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Two dimensional gel electrophoresis of the pattern of proteins synthesized in Escherichia coli under different phosphate (P) conditions reveals that less than 50% of the proteins have the same rates of synthesis during P limitation and during growth in abundant inorganic phosphate (Pi). The promoter regions of genes for proteins with induced or repressed synthesis contain sequences resembling the consensus sequence for PhoB binding. The mass of proteins that respond to P limitation or growth on phosphonate is around 30-40% of the cells' total mass.

A mutation in the structural gene, encoding release factor 1 (prf), suppresses cell division at nonpermissive temperatures in Salmonella typhimurium. However, RNA, DNA and protein synthesis are unaffected till two generations, and the mutants have a normal response to heat and SOS. The prfA101 mutation is a recessive GC-to-AT transition in the 168th codon, inhibits amber mutations and causes cell lysis. The inhibition of cell division is probably due to the formation of an aberrant protein that inhibits septation and does not involve any of the known regulatory pathways.

A cloned chromosomal segment of Escherichia coli was analyzed by two-dimensional gel electrophoresis to identify the genes in the bacterium. The segments for the experiment were chosen from an ordered genomic library and recloned into a new low-copy-number plasmid vector pFN476. The vector was used in the transcription system of bacteriophage T7. The genes resulting from the experiment were expressed in vivo. Two-dimensional gel electrophoresis analyzed the protein products and the DNA sequence information predicted their gel migration. Gene products on two-dimensional gels were identified by the results, though they can also be used to identify all gene products of E. Coli.

Mass spectrometric surface analysis of isoelectric focusing gels provides an ultrasensitive approach to proteome analysis. This 'virtual 2-D gel' approach, in which mass spectrometry is substituted for the size-based separation of SDS-PAGE, provides advantages in mass resolution and accuracy over classical 2-D gels and can be readily automated. Protein identities can be postulated from molecular mass ([+ or -] -0.1-0.2% for proteins of [is less than] 50 kDa in size) and pI ([+ or -] 0.3 pH unit) and confirmed by MALDI in-source decay of the intact protein (providing sequence spanning up to 43 residues) or by peptide mass mapping following gel-wide chemical cleavage. Additionally, post-translational modifications such as fatty acid acylation can be detected by the mass-resolved heterogeneity of component hydrocarbon chains. Sensitivity was evaluated by comparing the number of proteins detected by this method to equivalently loaded silver-stained 2-D gels. In the 5.7-6.0 pH range, E. coli is predicted to contain 435 proteins; virtual 2-D gels found 250 proteins ranging from [is greater than] 2 to [is less than] 120 kDa in size present at levels to tens of femtomoles, as compared to the 100 proteins found by silver-staining 2-D gels. Extrapolating this result to the total theoretical proteome suggests that this technology is capable of detecting over 2500 E. coli proteins.

Our purpose is to develop a serum assay to determine an individual's probability of having colorectal cancer (CRC). We have discovered a protein panel yielding encouraging, clinically significant results. We evaluated 431 serum samples from donors screened for CRC by colonoscopy. We compared the concentration of seven proteins in individuals with CRC versus individuals found to be CRC free. The assay monitored a single peptide from each of seven proteins. Comparing CRC to normal samples in univariate two-sample t-tests, 6 of the 7 proteins yielded a p-value less than 0.01. Logistic regression was used to construct a model for determination of CRC probability. The model was fit on a randomly chosen training set of 321 samples. Using 6 of the 7 proteins (ORM1, GSN, C9, HABP2, SAA2, and C3) and a cut point of 0.4, an independent test set of 110 samples yielded a sensitivity of 93.75%, a specificity of 82.89% and a prevalence-adjusted negative predictive value (NPV) of 99.9775% for the assay. The results demonstrate that the assay has promise as a sensitive, non-invasive diagnostic test to provide individuals with an understanding of their own probability of having CRC.

Genomics and proteomics technologies have yielded volumes of data for more than 20 years, and they continues to produce data at an astounding rate. Has all of this data helped us understand more about life, or it is just bogging us down in details that cannot be assembled into meaningful ideas? This review of the proteomics efforts over the last couple of decades is meant to emphasize that a new scientific discipline has emerged, Molecular Physiology, and that, indeed, this discipline is contributing to our understanding of life. Molecular physiology offers the reductionisms details of individual cellular molecules and offers the systems biology multivariant and high-dimensional datasets of cellular molecules.