Table I Recent large scale LC-MS/MS methylation site discovery experiments

Arginine and lysine methylation are abbreviated metR and metK, respectively.

OrganismSample preparationMS instrument platform(s)Methyl-PSM data filteringNo. of methylation sites reportedRef. (year)
Human (Jurkat cells)Peptide separation (HILIC)Q ExactiveHeavy-methyl SILAC249 metR6 (2012)
Trypanosoma bruceiPeptide separation (SCX)LTQ Orbitrap ETD (alternating CID and ETD)Thresholding to meet global target-decoy FDR estimates333 metR5 (2012)
T. bruceiPeptide separation (SCX)LTQ Orbitrap ETD (alternating CID and ETD)Thresholding to meet global target-decoy FDR estimates1332 metR9 (2013)
Human (HeLa cells)Antibody-based peptide immunoprecipitation and peptide separation (SCX)LTQ Orbitrap XLThresholding to meet global target-decoy FDR estimatesa552 metK4 (2013)
Human (HeLa cells)Antibody-based protein immunoprecipitation and SDS-PAGE, SDS-PAGE, or peptide separation (IEP)LTQ Orbitrap VelosHeavy-methyl SILAC397 metR and metK7 (2013)
Human (HCT116 cells) and mouseAntibody-based peptide immunoprecipitationOrbitrap Elite and Q ExactiveThresholding to meet global target-decoy FDR estimates>1000 metR and ∼160 metK8 (2013)
Arabidoposis thalianaSDS-PAGEbQ-TOF Ultima and LTQ-FTbSeparate target-decoy FDR estimates, in-depth manual inspection and curation of MS/MS data31 metR and metK11 (2014)
Human (HEK 293T cells)Antibody-based peptide immunoprecipitation and peptide separation (SCX)Q ExactiveThresholding to meet separate target-decoy FDR estimates1027 metR15 (2014)
Human (T cells)Antibody-based peptide immunoprecipitationQ ExactiveIsomethionine-methyl SILAC2,502 metR13 (2015)
Human (HeLa, K562, SW620, A549, SMM7721 cells)Antibody-based derivatized peptide immunoprecipitationOrbitrap Elite13CD3-methionine labeling with derivatized MML446 metK12 (2015)
S. cerevisiaeIn-solution digestion of cell lysatesLTQ Orbitrap XLGlobal target-decoy FDR estimates and arbitrary thresholding (heavy AdoMet labeling)c64 (various)d10 (2015)
S. cerevisiaeAntibody-based peptide immunoprecipitationQ Exactive and Orbitrap Elite (alternating CID and ETD)Heavy-methyl SILAC41 metR14 (2015)
S. cerevisiaeAntibody-based peptide immunoprecipitationLTQ Orbitrap Velos Pro ETDHeavy-methyl SILAC21 metR16 (2015)
  • a Samples from 13CD3-methionine labeled cells were analyzed but not used to validate methyl-PSMs, i.e. analysis of heavy samples was performed separately to light samples.

  • b Data were obtained from the AT_CHOLO database (57).

  • c Isotopic labeling employed to identify putative heavy/light pairs in first parse filtering; in-depth validation using heavy/light peptide data not performed.

  • d Including redundant identifications, i.e. multiple methyl-PSMs associated with methylation on different amino acid residues identified from individual MS/MS spectra.