PyQuant

What is PyQuant?

PyQuant is a versatile tool for an assortment of mass spectrometry based analyses.

Installation

Docker

Those who are comfortable using Docker may run PyQuant via the image at chrismit7/pyquant.
The only point of note is to remember that volumes on your local drive must be mounted in docker, for instance, if your files are located at /home/chris/msexperiment, you would run docker as such: docker run -v /home/chris/msexperiment:/msexperiment chrismit7/pyquant --search-file /msexperiment/search_file.msf -o /msexperiment/pyquant_results

non-windows operating systems

For mac and linux OS's, PyQuant is installable via the standard python packaging tool, pip.


                pip install Cython
                pip install pyquant

Windows Installation

Docker

Docker may be used to run PyQuant on Windows

The easy way

This approach may not work for every configuration, but is considerably less involved.

Install anaconda 64 bit for python 2.7: continuum.io/downloads#windows
In the terminal: pip install pyquant
Confirm you can view PyQuant via pyQuant --help

The hard way

The difficult aspect of building on Windows is setting up a compilation environment. Those unfamiliar with compilation on Windows should seek someone comfortable with doing so.
To ease this pain, we recommend using the Anaconda python 2.7 distribution.
The steps here should be followed to get a working Cython installation on Windows:
https://github.com/cython/cython/wiki/InstallingOnWindows
For brevity, they are summarized here, but are not guaranteed to be up to date:

conda install cython
Install Microsoft Visual C++ Compiler for Python 2.7

Patch C:\Anaconda2\Lib\distutils\msvc9compiler.py with the following code:

def find_vcvarsall(version):
    """Find the vcvarsall.bat file

    At first it tries to find the productdir of VS 2008 in the registry. If
    that fails it falls back to the VS90COMNTOOLS env var.
    """
    vsbase = VS_BASE % version
    vcpath = os.environ['ProgramFiles']
    vcpath = os.path.join(vcpath, 'Common Files', 'Microsoft',
        'Visual C++ for Python', '9.0', 'vcvarsall.bat')
    if os.path.isfile(vcpath): return vcpath
    vcpath = os.path.join(os.environ['LOCALAPPDATA'], 'Programs', 'Common', 'Microsoft', 'Visual C++ for Python', '9.0', 'vcvarsall.bat')
    if os.path.isfile(vcpath): return vcpath
    ...

Install pyquant via pip install pyquant

PyQuant Arguments

Below are the parameters for use with PyQuant

scan-file: The scan file(s) for the raw data. If not provided, assumed to be in the directory of the processed/tabbed/peaklist file.
scan-file-dir: The directory containing raw data.
precision: The precision for storing m/z values. Defaults to 6 decimal places.
precursor-ppm: The mass accuracy for the first monoisotopic peak in ppm.
isotope-ppm: The mass accuracy for the isotopic cluster.
spread: Assume there is spread of the isotopic label.

search-file: A search output or Proteome Discoverer msf file
skip: If true, skip scans with missing files in the mapping.
peptide: The peptide(s) to limit quantification to.
peptide-file: A file of peptide(s) to limit quantification to.
scan: The scan(s) to limit quantification to.

mva: Analyze files in 'missing value' mode.
rt-window: The maximal deviation of a scan's retention time to be considered for analysis.

label-scheme: The file corresponding to the labeling scheme utilized.
label-method: Predefined labeling schemes to use.
reference-label: The label to use as a reference (by default all comparisons are taken).

tsv: A delimited file containing scan information.
label: The column indicating the label state of the peptide. If not found, entry assumed to be light variant.
peptide-col: The column indicating the peptide.
rt: The column indicating the retention time.
mz: The column indicating the MZ value of the precursor ion. This is not the MH+.
scan-col: The column indicating the scan corresponding to the ion.
charge: The column indicating the charge state of the ion.
source: The column indicating the raw file the scan is contained in.

msn-id: The ms level to search for the ion in. Default: 2 (ms2)
msn-quant-from: The ms level to quantify values from. i.e. if we are identifying an ion in ms2, we can quantify it in ms1 (or ms2). Default: msn value-1
msn-ion: M/Z values to search for in the scans.
msn-peaklist: A file containing peaks to search for in the scans.
msn-ppm: The error tolerance for identifying the ion(s).

quant-method: The process to use for quantification. Default: Integrate for ms1, sum for ms2+.
reporter-ion: Indicates that reporter ions are being used. As such, we only analyze a single scan.
isotopologue-limit: How many isotopologues to quantify
overlapping-mz: This declares the mz values will overlap. It is useful for data such as neucode, but not needed for only SILAC labeling.
labels-needed: How many labels need to be detected to quantify a scan (ie if you have a 2 state experiment and set this to 2, it will only quantify scans where both occur.
min-scans: How many quantification scans are needed to quantify a scan.
min-resolution: The minimal resolving power of a scan to consider for quantification. Useful for skipping low-res scans
no-mass-accuracy-correction: Disables the mass accuracy correction.

peak-cutoff: The threshold from the initial retention time a peak can fall by before being discarded
max-peaks: The maximal number of peaks to find in the XIC. A lower value is useful for noisy ms¹.

html: Output a HTML summary.
resume: Will resume from the last run. Only works if not directing output to stdout.
sample: How much of the data to sample. Enter as a decimal (ie 1.0 for everything, 0.1 for 10%)
disable-stats: Disable confidence statistics on data.
out: The prefix for the file output

neucode: This will select parameters suitable for NeuCode data.
isobaric-tags: This will select parameters suitable for iTRAQ or TMT based data.
ms3: This will select parameters suitable for ms³ based TMT quantification.
maxquant: This will select parameters suitable for providing a MaxQuant 'evidence' txt file to PyQuant.

Usage Instructions

PyQuant is run through the pyQuant script. It may be invoked by using pyQuant from the command line following installation.

Here are some common cases and the commands used to run the given analysis

SILAC: --tsv xxx_evidence.txt --label-method K8R10 --maxquant

MS³ based TMT: --isobaric-tags --ms3 --label-method TMT10 --search-file xxx_.msf --reference-label 128N --precursor-ppm 10

Neucode: --neucode --resolution 200000 --search-file xxx.pep.xml --label-scheme neucode.tsv --overlapping-labels

iTRAQ: --label-method iTRAQ8 --isobaric-tags --search-file xxx_.msf --reference-label 114 --precursor-ppm 20