ArticlePancreas
Proteome-Wide Protein Expression Profiling Across Five Pancreatic Cell Lines.
Article in Pancreas. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
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- Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing.Cell chemical biology · 2020Article
- Selective Alanine Transporter Utilization Creates a Targetable Metabolic Niche in Pancreatic Cancer.Cancer discovery · 2020Article
- Monitoring protein communities and their responses to therapeutics.Nature reviews. Drug discovery · 2020Review
- NCOA4 maintains murine erythropoiesis via cell autonomous and non-autonomous mechanisms.Haematologica · 2019Article
- Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3.Journal of proteome research · 2018Article
- Global quantitative analysis of the human brain proteome in Alzheimer's and Parkinson's Disease.Scientific data · 2018Article
- Filter-Based Protein Digestion (FPD): A Detergent-Free and Scaffold-Based Strategy for TMT Workflows.Journal of proteome research · 2018Article
- Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling.Journal of proteome research · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
objectivesMass spectrometry-based proteomics enables near-comprehensive protein expression profiling. We aimed to compare quantitatively the relative expression levels of thousands of proteins across 5 pancreatic cell lines.
methodsUsing tandem mass tags (TMT10-plex), we profiled the global proteomes of 5 cell lines in duplicate in a single multiplexed experiment. We selected cell lines commonly used in pancreatic research: CAPAN-1, HPAC, HPNE, PANC1, and PaSCs. In addition, we examined the effects of different proteases (Lys-C and Lys-C plus trypsin) on the dataset depth.
resultsWe quantified over 8000 proteins across the 5 cell lines. Analysis of variance testing of cell lines within each data set resulted in over 1400 statistically significant differences in protein expression levels. Comparing the data sets, 10% more proteins and 30% more peptides were identified in the Lys-C/trypsin data set than in the Lys-C-only data set. The correlation coefficient of quantified proteins common between the data sets was greater than 0.85.
conclusionsWe illustrate protein level differences across pancreatic cell lines. In addition, we highlight the advantages of Lys-C/trypsin over Lys-C-only digests for discovery proteomics. These data sets provide a valuable resource of cell line-dependent peptide and protein differences for future targeted analyses, including those investigating on- or off-target drug effects across cell lines.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.