Proteome analyses of human induced pluripotent stem cells (iPSC) were carried 
out on a liquid chromatography-tandem mass spectrometry system using meter-scale 
monolithic silica-C18 capillary columns without prefractionation. Tryptic 
peptides from five different iPSC lysates and three different fibroblast lysates 
(4 μg each) were directly injected onto a 200 cm long, 100 μm i.d. monolithic 
silica-C18 column and an 8-h gradient was applied at 500 nL/min at less than 20 
MPa. We identified 98,977 nonredundant tryptic peptides from 9510 proteins 
(corresponding to 8712 genes), including low-abundance protein groups (such as 
329 protein kinases) from triplicate measurements within 10 days. The obtained 
proteome profiles of the eight cell lysates were categorized into two groups, 
iPSC and fibroblast, by hierarchical cluster analysis. Further quantitative 
analysis based on an exponentially modified protein abundance index approach 
combined with UniProt keyword enrichment analysis revealed that the iPSC group 
contains more "transcription regulation"-related proteins, while the fibroblast 
group contained more "transport"-related proteins. Our results indicate that 
this simplified one-shot proteomics approach with long monolithic columns is 
advantageous for rapid, deep, sensitive, and reproducible proteome analysis.