multiplierz.mzTools.silacAnalysis

SILAC quantitation methods enable relative quantity determination between two samples in a single MS run. In principle, determining the relative quantity between two peptides in the data is simply a matter of observing the relative intensity of the labelled- and unlabelled-state MS1 peaks; however, due to the noise and instability of MS1 measurements (which may be due to low-intensity MS1 signals, RT/MZ space that is crowded with other analytes, or other factors) automated ratio determination is difficult. Multiplierz uses a novel feature-detection algorithm to determine the full MS1 features corresponding to each analyte in a labelled pair (or triple), and calculates the ratio by comparison of these features rather than individual MS1 peaks.

SILAC3Plex(datafiles, resultfiles, mediumTags, heavyTags, **optional_arguments)
SILAC2Plex(datafiles, resultfiles, heavyTags, **optional_arguments)

Separate function calls are provided for processing 2-plex and 3-plex SILAC data. datafiles should be a list of paths the MS instrument data files to be analyzed; multiple files can be specified to analyze multi-fraction runs with a single function call. At present, these functions require resultfiles to be the PSM result table(s) as returned by a Multiplierz-enabled Mascot search; Comet and Tandem result files are not supported. The database search should be performed without explicit quantitation options enabled, but with the SILAC tags used specified as variable modifications; these tags should be specified in mediumTags and heavyTags as a dict from amino acid to modification name, so typical values would be

mediumTags = {'K':'Label:2H(4)', 'R':'Label:13C(6)'}
heavyTags = {'K':'Label:13C(6)15N(2)', 'R':'Label:13C(6)15N(4)'}

There are several optional arguments:

• mzRegex can be a regular expression (in Python regular expression format) that converts the spectrum description format in the target PSM files to a string indicating the precursor M/Z. For results that used the Multiplierz MGF extraction algorithm, and which therefore have description strings in the standard Multiplierz format, this is unnecessary.
• scanRegex, likewise, can be a regular expression indicating the scan number of the target PSM. Also unnecessary if the Multiplierz MGF extraction algorithm was used.
• tolerance sets the mass accuracy tolerance used in the feature detection and other steps of the process; this should be set according to the mass accuracy of your instrument. This is given in units of parts-per-million.

Additional notes

• Currently, only K and R tagging is supported. Attempting to use the SILAC analysis function for other label types may not give expected results.
• The output from a SILAC quantitation analysis is not a full representation of the peptide identification set given in the input file; peptides for which no quantitation is theoretically possible will be omitted. In particular, peptides that do not have labellable residues (K and R), or which are incompletely labelled (have some labelled K/R residues alongside unlabelled K/R residues) will be omitted.