hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data (original) (raw)

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). Protein methylation is a posttranslational modification (PTM) consisting in the addition of one or more methyl-groups to arginine and lysine residues of a protein. Lysine can be mono-, di-, or tri-methylated, while arginine can be mono-or di-methylated. Arginine di-methylation can, in turn, be either symmetrical or asymmetrical. While the functional implication of histone lysine and arginine methylation in the regulation of gene expression is well established, recent evidence revealed that this PTM is widespread at the proteome level, a notion that expands its regulatory potential well beyond chromatin structure and