HmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data. Issue 5 (18th February 2019)

• Record Type: Journal Article
• Authors: Massignani, Enrico; Cuomo, Alessandro; Musiani, Daniele; Jammula, SriGanesh; Pavesi, Giulio; Bonaldi, Tiziana
• Is Part Of: Proteomics. Volume 19:Issue 5(2019)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2019-02-18
• Subjects: data processing and analysis -- heavy methyl SILAC -- methylation -- MS–LC–MS/MS -- posttranslational modifications analysis -- stable isotope labeling; Proteins -- Separation -- Periodicals; Bioinformatics -- Periodicals; Proteomics -- Periodicals; Genomes -- Periodicals; Molecular genetics -- Periodicals; 572.605
• DOI: 10.1002/pmic.201800300
• Languages: English
• ISSNs: 1615-9853

Abstract

Abstract: 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 (https://bit.ly/2scCT9u ).