Proteomic validation of transcript isoforms, including those assembled from RNA-Seq data

Journal of Proteome Research

Volumn 14, Issue 9, 2015, Pages 3541-3554

  Tay, Aidan P ^a   Pang, Chi Nam Ignatius ^a   Twine, Natalie A ^a   Hart Smith, Gene ^a   Harkness, Linda ^b   Kassem, Moustapha ^b   Wilkins, Marc R ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b ODENSE UNIVERSITY HOSPITAL   (Denmark)

Author keywords

alternative splicing; isoform specific peptides; mesenchymal stem cell; proteotypic peptides; RNA seq; splice junction peptides

Indexed keywords

ISOPROTEIN; RNA ISOFORM; CODON; MESSENGER RNA;

AMINO ACID SEQUENCE; ARTICLE; GENOMICS; HAPLOTYPE; HUMAN; HUMAN CELL; MESENCHYMAL STEM CELL; OPEN READING FRAME; OSTEOBLAST; PRIORITY JOURNAL; PROTEOMICS; RNA SEQUENCE; RNA TRANSLATION; TANDEM MASS SPECTROMETRY; CELL CULTURE; CHEMISTRY; CODON; EXON; GENETICS; RNA SPLICING; SEQUENCE ANALYSIS; VALIDATION STUDY;

CELLS, CULTURED; CODON; EXONS; HUMANS; OPEN READING FRAMES; PROTEIN ISOFORMS; PROTEOMICS; RNA SPLICING; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TANDEM MASS SPECTROMETRY;

EID: 84941105408     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr5011394     Document Type: Article

References (74)

1. Djebali, S.; Davis, C. A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; Lagarde, J.; Lin, W.; Schlesinger, F.; Xue, C.; Marinov, G. K.; Khatun, J.; Williams, B. A.; Zaleski, C.; Rozowsky, J.; Roder, M.; Kokocinski, F.; Abdelhamid, R. F.; Alioto, T.; Antoshechkin, I.; Baer, M. T.; Bar, N. S.; Batut, P.; Bell, K.; Bell, I.; Chakrabortty, S.; Chen, X.; Chrast, J.; Curado, J.; Derrien, T.; Drenkow, J.; Dumais, E.; Dumais, J.; Duttagupta, R.; Falconnet, E.; Fastuca, M.; Fejes-Toth, K.; Ferreira, P.; Foissac, S.; Fullwood, M. J.; Gao, H.; Gonzalez, D.; Gordon, A.; Gunawardena, H.; Howald, C.; Jha, S.; Johnson, R.; Kapranov, P.; King, B.; Kingswood, C.; Luo, O. J.; Park, E.; Persaud, K.; Preall, J. B.; Ribeca, P.; Risk, B.; Robyr, D.; Sammeth, M.; Schaffer, L.; See, L. H.; Shahab, A.; Skancke, J.; Suzuki, A. M.; Takahashi, H.; Tilgner, H.; Trout, D.; Walters, N.; Wang, H.; Wrobel, J.; Yu, Y.; Ruan, X.; Hayashizaki, Y.; Harrow, J.; Gerstein, M.; Hubbard, T.; Reymond, A.; Antonarakis, S. E.; Hannon, G.; Giddings, M. C.; Ruan, Y.; Wold, B.; Carninci, P.; Guigo, R.; Gingeras, T. R. Landscape of transcription in human cells Nature 2012, 489 (7414) 101-8
2. Wang, E. T.; Sandberg, R.; Luo, S.; Khrebtukova, I.; Zhang, L.; Mayr, C.; Kingsmore, S. F.; Schroth, G. P.; Burge, C. B. Alternative isoform regulation in human tissue transcriptomes Nature 2008, 456 (7221) 470-6
3. Eksi, R.; Li, H. D.; Menon, R.; Wen, Y.; Omenn, G. S.; Kretzler, M.; Guan, Y. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data PLoS Comput. Biol. 2013, 9 (11) e1003314
4. Li, H. D.; Menon, R.; Omenn, G. S.; Guan, Y. The emerging era of genomic data integration for analyzing splice isoform function Trends Genet. 2014, 30 (8) 340-7
5. Li, H. D.; Menon, R.; Omenn, G. S.; Guan, Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence Proteomics 2014, 14 (23-24) 2709-18
6. Kim, M. S.; Pinto, S. M.; Getnet, D.; Nirujogi, R. S.; Manda, S. S.; Chaerkady, R.; Madugundu, A. K.; Kelkar, D. S.; Isserlin, R.; Jain, S.; Thomas, J. K.; Muthusamy, B.; Leal-Rojas, P.; Kumar, P.; Sahasrabuddhe, N. A.; Balakrishnan, L.; Advani, J.; George, B.; Renuse, S.; Selvan, L. D.; Patil, A. H.; Nanjappa, V.; Radhakrishnan, A.; Prasad, S.; Subbannayya, T.; Raju, R.; Kumar, M.; Sreenivasamurthy, S. K.; Marimuthu, A.; Sathe, G. J.; Chavan, S.; Datta, K. K.; Subbannayya, Y.; Sahu, A.; Yelamanchi, S. D.; Jayaram, S.; Rajagopalan, P.; Sharma, J.; Murthy, K. R.; Syed, N.; Goel, R.; Khan, A. A.; Ahmad, S.; Dey, G.; Mudgal, K.; Chatterjee, A.; Huang, T. C.; Zhong, J.; Wu, X.; Shaw, P. G.; Freed, D.; Zahari, M. S.; Mukherjee, K. K.; Shankar, S.; Mahadevan, A.; Lam, H.; Mitchell, C. J.; Shankar, S. K.; Satishchandra, P.; Schroeder, J. T.; Sirdeshmukh, R.; Maitra, A.; Leach, S. D.; Drake, C. G.; Halushka, M. K.; Prasad, T. S.; Hruban, R. H.; Kerr, C. L.; Bader, G. D.; Iacobuzio-Donahue, C. A.; Gowda, H.; Pandey, A. A draft map of the human proteome Nature 2014, 509 (7502) 575-81
7. Marko-Varga, G.; Omenn, G. S.; Paik, Y. K.; Hancock, W. S. A first step toward completion of a genome-wide characterization of the human proteome J. Proteome Res. 2013, 12 (1) 1-5
8. Blakeley, P.; Siepen, J. A.; Lawless, C.; Hubbard, S. J. Investigating protein isoforms via proteomics: a feasibility study Proteomics 2010, 10 (6) 1127-40
9. Picotti, P.; Lam, H.; Campbell, D.; Deutsch, E. W.; Mirzaei, H.; Ranish, J.; Domon, B.; Aebersold, R. A database of mass spectrometric assays for the yeast proteome Nat. Methods 2008, 5 (11) 913-4
10. Stastna, M.; Van Eyk, J. E. Analysis of protein isoforms: can we do it better? Proteomics 2012, 12 (19-20) 2937-48
11. Krieger, J. R.; Taylor, P.; Gajadhar, A. S.; Guha, A.; Moran, M. F.; McGlade, C. J. Identification and selected reaction monitoring (SRM) quantification of endocytosis factors associated with Numb Mol. Cell Proteomics 2013, 12 (2) 499-514
12. Shargunov, A. V.; Krasnov, G. S.; Ponomarenko, E. A.; Lisitsa, A. V.; Shurdov, M. A.; Zverev, V. V.; Archakov, A. I.; Blinov, V. M. Tissue-specific alternative splicing analysis reveals the diversity of chromosome 18 transcriptome J. Proteome Res. 2014, 13 (1) 173-82
13. Pang, C. N.; Tay, A. P.; Aya, C.; Twine, N. A.; Harkness, L.; Hart-Smith, G.; Chia, S. Z.; Chen, Z.; Deshpande, N. P.; Kaakoush, N. O.; Mitchell, H. M.; Kassem, M.; Wilkins, M. R. Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing J. Proteome Res. 2014, 13 (1) 84-98
14. Zhu, Y.; Hultin-Rosenberg, L.; Forshed, J.; Branca, R. M.; Orre, L. M.; Lehtio, J. SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data Mol. Cell Proteomics 2014, 13 (6) 1552-62
15. Evans, V. C.; Barker, G.; Heesom, K. J.; Fan, J.; Bessant, C.; Matthews, D. A. De novo derivation of proteomes from transcriptomes for transcript and protein identification Nat. Methods 2012, 9 (12) 1207-11
16. Thorvaldsdottir, H.; Robinson, J. T.; Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Brief. Bioinf. 2013, 14, 178-92
17. Gaudet, P.; Argoud-Puy, G.; Cusin, I.; Duek, P.; Evalet, O.; Gateau, A.; Gleizes, A.; Pereira, M.; Zahn-Zabal, M.; Zwahlen, C.; Bairoch, A.; Lane, L. neXtProt: organizing protein knowledge in the context of human proteome projects J. Proteome Res. 2013, 12 (1) 293-8
18. Flicek, P.; Amode, M. R.; Barrell, D.; Beal, K.; Billis, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; Coates, G.; Fitzgerald, S.; Gil, L.; Giron, C. G.; Gordon, L.; Hourlier, T.; Hunt, S.; Johnson, N.; Juettemann, T.; Kahari, A. K.; Keenan, S.; Kulesha, E.; Martin, F. J.; Maurel, T.; McLaren, W. M.; Murphy, D. N.; Nag, R.; Overduin, B.; Pignatelli, M.; Pritchard, B.; Pritchard, E.; Riat, H. S.; Ruffier, M.; Sheppard, D.; Taylor, K.; Thormann, A.; Trevanion, S. J.; Vullo, A.; Wilder, S. P.; Wilson, M.; Zadissa, A.; Aken, B. L.; Birney, E.; Cunningham, F.; Harrow, J.; Herrero, J.; Hubbard, T. J.; Kinsella, R.; Muffato, M.; Parker, A.; Spudich, G.; Yates, A.; Zerbino, D. R.; Searle, S. M. Ensembl 2014 Nucleic Acids Res. 2014, 42, D749-55
19. Pruitt, K. D.; Brown, G. R.; Hiatt, S. M.; Thibaud-Nissen, F.; Astashyn, A.; Ermolaeva, O.; Farrell, C. M.; Hart, J.; Landrum, M. J.; McGarvey, K. M.; Murphy, M. R.; O'Leary, N. A.; Pujar, S.; Rajput, B.; Rangwala, S. H.; Riddick, L. D.; Shkeda, A.; Sun, H.; Tamez, P.; Tully, R. E.; Wallin, C.; Webb, D.; Weber, J.; Wu, W.; DiCuccio, M.; Kitts, P.; Maglott, D. R.; Murphy, T. D.; Ostell, J. M. RefSeq: an update on mammalian reference sequences Nucleic Acids Res. 2014, 42, D756-63
20. Lane, L.; Bairoch, A.; Beavis, R. C.; Deutsch, E. W.; Gaudet, P.; Lundberg, E.; Omenn, G. S. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins J. Proteome Res. 2014, 13 (1) 15-20
21. Lee, Y.; Lee, Y.; Kim, B.; Shin, Y.; Nam, S.; Kim, P.; Kim, N.; Chung, W. H.; Kim, J.; Lee, S. ECgene: an alternative splicing database update Nucleic Acids Res. 2007, 35, D99-103
22. Menon, R.; Im, H.; Zhang, E. Y.; Wu, S. L.; Chen, R.; Snyder, M.; Hancock, W. S.; Omenn, G. S. Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes J. Proteome Res. 2014, 13 (1) 212-27
23. Tavares, R.; de Miranda Scherer, N.; Pauletti, B. A.; Araujo, E.; Folador, E. L.; Espindola, G.; Ferreira, C. G.; Paes Leme, A. F.; de Oliveira, P. S.; Passetti, F. SpliceProt: a protein sequence repository of predicted human splice variants Proteomics 2014, 14 (2-3) 181-5
24. Woo, S.; Cha, S. W.; Merrihew, G.; He, Y.; Castellana, N.; Guest, C.; Maccoss, M.; Bafna, V. Proteogenomic database construction driven from large scale RNA-seq data J. Proteome Res. 2014, 13, 21-8
25. Sheynkman, G. M.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq Mol. Cell Proteomics 2013, 12, 2341-53
26. Woo, S.; Cha, S. W.; Na, S.; Guest, C.; Liu, T.; Smith, R. D.; Rodland, K. D.; Payne, S.; Bafna, V. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data Proteomics 2014, 14 (23-24) 2719-30
27. Tang, F.; Barbacioru, C.; Bao, S.; Lee, C.; Nordman, E.; Wang, X.; Lao, K.; Surani, M. A. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis Cell Stem Cell 2010, 6 (5) 468-78
28. Klimmeck, D.; Cabezas-Wallscheid, N.; Reyes, A.; von Paleske, L.; Renders, S.; Hansson, J.; Krijgsveld, J.; Huber, W.; Trumpp, A. Transcriptome-wide profiling and posttranscriptional analysis of hematopoietic stem/progenitor cell differentiation toward myeloid commitment Stem Cell Rep. 2014, 3 (5) 858-75
29. Kroll, J. E.; de Souza, S. J.; de Souza, G. A. Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites Peer J. 2014, 2, e673
30. Skarn, M.; Namlos, H. M.; Noordhuis, P.; Wang, M. Y.; Meza-Zepeda, L. A.; Myklebost, O. Adipocyte differentiation of human bone marrow-derived stromal cells is modulated by microRNA-155, microRNA-221, and microRNA-222 Stem Cells Dev. 2012, 21 (6) 873-83
31. Al-toub, M.; Almusa, A.; Almajed, M.; Al-Nbaheen, M.; Kassem, M.; Aldahmash, A.; Alajez, N. M. Pleiotropic effects of cancer cells' secreted factors on human stromal (mesenchymal) stem cells Stem Cell Res. Ther. 2013, 4 (5) 114
32. Salomonis, N.; Nelson, B.; Vranizan, K.; Pico, A. R.; Hanspers, K.; Kuchinsky, A.; Ta, L.; Mercola, M.; Conklin, B. R. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors PLoS Comput. Biol. 2009, 5 (11) e1000553
33. Larsen, K. H.; Frederiksen, C. M.; Burns, J. S.; Abdallah, B. M.; Kassem, M. Identifying a molecular phenotype for bone marrow stromal cells with in vivo bone-forming capacity J. Bone Miner. Res. 2010, 25 (4) 796-808
34. Twine, N. A.; Chen, L.; Pang, C. N.; Wilkins, M. R.; Kassem, M. Identification of differentiation-stage specific markers that define the ex vivo osteoblastic phenotype Bone 2014, 67, 23-32
35. FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc (April 3, 2013).
36. Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S. L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol. 2013, 14 (4) R36
37. Trapnell, C.; Hendrickson, D. G.; Sauvageau, M.; Goff, L.; Rinn, J. L.; Pachter, L. Differential analysis of gene regulation at transcript resolution with RNA-seq Nat. Biotechnol. 2013, 31 (1) 46-53
38. Hart-Smith, G.; Raftery, M. J. Detection and characterization of low abundance glycopeptides via higher-energy C-trap dissociation and orbitrap mass analysis J. Am. Soc. Mass Spectrom. 2012, 23 (1) 124-40
39. Vizcaino, J. A.; Deutsch, E. W.; Wang, R.; Csordas, A.; Reisinger, F.; Rios, D.; Dianes, J. A.; Sun, Z.; Farrah, T.; Bandeira, N.; Binz, P. A.; Xenarios, I.; Eisenacher, M.; Mayer, G.; Gatto, L.; Campos, A.; Chalkley, R. J.; Kraus, H. J.; Albar, J. P.; Martinez-Bartolome, S.; Apweiler, R.; Omenn, G. S.; Martens, L.; Jones, A. R.; Hermjakob, H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nat. Biotechnol. 2014, 32 (3) 223-6
40. Wright, J. C.; Collins, M. O.; Yu, L.; Kall, L.; Brosch, M.; Choudhary, J. S. Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator Mol. Cell Proteomics 2012, 11 (8) 478-91
41. Wang, M.; Herrmann, C. J.; Simonovic, M.; Szklarczyk, D.; von Mering, C. Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines Proteomics 2015, 10.1002/pmic.201400441
42. R Development Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2008.
43. Huang da, W.; Sherman, B. T.; Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Nucleic Acids Res. 2009, 37 (1) 1-13
44. Bianchi, V.; Colantoni, A.; Calderone, A.; Ausiello, G.; Ferre, F.; Helmer-Citterich, M. DBATE: database of alternative transcripts expression Database 2013, 2013, bat050
45. Mallick, P.; Schirle, M.; Chen, S. S.; Flory, M. R.; Lee, H.; Martin, D.; Ranish, J.; Raught, B.; Schmitt, R.; Werner, T.; Kuster, B.; Aebersold, R. Computational prediction of proteotypic peptides for quantitative proteomics Nat. Biotechnol. 2007, 25 (1) 125-31
46. Ivanov, I. P.; Firth, A. E.; Michel, A. M.; Atkins, J. F.; Baranov, P. V. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences Nucleic Acids Res. 2011, 39 (10) 4220-34
47. Gonzalez-Porta, M.; Frankish, A.; Rung, J.; Harrow, J.; Brazma, A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene Genome Biol. 2013, 14 (7) R70
48. Ezkurdia, I.; Rodriguez, J. M.; Carrillo-de Santa Pau, E.; Vazquez, J.; Valencia, A.; Tress, M. L. Most highly expressed protein-coding genes have a single dominant isoform J. Proteome Res. 2015, 14, 1880-7
49. Lundberg, E.; Fagerberg, L.; Klevebring, D.; Matic, I.; Geiger, T.; Cox, J.; Algenas, C.; Lundeberg, J.; Mann, M.; Uhlen, M. Defining the transcriptome and proteome in three functionally different human cell lines Mol. Syst. Biol. 2010, 6, 450
50. Varrin-Doyer, M.; Nicolle, A.; Marignier, R.; Cavagna, S.; Benetollo, C.; Wattel, E.; Giraudon, P. Human T lymphotropic virus type 1 increases T lymphocyte migration by recruiting the cytoskeleton organizer CRMP2 J. Immunol 2012, 188 (3) 1222-33
51. Hamajima, N.; Matsuda, K.; Sakata, S.; Tamaki, N.; Sasaki, M.; Nonaka, M. A novel gene family defined by human dihydropyrimidinase and three related proteins with differential tissue distribution Gene 1996, 180 (1-2) 157-63
52. Rahajeng, J.; Giridharan, S. S.; Naslavsky, N.; Caplan, S. Collapsin response mediator protein-2 (Crmp2) regulates trafficking by linking endocytic regulatory proteins to dynein motors J. Biol. Chem. 2010, 285 (42) 31918-22
53. Morgan-Fisher, M.; Couchman, J. R.; Yoneda, A. Phosphorylation and mRNA splicing of collapsin response mediator protein-2 determine inhibition of rho-associated protein kinase (ROCK) II function in carcinoma cell migration and invasion J. Biol. Chem. 2013, 288 (43) 31229-40
54. Mientjes, E. J.; Willemsen, R.; Kirkpatrick, L. L.; Nieuwenhuizen, I. M.; Hoogeveen-Westerveld, M.; Verweij, M.; Reis, S.; Bardoni, B.; Hoogeveen, A. T.; Oostra, B. A.; Nelson, D. L. Fxr1 knockout mice show a striated muscle phenotype: implications for Fxr1p function in vivo Hum. Mol. Genet. 2004, 13 (13) 1291-302
55. Dinkel, H.; Van Roey, K.; Michael, S.; Davey, N. E.; Weatheritt, R. J.; Born, D.; Speck, T.; Kruger, D.; Grebnev, G.; Kuban, M.; Strumillo, M.; Uyar, B.; Budd, A.; Altenberg, B.; Seiler, M.; Chemes, L. B.; Glavina, J.; Sanchez, I. E.; Diella, F.; Gibson, T. J. The eukaryotic linear motif resource ELM: 10 years and counting Nucleic Acids Res. 2014, 42, D259-66
56. Gilmour, P. S.; O'Shea, P. J.; Fagura, M.; Pilling, J. E.; Sanganee, H.; Wada, H.; Courtney, P. F.; Kavanagh, S.; Hall, P. A.; Escott, K. J. Human stem cell osteoblastogenesis mediated by novel glycogen synthase kinase 3 inhibitors induces bone formation and a unique bone turnover biomarker profile in rats Toxicol. Appl. Pharmacol. 2013, 272 (2) 399-407
57. Chen, F. C.; Wang, S. S.; Chen, C. J.; Li, W. H.; Chuang, T. J. Alternatively and constitutively spliced exons are subject to different evolutionary forces Mol. Biol. Evol. 2006, 23 (3) 675-82
58. Ederveen, T. H.; Overmars, L.; van Hijum, S. A. Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction PLoS One 2013, 8 (5) e63523
59. Blakeley, P.; Overton, I. M.; Hubbard, S. J. Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies J. Proteome Res. 2012, 11 (11) 5221-34
60. Banfai, B.; Jia, H.; Khatun, J.; Wood, E.; Risk, B.; Gundling, W. E., Jr.; Kundaje, A.; Gunawardena, H. P.; Yu, Y.; Xie, L.; Krajewski, K.; Strahl, B. D.; Chen, X.; Bickel, P.; Giddings, M. C.; Brown, J. B.; Lipovich, L. Long noncoding RNAs are rarely translated in two human cell lines Genome Res. 2012, 22 (9) 1646-57
61. Juntawong, P.; Bailey-Serres, J. Dynamic light regulation of translation status in Arabidopsis thaliana Front. Plant Sci. 2012, 3, 66
62. Menschaert, G.; Van Criekinge, W.; Notelaers, T.; Koch, A.; Crappe, J.; Gevaert, K.; Van Damme, P. Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events Mol. Cell Proteomics 2013, 12 (7) 1780-90
63. Bazzini, A. A.; Johnstone, T. G.; Christiano, R.; Mackowiak, S. D.; Obermayer, B.; Fleming, E. S.; Vejnar, C. E.; Lee, M. T.; Rajewsky, N.; Walther, T. C.; Giraldez, A. J. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation EMBO J. 2014, 33 (9) 981-93
64. Wilhelm, M.; Schlegl, J.; Hahne, H.; Moghaddas Gholami, A.; Lieberenz, M.; Savitski, M. M.; Ziegler, E.; Butzmann, L.; Gessulat, S.; Marx, H.; Mathieson, T.; Lemeer, S.; Schnatbaum, K.; Reimer, U.; Wenschuh, H.; Mollenhauer, M.; Slotta-Huspenina, J.; Boese, J. H.; Bantscheff, M.; Gerstmair, A.; Faerber, F.; Kuster, B. Mass-spectrometry-based draft of the human proteome Nature 2014, 509 (7502) 582-7
65. Buljan, M.; Chalancon, G.; Eustermann, S.; Wagner, G. P.; Fuxreiter, M.; Bateman, A.; Babu, M. M. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks Mol. Cell 2012, 46 (6) 871-83
66. Ellis, J. D.; Barrios-Rodiles, M.; Colak, R.; Irimia, M.; Kim, T.; Calarco, J. A.; Wang, X.; Pan, Q.; O'Hanlon, D.; Kim, P. M.; Wrana, J. L.; Blencowe, B. J. Tissue-specific alternative splicing remodels protein-protein interaction networks Mol. Cell 2012, 46 (6) 884-92
67. Davis, M. J.; Shin, C. J.; Jing, N.; Ragan, M. A. Rewiring the dynamic interactome Mol. BioSyst. 2012, 8 (8) 2054-66
68. Engstrom, P. G.; Steijger, T.; Sipos, B.; Grant, G. R.; Kahles, A.; Ratsch, G.; Goldman, N.; Hubbard, T. J.; Harrow, J.; Guigo, R.; Bertone, P. Consortium, R., Systematic evaluation of spliced alignment programs for RNA-seq data Nat. Methods 2013, 10 (12) 1185-91
69. Sharon, D.; Tilgner, H.; Grubert, F.; Snyder, M. A single-molecule long-read survey of the human transcriptome Nat. Biotechnol. 2013, 31 (11) 1009-14
70. Tran, J. C.; Zamdborg, L.; Ahlf, D. R.; Lee, J. E.; Catherman, A. D.; Durbin, K. R.; Tipton, J. D.; Vellaichamy, A.; Kellie, J. F.; Li, M.; Wu, C.; Sweet, S. M.; Early, B. P.; Siuti, N.; LeDuc, R. D.; Compton, P. D.; Thomas, P. M.; Kelleher, N. L. Mapping intact protein isoforms in discovery mode using top-down proteomics Nature 2011, 480 (7376) 254-8
71. Nagaraj, N.; Wisniewski, J. R.; Geiger, T.; Cox, J.; Kircher, M.; Kelso, J.; Paabo, S.; Mann, M. Deep proteome and transcriptome mapping of a human cancer cell line Mol. Syst. Biol. 2011, 7, 548
72. Meyer, J. G.; Kim, S.; Maltby, D. A.; Ghassemian, M.; Bandeira, N.; Komives, E. A. Expanding proteome coverage with orthogonal-specificity alpha-lytic proteases Mol. Cell Proteomics 2014, 13 (3) 823-35
73. Omenn, G. S.; Guan, Y.; Menon, R. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines J. Proteomics 2014, 107, 103-12
74. Woo, S.; Cha, S. W.; Na, S.; Guest, C.; Liu, T.; Smith, R. D.; Rodland, K. D.; Payne, S.; Bafna, V. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next generation sequencing data Proteomics 2014, 14, 2719-30