Proteomics mass analysis

Dunlop, K. Y. Li, L. Automated Mass Analysis of low-molecular-mass bacterial proteome by liquid chromatography-electrospray ionization mass spectrometry. J. Chromatogr. A 2001, 925,123-132. 

Field, H.I., Fenyo, D., Beavis, R.C. (2002). RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2, 36 17. 

Ion traps are favored for proteomics studies because of their ability to perform multistage mass analysis (MSn), thereby increasing the structural information obtained from molecules. Ion traps, however, do not provide information for ions that have lower mass-to-charge values (the one-third rule). Additionally, the sensitivity of ion traps can also be limiting because only about 50% of the ions within a trap are ejected to the detector. Ion traps are also subject to a space charging phenomenon that may occur when the concentration of ions in the trap is high and produces ion repulsion within the trap. Nevertheless, the versatility and robustness of ion trap MS underlies its popularity for several proteomics-related applications. 

H. I. Field, D. Fenyo, and R. C. Beavis. RADARS, a Bioinformatics Solution that Automates Proteome Mass Spectral Analysis, Optimises Protein Identification, and Archives Data in a Relational Database. Proteomics, 2, no. 1 (2002) 36-47. 

Zimmer, J. S., Monroe, M. E., Qian, W. J., and Smith, R. D. (2006). Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom. Rev. 25 450-482. 

Although reliable, this technique may lead to false positive results in some cases. To overcome this problem many proteomic companies are now adopting the technique of tandem mass spectrometry to unambiguously identify protein sequences. This technique subjects proteins to successive routines of fragmentation and mass analysis in order to provide the actual amino acid sequence. 

The methods for each study are divided into the initial protein separation step, a second separation step if applicable, the type of mass analysis, and the software used for peptide identification. ID = one dimensional polyacrylamide gel electrophoresis, 2D = two dimensional polyacrylamide gel electrophoresis, MS = mass spectrometry (peptide mass fingerprinting), MS/MS = tandem mass spectrometry, MALDI-TOF = matrix assisted laser desorption/ionization-time of flight, MS FIT = software from Protein Prospector, http //prospector.ucsf edu/, ESI = electrospray ionization, Q-TOF = quadrupole-time of flight, PPSS2 =Protana s Proteomic Software Suite (ProtanaEngineering, Odense, Denmark), Mascot = Matiix Science, http //www.matrixscience.com/, TOF-TOF = MALDI plus TOF tandem mass spectrometry, RP-HPLC = reverse phase high performance liquid chromatography, Q-IT = quadrupole ion trap, LIT = linear ion trap. Bioworks = Thermo Electron Corporation. 

Protein identification in a proteome by tiyptic digestion and RPLC-MS relies on the abihty of trypsin to achieve efficient digestion of the proteins in the nuxture, the ability of RPLC to separate the resulting peptides, and deliver them to nano-ESI-MS for mass analysis. The peptides in a complex mixture widely differ in their physicochemical properties, which in turn influence both LC and nano-ESI-MS performance. Data were compared for experimentally detected and in-silico predicted peptides from three different complex protein mixtmes [38]. The peptides detected actnally form only a small subset of the peptides present. 

Another area where TOF-MS has an advantage is in high-mass analysis where its mass range is nearly unlimited. In MALDI-TOF, for example, it is not unusual to detect proteins with molecular weights exceeding 100,000. The ability for high-mass analysis is expected to increase in importance as clinical laboratories embrace proteomic-based diagnostic methods. 

Angel Garcia andYotis A. Senis (Editors) Platelet Proteomics Principles, Analysis, and Applications Luigi Mondello Comprehensive Chromatography in Combination with Mass Spectrometry Jian Wang, James MacNeil, and Jack F. Kay Chemical Analysis of Antibiotic Residues in Food... 

DCIM-MS has been coupled to liquid chromatography (LC) for analyzing complex peptide samples [36], Peptides eluting from the LC column were analyzed on an IMS-Q-TOF mass spectrometer. The ions generated from the source were accumulated in an ion trap and injected periodically into the drift tube. After mass analysis by the quadrupole, ions were subjected to collision-induced dissociation (CID) within an octopole collision cell and the product ions were analyzed by a TOF analyzer. Using this instrumental configuration, the urinary proteome [37], the Drosophila melano-gaster head proteome [38], and the human plasma proteome [39] have been analyzed. While many additional measurements, compared to standard mass spectrometry-based proteomics experiments, were obtained (for example, collision cross-sections), these were not used to improve upon protein identification results. 

After the first demonstration of multiply charged gas-phase proteins ions, all major instrument manufacturers developed atmospheric-pressure ion sources, equipped with electrospray interfaces for both protein characterization and LC-MS applications. Within 5 years, electrospray interfacing became the method of choice in LC-MS coupling. It led to a large increase in the use of MS for the characterization and identification of labile and polar analytes as well as to routine quantitative analysis. The advent of electrospray ionization for peptide and protein analysis stimulated further development and analytical application of existing and new mass analysis approaches, such as quadrupole ion traps, Fourier-transform ion-cyclotron resonance MS, and quadru-pole-time-of-flight hybrid instruments. It opened new application areas, such proteomics. LC-MS... 

Baker, H., Patel, V., Mohnolo, A.A., ShiHitoe, E.J., Ensley, J.F., Yoo, G.H., Meneses-Garcia, A., Myers, J.N., El-Na ar, A.K., Gutkind, J.S., and Hancock, W.S. (2005) Proteome-wide analysis of head and neck squamous cell carcinomas using laser-capture microdissection and tandem mass spectrometry. Oral Oncol, 41,183-199. 

Fig. 8. Drug-induced proteome changes predict for therapeutic resistance. (A) Mice bearing established >300 mm Fo5 (Flerceptin-resistant) and 1282 (Flerceptin-sensitive) tumors were treated with Flerceptin 30 mg/kg i.p. twice a week. Each data point represents mean tumor volume SD (Fo5, = 3 1282, n = 6). (B) Fo5 and 1282 tumors of equivalent size were harvested 24 and 48 h after a single dose of Herceptin i.p. and subjected to mass spectral proteomic profiling analysis. An example of a statistically significant change observed after Herceptin treatment in the 1282 tumors not observed in the Fo5 tumors is shown. The solid line trace (—) represents control, untreated tumors while the dotted line trace ( ) represents Herceptin-treated tumors. (Reprinted with permission from the American Association for Cancer Research from Cancer Research 64 9093-9100, 2004.)...

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