"Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes"

Hyeon D.Y.; Nam D.; Han Y.; Kim D.K.; Kim G.; Kim D.; Bae J.; Back S.; Mun D.-G.; Madar I.H.; Lee H.; Kim S.-J.; Kim H.; Hyun S.; Kim C.R.; Choi S.A.; Kim Y.R.; Jeong J.; Jeon S.; Choo Y.W.; Lee K.B.; Kwon W.; Choi S.; Goo T.; Park T.; Suh Y.-A.; Kim H.; Ku J.-L.; Kim M.-S.; Paek E.; Park D.; Jung K.; Baek S.H.; Jang J.-Y, Hwang D.; Lee S.-W.; Nature Cancer, 4, 290-307, 2023

We report a proteogenomic analysis of pancreatic ductal adenocarcinoma (PDAC). Mutation–phosphorylation correlations identified signaling pathways associated with somatic mutations in significantly mutated genes. Messenger RNA–protein abundance correlations revealed potential prognostic biomarkers correlated with patient survival. Integrated clustering of mRNA, protein and phosphorylation data identified six PDAC subtypes. Cellular pathways represented by mRNA and protein signatures, defining the subtypes and compositions of cell types in the subtypes, characterized them as classical progenitor (TS1), squamous (TS2–4), immunogenic progenitor (IS1) and exocrine-like (IS2) subtypes. Compared with the mRNA data, protein and phosphorylation data further classified the squamous subtypes into activated stroma-enriched (TS2), invasive (TS3) and invasive-proliferative (TS4) squamous subtypes. ...

Novel Online Three-Dimensional Separation Expands the Detectable Functional Landscape of Cellular Phosphoproteome

Kang C.; Huh S.; Nam D.; Kim H.; Hong J.; Hwang D.; Lee S.-W.; Anal. Chem., 94, 35, 12185–12195, 2022

Protein phosphorylation is a prevalent post-translational modification that regulates essentially every aspect of cellular processes. Currently, liquid chromatography-tandem mass spectrometry (LC-MS/MS) with an extensive offline sample fractionation and a phosphopeptide enrichment method is a best practice for deep phosphoproteome profiling, but balancing throughput and profiling depth remains a practical challenge. We present an online three-dimensional separation method for ultradeep phosphoproteome profiling that combines an online two-dimensional liquid chromatography separation and an additional gas-phase separation. ...

Proteogenomic Characterization of Human Early-Onset Gastric Cancer

Mun, D.-G.; Bhin, J.; Kim, S.; Kim, H.; Jung, J. H.; Jung, Y.; Jang, Y. E.; Park, J. M.; Kim, H.; Jung, Y.; Lee, H.; Bae, J.; Back, S.; Kim, S.-J.; Kim, J.; Park, H.; Li, H.; Hwang, K.-B.; Park, Y. S.; Yook, J. H.; Kim, B. S.; Kwon, S. Y.; Ryu, S. W.; Park, D. Y.; Jeon, T. Y.; Kim, D. H.; Lee, J.-H.; Han, S.-U.; Song, K. S.; Park, D.; Park, J. W.; Rodriguez, H.; Kim, J. Lee, H.; Kim, K. P.; Yang, E. G.; Kim, H. K.; Paek, E.; Lee, S.; Lee, S.-W.; Hwang, D. Cancer Cell 2019, 35, 111-124.

We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and. ...

Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to increase sensitivity and accuracy in peptide identifications from tandem mass spectra of co-fragmentation

Madar, I. H.; Ko, S.-I.; Kim, H.; Mun, D.-G.; Kim, S.; Smith, R.; Lee, S.-W. Anal. Chem. 2017, 89(2), 1244-1253

Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation. We describe a composite method of utilizing MS data to assign accurate monoisotopic masses to MS/MS spectra, including those subject to cofragmentation. The method, “multiplexed post-experiment monoisotopic mass refinement” (mPE-MMR), consists of the following: multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra, multiplexing of charge states to assign correct charges to the precursor ions of MS/MS spectra with no charge information, and mass correction for inaccurate monoisotopic peak picking. ...

Efficient exploitation of separation space in two-dimensional liquid chromatography system for comprehensive and efficient proteomic analyses

Lee, H.; Mun, D.-G.; So, J. E.; Bae, J.; Kim, H.; Masselon, C.; Lee, S.-W. Anal. Chem 2016, 88, 11734-11741.

Proteomics aims to achieve complete profiling of the protein content and protein modifications in cells, tissues, and biofluids and to quantitatively determine changes in their abundances. This information serves to elucidate cellular processes and signaling pathways and to identify candidate protein biomarkers and/or therapeutic targets. Analyses must therefore be both comprehensive and efficient. Here, we present a novel online two-dimensional reverse-phase/reverse-phase liquid chromatography separation platform, which is based on a newly developed online noncontiguous fractionating and concatenating device (NCFC fractionator). In bottom-up proteomics analyses of a complex proteome, this system provided significantly improved exploitation of the separation space of the two RPs, considerably increasing the numbers of peptides identified compared to a contiguous 2D-RP/RPLC method. ...