Description, Instructions, and Tips for MS-Filter


This document provides instructions for MS-Filter.

Contents of this document:

Links to topics in the general instructions:

Introduction and Background

MS-Filter processes either a single MSMS peak list file or an archive of peak list files. The spectra matching the filter parameters are either removed from or retained in the peak lists dependent on whether you elect to Keep Spectra Matching Criteria or Remove Spectra Matching Criteria. A further option is to Create Both Sets of Spectra. The program outputs links to allow the processed peak lists to be downloaded. Multiple peak list formats are supported, however the peak lists returned are always in mgf format. Filtering can be based on:

  • the precursor M+H range;
  • the precursor RT range;
  • the precursor charge;
  • the presence of a loss fragment from the precursor ion;
  • the presence of an fragment ion of a given m/z.

The idea of the program is to pre-process peak lists for targeted MSMS searches.

Precursor M+H

The spectra can be filtered by precursor M+H by entering a precursor M+H range. To disable this feature check the All checkbox.

Precursor RT

The spectra can be filtered by precursor RT (retention time) by entering a precursor RT range in minutes. To disable this feature check the All checkbox. Note the part of the number after the decimal point represents fractional minutes rather than seconds.

Precursor Charge

The spectra can be filtered by precursor charge by selecting the precursor charges you wish to retain or eliminate. To disable this feature check the All checkbox.

Loss Composition

If you enter a loss composition the spectral filtering depends on the presence of a loss peak from the precursor ion. The loss peak must also be of the same charge as the precursor except in cases where the spectra contain charge reduced precursor peaks. For charge reduced spectra the loss peak much have a charge one less than the precursor charge.

Fragment M/Zs

If you enter one or more fragment m/z values then the spectral filtering is based on the presence of fragment ions.

Diff M/Z

If you enter one or more diff m/z values then the spectral filtering is based on the presence of mass differences between fragment ions. You can also specify how many times the mass differences must occur to pass the filter.

Min Matches

This is the minimum number of the fragment ions that must match for the spectrum to be retained. This parameter is ignored if no fragment values are entered

Report Options

If you select a report when running MS-Viewer it can be sorted by up to 6 levels. You need to select column numbers, sort types and either ascending or descending order.

Glycosylation Options

The N Motif option limits N-glycosylation hits to N residues which match the motif N[^P][ST]. Note that if the motif extends beyond the peptide then the motif is assumed to have matched.

Peak List File

MS-Filter accepts peak lists in mgf, dta, pkl, mzXML and mzData file formats. There is no need to specify the file format; Protein Prospector will try and automatically recognize it. Compressed files in zip, 7z, rar, gz, z, bz2 and cmn are supported along with tar archives and compressed tar archives (.tar, .tgz, .tar.gz, .taz, .tar.z). These compressed files may contain multiple peak list files.

MS-Filter always generates mgf files whatever the input format.