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The relative abundance of the extracted proteins was determined by comparison to protein extracts from DLBCL cell lines cultured in medium containing heavy isotope labeled amino acids. To improve coverage and maximize the number of identified/quantified proteins, extracted proteins were processed according to two different workflows. First, proteins were separated by denaturing polyacrylamide gel-electrophoresis and in-gel digested peptides were extracted for further analysis. In parallel, protein extracts were subjected to in-solution digestion according to the FASP protocol followed selleck chemicals llc by peptide fractionation on a strong anion-exchange resin. Proteins were identified by mass spectrometric analysis of tryptic peptides on an LTQ-FTICR hybrid instrument and the relative quantities were calculated based on the ion intensities. The two workflows were run in parallel but the raw data were merged and data processing was performed in one single batch. The experimental workflow is schematically outlined in Figure 1. Figure 1 The experimental workflow. In total, 3,588 unique protein groups were identified at 1% FDR, among which B-cell lineage specific markers (e.g., CD20, CD22, CD40, and CD79a) were present as well as proteins involved in B-cell receptor mediated signaling (e.g., mitogen-activated protein kinase 3 (MAPK3), spleen tyrosine kinase (SYK), Bruton's tyrosine kinase (BTK), and protein kinase C (PKC)) (Supplemental I-BET151 solubility dmso Table 2). Recently, a thorough proteome investigation of established DLBCL cell lines has been performed Oxygenase [14], and a comparison of the proteins identified in our study revealed a substantial overlap with 2,572 proteins being identified in both studies; this constitutes 72% of the proteins identified in our study. We successfully quantified 3,027 (84%) of the identified proteins in at least one of the samples. Identification and quantification in all samples were obtained for 1305 proteins and 87 of these proteins were significantly (Student's t-test, P