 1323, 10.1021/pr900863u

Swaney, 2013, Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation, Nat. Methods, 10, 676, 10.1038/nmeth.2519

Szklarczyk, 2015, STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res., 43, D447, 10.1093/nar/gku1003

Thakur, 2011, Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation, Mol. Cell. Proteomics, 10, M110, 10.1074/mcp.M110.003699

The, 2016, Fast and accurate protein false discovery rates on large-scale proteomics data sets with percolator 3.0, J. Am. Soc. Mass Spectrom., 27, 1719, 10.1007/s13361-016-1460-7

Ting, 2011, MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics, Nat. Methods, 8, 937, 10.1038/nmeth.1714

Trapnell, 2010, Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotechnol., 28, 511, 10.1038/nbt.1621

Tyanova, 2016, The MaxQuant computational platform for mass spectrometry-based shotgun proteomics, Nat. Protoc., 11, 2301, 10.1038/nprot.2016.136

Tyanova, 2016, The Perseus computational platform for comprehensive analysis of (prote)omics data, Nat. Methods, 13, 731, 10.1038/nmeth.3901

Van Hoof, 2009, Phosphorylation dynamics during early differentiation of human embryonic stem cells, Cell Stem Cell, 5, 214, 10.1016/j.stem.2009.05.021

Vizcaino, 2014, ProteomeXchange provides globally coordinated proteomics data submission and dissemination, Nat. Biotechnol., 32, 223, 10.1038/nbt.2839

von Stechow, 2015, Recent findings and technological advances in phosphoproteomics for cells and tissues, Expert Rev. Proteomics, 12, 469, 10.1586/14789450.2015.1078730

Wang, 2011, Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells, Proteomics, 11, 2019, 10.1002/pmic.201000722

Wilhelm, 2014, Mass-spectrometry-based draft of the human proteome, Nature, 509, 582, 10.1038/nature13319

Wisniewski, 2009, Universal sample preparation method for proteome analysis, Nat. Methods, 6, 359, 10.1038/nmeth.1322

Wisniewski, 2014, A “proteomic ruler” for protein copy number and concentration estimation without spike-in standards, Mol. Cell. Proteomics, 13, 3497, 10.1074/mcp.M113.037309

Wolters, 2001, An automated multidimensional protein identification technology for shotgun proteomics, Anal. Chem., 73, 5683, 10.1021/ac010617e

Yamana, 2013, Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot Nanolc-MS/MS analysis with meter-scale monolithic silica columns, J. Proteome Res., 12, 214, 10.1021/pr300837u

Zeiler, 2012, A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines, Mol. Cell. Proteomics, 11, 10.1074/mcp.O111.009613