/msSLASH

Spectral library searching tool based on locality sensitive hashing

Primary LanguageC++GNU General Public License v3.0GPL-3.0

Introduction

msSLASH (standing for mass spectral Searching using LocAlity Sensitive Hashing) was developed by Lei Wang, Sujun Li and Haixu Tang*, for performing rapid MSMS spectral library searching while preserving sensitivity. Multithreading is enabled in this package.

Prerequisites

g++ with version 5.1.0+ is required.

Installation

  1. cd to the main directory of msSLASH.
  2. Type ./install.sh
  3. Two executable files will be placed under bin directory: ./msSLASH for searching with locality sensitive hashing technique and ./bruteforce for searching using naive method, respectively. The bruteforce method literally compares input spectrum with each candidate of similar precursor and same charge, using the same scoring function as msSLASH, thus serving as benchmark

Usage

  • This process will search input spectra dataset against designated target library and the respective decoy library. A csv file will be generated at the end to hold the searching results.

    1. cd bin
    2. Usage: ./msSLASH -e experimental_spectra -d decoy_library -l target_library [-c fragment_precision] [-t threads] [-n hash_func_num] [-i iteration] [-s min_similarity] [-a min_mz] [-r rescale_method] [-o output_file] [-m precursor_mass_tolerance].
    3. Typical example: ./msSLASH -n 100 -i 10 -t 20 -l $target -e $exp -d $decoy -o $out_file -r 1 -m 0.05 --precision 0.5 --min_mz 0 -u. You will find the searching result file with name $out_file if specified, otherwise you will find it in the same dir as the $exp, with suffix .msSLASH.tsv.
    4. Description Type ./msSLASH -h to see full list of command options.

      • -u, --unfragment

        [Bool] Filter unfragmented ms2 if specified This parameter is optional. The default value is '0'.

      • -i, --iteration

        [Int] iteration for searching with LSH This parameter is optional. The default value is '100'.

      • -n, --hash

        [Int] Hash functions per hash table. This parameter is optional. The default value is '8'.

      • -t, --threads

        [Int] Threads to use. This parameter is optional. The default value is '20'.

      • -a, --min_mz

        [Float] min mz for peaks to consider. This parameter is optional. The default value is '200'.

      • -s, --similarity

        [Float] Minimum cosine similalrity when reporting a hit. This parameter is optional. The default value is '0'.

      • -c --precision

        [Float] fragment precision in Da. This parameter is optional. The default value is '0.500000'.

      • -m --precursor_mass_tolerance

        [Float] precursor mass tolerance in Da. This parameter is optional. The default value is '0.050000'.

      • -r --rescale

        [Int] PEAK_INTENSITY_RESCALE_METHOD. This parameter is optional. The default value is '1'.

      • -o --out_file

        [String] out file contanining msSLASH searching results. This parameter is optional. The default value is ''.

      • -d --decoy (required)

        [String] decoy library mgf file.

      • -e --experimental (required)

        [String] experimental mgf file.

      • -l --library (required)

        [String] library mgf file.

  • It is very important to select proper paramters for msSLASH to search spectral library with high sensitivity and specificity. Specifically:

    1. hash_func_num controls the collision probability of two spectra in a single hash table, the more hash functions, the smaller collision probabiilty, the more buckets, the faster msSLASH program. 7~10 is a good starting point for MassIVE HCD spectral library, NIST CID library, and predicted human proteome library.
    2. iteration controls the number of hash tables to use with the aim to increase the probabiilty of two similar spectra to collide in at least one hash table, the more iterations, the higher collision probability, the less clusters, the slower mcCRUSH program. 100 iterations is a good starting point to play with.
    3. rescale specifies transformation that will be applied to each peaks. 0 for no transformation, 1 for log transformation, 2 for sqrt transformation.
    4. precision specifies the fragment precision in Da. Preferably set to value equivalently 1Th, i.e. 0.5Da for doubly charged spectra, 0.33 Da for tribly charged spectra

Citation

TBD

Questions

Please contact Lei Wang (wang558@indiana.edu) for assistance.

Acknowledgement

This work was supported by the NIH grant 1R01AI108888 and the Indiana University Precision Health Initiative.