---
title: "MSconvert Instructions"
output: 
  rmarkdown::html_vignette:
    fig_width: 6
    fig_height: 2
description: |
  MRMhub: postprocessing and quality control of small molecule mass spectrometry data 
vignette: >
  %\VignetteIndexEntry{MSconvert Instructions}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
editor_options: 
  markdown: 
    wrap: 72
bibliography: references.bib
---

# 

INTEGRATOR uses mzML files as input. Users can use the MSconvert tool,
available as part of the Proteowizard software to convert proprietary
raw data files (.wiff for SCIEX/Watersm, .raw files for Thermo Fisher,
.d folders for Agilent, etc) into mzML format. This step can only be
done on Windows PC.

1.  Download or upgrade a recent version ProteoWizard
    (<https://proteowizard.sourceforge.io>) on a Windows computer.
    Having a recent versions ensures successfull conversion of actual
    vendor-specific formats.

2.  Start “MSConvert” via the START menu, or by right-clicking on the
    raw files to be converted and selecting MSConvertGUI.

3.  In the MSConvert window, use the “Browse” button to select the raw
    files to be converted. Note: .wiff and .wiff.scan files need to be
    located in the same folder).

4.  Set following options: “*mzML*” for “*Output format”*, “*32-bit*”
    for “*Binary encoding precision*”, check “*Write index*" and to
    improve performance, increase "Files to convert in parallel" to the
    number of available CPU cores.

5.  Run conversion by clicking "Start", and copy the mzML files to the
    MRMhub subfolder mzML

![](images/paste-7.png){fig-align="center" width="465"}

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