hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data

Enrico Massignani, Alessandro Cuomo, Daniele Musiani, Sri Ganesh Jammula, Giulio Pavesi, Tiziana Bonaldi

Research output: Contribution to journalArticlepeer-review


Heavy methyl Stable Isotope Labeling with Amino acids in Cell culture (hmSILAC) is a metabolic labeling strategy employed in proteomics to increase the confidence of global identification of methylated peptides by MS. However, to this day, the automatic and robust identification of heavy and light peak doublets from MS-raw data of hmSILAC experiments is a challenging task, for which the choice of computational methods is very limited. Here, hmSEEKER, a software designed to work downstream of a MaxQuant analysis for in-depth search of MS peak pairs that correspond to light and heavy methyl-peptide within MaxQuant-generated tables is described with good sensitivity and specificity. The software is written in Perl, and its code and user manual are freely available at Bitbucket (

Original languageEnglish
Article number1800300
Issue number5
Publication statusPublished - Mar 2019


  • data processing and analysis
  • heavy methyl SILAC
  • methylation
  • posttranslational modifications analysis
  • stable isotope labeling

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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