Low molecular weight proteome

Banks RE, Stanley AJ, Cairns DA, Barrett JH, Clarke P, Thompson D, et al. Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin Chem 2005 51(9) 1637 1649. 

Brouwers FM, Petricoin EF, III, Ksinantova L, Breza J, Rajapakse V, Ross S, et al. Low molecular weight proteomic information distinguishes metastatic from benign pheochro-mocytoma. Endocr Relat Cancer 2005 12(2) 263-272. 

Figure 5.9 shows a snapshot of an LC CID MS/MS analysis of a tryptic digest of a standard six-protein mixture. The top mass spectrum (scan 1345 in this experiment) is an FT-ICR survey scan. In the subsequent scan ( 1346), CID MS/MS of the precursor ion m/z 524.9 is performed in the linear ion trap. That precursor ion is the most abundant ion in the survey scan that has not been subjected previously to MS/MS, that is, is not on the exclusion list. Scan 1347 is the CID mass spectrum of precursor mJz 6253, the second most abundant ion, not on the exclusion list, in the survey scan. The sequence ends with CID of precursor m/z 707.6, the third most abundant ion, not on the exclusion list, in the survey scan. The subsequent scan (not shown) is an FT-ICR survey scan. An alternative workflow favored by some researchers is one FT-ICR survey MS scan followed by CID in the linear ion trap of the 10 most-abundant ions [107]. These parallel-processing approaches have been applied to a diverse range of studies including analysis of the chicken egg white proteome [108], the low molecular weight proteome of Halobacterium salinarum [109], the endocervical mucas proteome [110], sumoylation in Saccharomyces cerevisiae [111], and the tear fluid proteome [112]. 

Alvarez MTB, Shah DJ, Thulin CD, Graves SW. Tissue proteomies of the low-molecular weight proteome using an integrated cLC-ESI-QTOFMS approach. Proteomies. 2013 13(9) 1400-11. 

The most prominent field of applications for microchip—MS concerns identification and analysis of large molecules in the field of proteomics according to the reduced separation time compared to conventional approaches such as gel-based methods for protein analysis. High-throughput analyses, with lower contamination and disposability, are other features of microfabricated devices that allow the fast screening of proteomic samples in the clinical field. Applications also include the analysis of low-molecular-weight compounds such as peptides or pharmaceutical samples. 

Beyond peptides and proteins, MALDI MS imaging of tissue section for the detection of low-molecular-weight compounds can also be achieved. Of particular interest is the posttreatment location of pharmaceutical compounds in targeted tissues or organs. Further, in parallel to location, the effects of a drug on the local proteome can be observed as a function of dose or time. Variations in the proteome are indicative of drug efficacy.116... 

Over the recent years, proteomic technologies evolved rapidly and now offer new perspectives in discovery of new cancer biomarkers based on the detection of low molecular weight proteins or peptides by MS. Two main peptidomic approaches are currently under investigation. These include pattern recognition and single/oligo biomarker detection. 

With respect to technical differences, it should be emphasized that, for metabolomic analyses, there is no single analytical technique that allows determination of all low-molecular-weight compounds, unlike genomic and proteomic analyses. In metabolomics, various complementary analytical techniques are often used in combination with advanced bioinformatics tools for analysis of large data sets. 

Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD. Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics 2003 2(10) 1096-103. 

In chemical genomics and proteomics, tiny low molecular weight probe molecules are used to perturb the functions of individual genes and proteins. The functional consequences of that perturbation are then examined and analyzed. By using small, yet relatively complex, molecular structures to disrupt cellular events and behavior, biologists can often pick apart some of the most complex and intricate signaling processes that are operational within cells, and thus provide a biomolecular panoptic that would otherwise be unattainable by purely biological means. ... 

Proteomics based on the 2-DE approach, of course, suffers from problems associated with the analysis of membrane proteins, so that such mitochondrial proteins are poorly represented on 2-D profiles. In addition, many mitochondrial proteins are more basic than cytosolic proteins, mitochondria are rich in low molecular weight (<10 kDa) proteins, and mitochondrial proteins are poorly described in databases (Lescuyer et al.,... 

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