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1.
Figure 10

Figure 10. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Recalibration of Data Acquired on a Quadrupole Time-of-Flight (QTOF) Mass Spectrometer. Fragment ion mass errors for the peptide ADISSDQIAAIGITNQR (based on Mascot assignment), derived from the protein glycerol kinase (a) before and (b) after recalibration.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
2.
Figure 4

Figure 4. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Generation of Publication Quality Images. A Scrapbook tool allows manipulation of Peak Viewer plot properties such as axes labels, titles, and size. Multi-plot comparison via the mirror and overlay functions provide further modes for in-depth, manual data interrogation. Users may export publication quality images from all Scrapbook plots.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
3.
Figure 9

Figure 9. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Instrument Calibration Quality Control Report. An .mz script is used to automatically generate a spreadsheet report that indicates mass errors (in ppm) for a set of standard peptides. Images of the precursor isotope distribution and reconstructed ion chromatogram are embedded within the report for rapid confirmation of mass spectrometry and chromatographic performance.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
4.
Figure 7

Figure 7. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Quantitative Comparison of Phosphopeptide Enrichment Methods. Histogram distributions of peak heights for unique and overlapping phosphopeptides detected in conjunction with (a) (TiO2)-, and (b) (Nb2O5)-based enrichment. The intensity distributions for phosphopeptides assigned uniquely to either metal oxide did not differ significantly from the intensity distributions for commonly detected phosphopeptides, indicating that the unique precursors were not confined to low signal-to-noise regions. Reprinted from [23] by permission from the American Chemical Society.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
5.
Figure 6

Figure 6. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

User-defined Customization Through .mz Scripts. A short .mz script (a) opens each MS/MS spectrum within a given LC-MS acquisition and returns those scans that contain the phosphotyrosine immonium ion (m/z = 216). The tab-delimited multiplierz output is readily opened in Excel and (b) a histogram view facilitates rapid evaluation of enrichment efficiency. In this example, the majority of peptides in the heart of the LC gradient (~25 - 65 min.) contain phosphotyrosine residues as evidenced by the presence of an m/z = 216 immonium ion.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
6.
Figure 1

Figure 1. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

A Common API and Desktop Environment for Mass Spectrometry Data Analysis. The multiplierz environment provides a central point for user interaction with proprietary data files (via mzAPI), protein/peptide identification algorithms, publicly available annotation databases, and commercial reporting and spreadsheet tools. Our proposal calls for manufacturers to provide a minimal set of libraries for access to their native data files. Ad hoc data analysis tasks are supported through multiplierz scripting capability, including programmatic access for integration into data analytic pipelines.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
7.
Figure 3

Figure 3. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Dynamic Visualization of Proprietary Mass Spectrometry Data Files. The Peak Viewer tool in multiplierz provides interactive plots for precursor RICs, and corresponding MS and MS/MS scans, in centroid or profile modes. Green squares in the RIC denote MS scans and red triangles indicate MS/MS events. In addition, users may adjust the time or m/z range displayed in each data window. Verification of peptide sequence is facilitated by overlay of theoretical fragment ions on the MS/MS spectra. Users may dynamically evaluate multiple peptide assignment options by changing the proposed sequence or post-translational modification state in the left-most pane.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
8.
Figure 8

Figure 8. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Label-Free Relative Protein Quantification. A multiplierz Excel report provides data analytic figures of merit, including: (a) the ratio of each protein across two conditions with an embedded box plot that illustrates the distribution of feature-level ratios, where each feature is defined as a (peptide, modification, charge state) combination; (b) p-value for the significance of the ratio; (c) the number (N) of features underlying the protein quantification; (d) the ratio and embedded RIC plot (showing all RICs used to quantify the peptide - colored by sample source) from the peptide most representative of the final protein ratio; (e) "expected" field is added manually by the user based on the experimental design. Users may also generate associated graphs using native plotting capabilities in Excel.

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
9.
Figure 5

Figure 5. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Multiplierz -based Workflow for Analysis of LC Column Geometry and Flow Rate. Relative performance improvement for analysis of peptides derived from whole cell lysate as a function of column size and flow rate (a). Original data contained ~90,000 MS/MS scans (b) encompassing almost 23,000 peptide assignments (combination of sequence, charge state, and modification), across 11 LC-MS acquisitions. In addition, multiplierz used Mascot-derived peptide identifications (c) to generate RICs, calculate full chromatographic peak width at half-maximum (FWHM), and determine precursor apex intensity (d). Common peptide sequences and associated analytical metrics are extracted (e) into a final, spreadsheet based report (f).

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.
10.
Figure 2

Figure 2. From: multiplierz: an extensible API based desktop environment for proteomics data analysis.

Integration of Commercial Tools for multiplierz Reports. A spreadsheet-based report from multiplierz analysis of 11 LC-MS analyses, designed to interrogate performance of LC column geometry and flow rate (see also Figure 5 and Additional File 5). For clarity the spreadsheet shows peptide entries and characterization data from the two extremes in column size and flow rate. Informative images are embedded within spreadsheet cell comments and are accessed by mouse-over, thus facilitating rapid visual inspection. Optional embedded images include: 1.) MS/MS spectra that are annotated with b- and y-type fragment ion labels, peptide sequence, search engine score (in this case Mascot peptide score), and precursor charge state. A color scheme highlights modified amino acids (in this case oxidized methionine) and those residues inferred from b- and y-type fragment ion assignments (horizontal lines, red and blue denote singly- and doubly-charged ions, respectively). 2.) RIC images in which MS scans are annotated with green squares, while yellow circles and blue triangles denote MS/MS scans for the precursor of interest, with the latter indicating the specific MS2 event described in the selected row of the spreadsheet. 3.) precursor region of the MS spectrum (not shown).

Jignesh R Parikh, et al. BMC Bioinformatics. 2009;10:364-364.

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