mscalib -- Calibration of Peptide and Protein Mass Spectra

Manuscript

The package provides a manuscript in which two of the calibration methods, implemented in this pacakges, are described in detail. Furthermore there is a study of their performance in comparison with some other methods, also implemented by mscalib, using serveral thousand peptide mass fingerprint spectra.

Vignettes

The pacakge provides three vignette (*.Rnw files) which describe three different calibration processes:
  1. The calibration pipeline based on iterative internal calibration.
  2. A calibration pipeline based on MST calibration and internal calibration.
  3. A calibration pipeline based on Peptide role calibration, Thin plate splines and Finding the optimal alignment of a set of Peak-lists using the Maximum spanning tree.
While the Rnw file of the first vignette is in this directory the Rnw file of second and third vignette can found in the samples directory of the package. It is possible to execute those vignettes by typing. 
    library(tools)
    Sweave(file.path(.path.package("mscalib"), "samples/MSIInternal.Rnw"))
    Sweave(file.path(.path.package("mscalib"), "samples/PeproleMSTCalibration.Rnw"))
(They are not included in the doc directory because they are computationally intensive.)

R files

Furthermore in the Sample directory: 
    file.path(.path.package("mscalib"), "samples")
we provide six R files wich implement six different calibration scenarios.
  1. Peptide role based calibration (LR/PR)
  2. Internal calibration (IC)
  3. Minimum Spanning Tree (MST) calibration
  4. Thin plate spline (TPS) calibration
  5. TPS calibration with subsequent internal calibration
  6. TPS calibration with subsequent MST calibration

We described and compared this scenarios in the study:
High throughput calibration of Mass Spectrometric PMF Data - without specific external or internal calibrations by W.E.Wolski et al.

The functionality of the packages msbase and mscalib can be extended by the package msmascot which provides an R interface to the Mascot search server version 1.8.1 (Matrixscience).

W.E. Wolski
Last modified: Tue Apr 26 15:55:33 BST 2005