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Assessing LC-MS Data Quality

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About MScout

MScout is a tool for assessing peak capacity, dynamic range, and signal-to-noise in low-resolution liquid-chromatography mass-spectrometry (LC-MS) data. MScout reads in mass spectra and finds peaks above a user-selected signal-to-noise ratio, using an algorithm adapted from Horn et al. [1]. These peaks are then checked to see if they persist in the time domain, i.e., if they behave like a real peptide eluting from an LC column. As peaks are checked for behavior in the time domain, chromatography peak widths are calculated, and the chromatographic peak capacity is computed. At the end of the calculations, dynamic range is computed by dividing the intensity of the most intense peak by the intensity of the least intense peak.

MScout is also capable of comparing signals between separate LC-MS runs. This capability was developed to analyze LC-FAIMS-MS data, in which there are separate MS1 files for each compensation voltage (CV) used. MScout was used specifically for this purpose in our recent evaluation of FAIMS (high-field asymmetric waveform ion mobility spectrometry) on an ion trap mass spectrometer [2].

Note. MScout is intended for use with low-resolution data such as that obtained on ion trap or triple-quadrupole instruments. Results from higher-resolution datasets are unpredictable. For high-resolution data, try using Hardklör.

Running MScout

MScout is a command-line program. The general format for usage for the 64-bit version is

% mscout64 <options> <input MS1 file(s)>

To run the 32-bit version, simply replace mscout64 with mscout32.

MScout currently accepts only MS1 files as input. See reference [3] for details. Download MakeMS2 to convert your RAW files from Thermo Scientific instruments into the MS1 format.

An example command is

% mscout64 -rti=0 -rtf=120 -time=0.2 -mz=0.5 -sn=3 -histograms=0 -siglist=1 ./ms1-files/052107-faims-yeast-03-CV-*.ms1

See Running MScout for more details.

  1. McDonald, W.H. et al. "MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications." Rapid Commun. Mass Spectrom. 18, 2162-2168 (2004)
  2. Horn, D. M., Zubarev, R. A., McLafferty, F. W. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332.
  3. Canterbury, J.D., Yi, X., Hoopmann, M.R., MacCoss, M.J. "Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics" submitted.
MScout is Copyright © 2008 University of Washington. All rights reserved. Written by Jesse D. Canterbury, Michael R. Hoopmann, and Michael J. MacCoss, in the Department of Genome Sciences at the University of Washington