Chromatogram base peak

FIGURE 14.17 Ultrahigh resolution nano LC-MS separation of base peak chromatogram of 2351 peptides identified in trypsin digest of mouse brain lysate P2 fraction using Micro-Tech XtremeSimple nano-LC and Thermo Electron LTQ. Column 100 cm x 75 fim C18 column, 3 /mi, 8000 psi column head pressure. Solvent composition time 350 min gradient, 5 to 35% B. Solvent A 2% acetonitrile, 0.1% formic acid. Solvent B 95% acetonitrile, 0.1% formic acid. Data analysis Sequest, PeptideProphet, and Protein Prophet. 

Fig. 18a-c. Base peak chromatograms for the LC/MS analyses of a cytochrome c Lys-C digest (0.7 pmol injected) on a a poly(styrene-co-divinylbenzene) monolith-filled needle b Vydac C18-packed needle c Poros R2-packed needle. (Reprinted with permission from [128]. Copyright 1998 American Chemical Society)... 

Figure 6.3. Metabolite profile of razaxaban (C24H2oNg02F4) in dog bile (a) base peak chromatogram of unprocessed LC-MS data (b) base peak chromatogram of processed LC-MS data (c) corresponding radioactivity chromatogram. The arrows annotate the retention time of the peak shown in Fig. 6.2. Bile was collected from dogs orally administered with 14C-labeled razaxaban (20 mg/kg). HPLC solvents were 10mM NH4HC03 (pH 9.0) and acetonitrile. A portion of the HPLC effluent was collected in 15-s fractions for the radioactivity chromatogram. Another portion of the HPLC effluent was directed to a Q-TOF Ultima mass spectrometer.

Figure 6.12. Base peak chromatograms obtained from 75-/xL urine samples spiked with clozapine metabolites using LTQ-FTICR. (a,b) Samples spiked with oxidative metabolites, where (a) was from unprocessed data and (b) from MDF-processed data. (c,d) Samples spiked with GSH metabolites, where (c) was from unprocessed data and (dj from MDF-processed data. The MDF settings were 0.04 Da in mass defect dimension and 50 Da around the parent or the parent-plus-GSH mass, respectively.

Figure 6.1 The base peak chromatograms of mixtures of rice, lentil, and human nail proteins containing 4.0 (A), 40 (B), and 320 ng (E) of each sample [30].

Figure 11-17. The software intelligently flags compounds falling below the pre-set stability threshold, automatically re-injects the compounds, and analyzes them in the MS/MS mode. (A) Base peak chromatograms from the MRM scans show a nnmber of metabolites detected for buspirone. (B) MS/MS spectrum of one of the low-level hydroxylated metabolites. (C) MS/MS spectrum of one of the low-level N-demethylated metabolites.

Figure 3. Effect of detergent on tryptic map of the heavy chain of monoclonal antibody CEA11.H5. A. ESI base peak chromatogram for sample containing 1% reduced Triton X1(X). B. ESI base peak chromatogram for equivalent sample containing 0.25% PVP360.

Figure 20.4 Base-peak chromatogram of RNase B oligosaccharide alditols, acquired using a graphitized carbon column in LC-MS. Peak annotation (a)...

Figure 7.10 Biomarker detection with an LC-MS chip. (A) Base-peak chromatogram of SCX fraction 7 of the MCF7 protein digest showing the distribution of putative biomarker peptides across the LC-MS run. (Adapted with permission from ref. 33). (B) Mass spectrum that enabled the selection of a PCNA peptide for collision-induced dissociation. Conditions were the same as for Figure 7.9.

Copyright 2004. With permission from American Chemical Society.) (b) Base peak chromatogram of a BSA tryptic peptide mixture (600 fmol injection). Reprinted from Xie, J., et al.. Anal. Chem., 77, 6947-6953,... 

Finally, the base peak chromatogram (BPC) is a chromatogram obtained by plotting the signal of the ions giving the base peak detected in each of a series of mass spectra recorded as a function of retention time. 

BPC Base peak chromatogram Base peak intensity of each spectrum plotted vs. retention time. 

Fig. 4. Illustration of proteomic analysis of the rat synaptic plasma-membrane fraction by combination of SDS-PAGE and gradient reversed-phase LC/ESI-MS/MS (GeLC/MS/MS) on a quadrupole ion-trap instrument [21]. (A) The developed gel is cut into bands and the bands are (i) destained, digested (trypsin), and the sample is desalted for injection into the column. (B) Base-peak chromatogram obtained from the tryptic digest of the 98-120 kDa. Data-dependent acquisition is employed, where in one acquisition cycle (ii) a full-scan mass spectrum is acquired (C), followed by (iii) CID-MS/MS of the most intense ion (m/z 915.5) in this mass spectrum (D). (However, MS/MS is not initiated, when ion intensity in the full-scan mass spectrum is below a preset threshold.) Database search (iv) matches the MS/MS to the protein(s) (Table 1, major sequence ions of the peptide are indicated in chart D).

Figure 9 Hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry (HILIC-ESI-MS) base peak chromatogram of a polar Parmesan cheese extract fraction.

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