MOESM1 of Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code
Creators: name: Sidoli, Simone
name: Congcong Lu
name: Coradin, Mariel
name: Xiaoshi Wang
name: Karch, Kelly
name: Chrystian Ruminowicz
name: Garcia, Benjamin
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Developmental Biology

description: Additional file 1: Figure S1. Analysis of EMT cells labeled using heavy lysine/arginine (heavy KR) during mesenchymal transition. (A) Workflow for metabolic labeling of EMT cells at the histone sequence level (heavy KR). (B) Pearson’s correlation values between technical and biological replicates (rep 2-1 implies second biological, first technical), differentiated between combinatorial PTMs quantified on unlabeled histone tails (old histones) and heavy labeled histone tails (new). (C) Bar plot representing the relative abundance of single histone PTMs on heavy labeled histone tails at day 1 (top) and day 2 (bottom). Unlabeled histone tails were excessively low abundant to provide a confident quantification of single histone PTMs. Figure S2. Annotated MS/MS spectrum of the histone H3 N-terminal tail modified as K27me2. From the top to bottom, (i) annotated sequence with highlights of identified fragments and modified site, (ii) annotated spectrum, (iii) observed mass, identified modification and Mascot (Matrix Science) identification scores, (iv) distribution of the fragment mass error, expressed in Da (left) and ppm (right). Figure S3. Annotated MS/MS spectrum of the histone H3 N-terminal tail modified as K27me2:2. From the top to bottom, (i) annotated sequence with highlights of identified fragments and modified site, (ii) annotated spectrum, (iii) observed mass, identified modification and Mascot (Matrix Science) identification scores, (iv) distribution of the fragment mass error, expressed in Da (left) and ppm (right). Figure S4. Annotated MS/MS spectrum of the histone H3 N-terminal tail modified as K14acK27me2:2. From the top to bottom, (i) annotated sequence with highlights of identified fragments and modified site, (ii) annotated spectrum, (iii) observed mass, identified modification and Mascot (Matrix Science) identification scores, (iv) distribution of the fragment mass error, expressed in Da (left) and ppm (right). Figure S5. Annotated MS/MS spectrum of the histone H3 N-terminal tail modified as K23me1:1K27me2:2. From the top to bottom, (i) annotated sequence with highlights of identified fragments and modified site, (ii) annotated spectrum, (iii) observed mass, identified modification and Mascot (Matrix Science) identification scores, (iv) distribution of the fragment mass error, expressed in Da (left) and ppm (right). Figure S6. Relative abundance of all quantified methylations during EMT stimulation combined with heavy methyl labeling. Each plot represents the trend line of differently methylated PTM sites. Error bar represents standard deviation between three biological replicates (two for day 0). Figure S7. Sum of all quantitative values of peptides identified in the EMT cell lines incubated with heavy methionine during transition. The relative abundances represent the total quantification of peptides carrying no heavy labeled methylations (in blue) versus peptides carrying at least one heavy labeled methylation (in orange). Evidently, cells growing in a non-confluent state acquire heavy methylation faster than confluent cells, which have reduced growth rate.