TY - JOUR
T1 - hmSEEKER
T2 - Identification of hmSILAC Doublets in MaxQuant Output Data
AU - Massignani, Enrico
AU - Cuomo, Alessandro
AU - Musiani, Daniele
AU - Jammula, Sri Ganesh
AU - Pavesi, Giulio
AU - Bonaldi, Tiziana
PY - 2019/3
Y1 - 2019/3
N2 - 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).
AB - 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).
KW - data processing and analysis
KW - heavy methyl SILAC
KW - methylation
KW - MS–LC–MS/MS
KW - posttranslational modifications analysis
KW - stable isotope labeling
UR - http://www.scopus.com/inward/record.url?scp=85061896596&partnerID=8YFLogxK
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U2 - 10.1002/pmic.201800300
DO - 10.1002/pmic.201800300
M3 - Article
C2 - 30656827
AN - SCOPUS:85061896596
VL - 19
JO - Proteomics
JF - Proteomics
SN - 1615-9853
IS - 5
M1 - 1800300
ER -