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).

hmSEEKER : identification of hmSILAC Doublets in MaxQuant Output Data / E. Massignani, A. Cuomo, D. Musiani, S. Jammula, G. Pavesi, T. Bonaldi. - In: PROTEOMICS. - ISSN 1615-9853. - 19:5(2019 Mar), pp. e1800300.1-e1800300.6.

hmSEEKER : identification of hmSILAC Doublets in MaxQuant Output Data

E. Massignani
Primo
;
G. Pavesi
;
T. Bonaldi
2019

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).
MS-LC-MS/MS; data processing and analysis; heavy methyl SILAC; methylation; posttranslational modifications analysis; stable isotope labeling
Settore BIO/11 - Biologia Molecolare
Settore INF/01 - Informatica
mar-2019
Article (author)
File in questo prodotto:
File Dimensione Formato  
Massignani_et_al-2019-PROTEOMICS.pdf

accesso aperto

Tipologia: Publisher's version/PDF
Dimensione 1.01 MB
Formato Adobe PDF
1.01 MB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/628242
Citazioni
  • ???jsp.display-item.citation.pmc??? 4
  • Scopus 13
  • ???jsp.display-item.citation.isi??? 11
social impact