Tremolo

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Contact: Mingxun Wang [miw023 (at) cs.ucsd.edu]

Summary

Tremolo is a spectral library search tool that leverages the Spectral Library Generating Function (SLGF) concept to identify spectrum-spectrum matches (SSMs). The SLGF models the variability of replicate spectra as compared to reference library spectra. Given a similarity function (in our case cosine), SLGF yields an expected score distribution for each reference library spectrum. Tremolo is able to assign p-values to SSMs and it has been shown to increase the sensitivity of spectral library searches.

Documentation

Spectral Libraries

Spectral libraries used for searching are derived from NIST peptide libraries. However, the NIST libraries cannot be used directly as precomputation is required to calculate the expected score distributions for each reference library spectrum.

Currently the following libraries are available for download and soon the SLGF precomputation software will be available soon.

Human_NIST_SLGF.zip
Yeast_NIST_SLGF.zip

Tremolo

Usage: main_execmodule ExecSpectralLibrarySearchSLGF <params_file>

Example command line:

./main_execmodule ExecSpectralLibrarySearchSLGF ./exampleparams.params

Convert command line:

./convert <input mzXML>

This will output the pklbin file in the current directory with a modified extension to pklbin.

Parameter Documentation

EXISTING_LIBRARY_MGF - MGF of Target High Abundance Spectral Library
EXISTING_LIBRARY_MGF_DECOY - MGF of Decoy High Abundance Spectral Library
ANNOTATEDMGF_TARGET_LOW - MGF of Target Low Abundance Spectral Library
ANNOTATEDMGF_DECOY_LOW - MGF of Decoy Low Abundance Spectral Library

searchspectra - input search spectra, must be in pklbin or mgf format
  (converter supplied), deliminated by spaces

AMINOACIDMASS_FILE - amino acid masses file
MODEL_FILE - Dancik model file

RESULTS_DIR - output PSM tsv path

tolerance.PM_tolerance - precursor tolerance in Th

Output

Outputs are in tab-delimited format. Each column is denoted with headers and the relevant columns and meanings are as follows:

#Scan# - scan number of the searched spectra
SpectrumFile - original file name of the searched file 
Annotation - Peptide ID
MQScore - match score
FDR - False discovery rate
isDecoy - ID is from decoy library

Downloads

Tremolo_8_21_2013.zip

Publications

Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance.
Mingxun Wang, Nuno Bandeira.
Journal of Proteome Research, Epub ahead of print