Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome

Víctor Segura, Juan Alberto Medina-Aunon, Maria I. Mora, Salvador Martínez-Bartolomé, Joaquín Abian, Kerman Aloria, Oreto Antúnez, Jesús M. Arizmendi, Mikel Azkargorta, Silvia Barceló-Batllori, Jabier Beaskoetxea, Joan J. Bech-Serra, Francisco Blanco, Mariana B. Monteiro, David Cáceres, Francesc Canals, Monserrat Carrascal, José Ignacio Casal, Felipe Clemente, Nuria ColoméNoelia Dasilva, Paula Díaz, Félix Elortza, Patricia Fernández-Puente, Manuel Fuentes, Oscar Gallardo, Severine I. Gharbi, Concha Gil, Carmen González-Tejedo, María Luisa Hernáez, Manuel Lombardía, Maria Lopez-Lucendo, Miguel Marcilla, José M. Mato, Marta Mendes, Eliandre Oliveira, Irene Orera, Alberto Pascual-Montano, Gorka Prieto, Cristina Ruiz-Romero, Manuel M. Sánchez Del Pino, Daniel Tabas-Madrid, Maria L. Valero, Vital Vialas, Joan Villanueva, Juan Pablo Albar, Fernando J. Corrales*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

23 Citations (Scopus)


The Spanish team of the Human Proteome Project (SpHPP) marked the annotation of Chr16 and data analysis as one of its priorities. Precise annotation of Chromosome 16 proteins according to C-HPP criteria is presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of DNA Elements (ENCODE) data sets were used to obtain further information relative to cell/tissue specific chromosome 16 coding gene expression patterns and to infer the presence of missing proteins. Twenty-four shotgun 2D-LC-MS/MS and gel/LC-MS/MS MIAPE compliant experiments, representing 41% coverage of chromosome 16 proteins, were performed. Furthermore, mapping of large-scale multicenter mass spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines into RNA-Seq data allowed further insights relative to correlation of chromosome 16 transcripts and proteins. Detection and quantification of chromosome 16 proteins in biological matrices by SRM procedures are also primary goals of the SpHPP. Two strategies were undertaken: one focused on known proteins, taking advantage of MS data already available, and the second, aimed at the detection of the missing proteins, is based on the expression of recombinant proteins to gather MS information and optimize SRM methods that will be used in real biological samples. SRM methods for 49 known proteins and for recombinant forms of 24 missing proteins are reported in this study.

Original languageEnglish
Pages (from-to)158-172
Number of pages15
JournalJournal of Proteome Research
Issue number1
Publication statusPublished - 3 Jan 2014
Externally publishedYes


  • bioinformatics
  • Chromosome 16
  • Human Proteome Project
  • proteomics
  • transcriptomics


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