Run qTrace
Run qTrace
Description
Perform petide quantitation on MS1 full or SIM scans. All peptides that are to be quantified must be specified either via the peptides parameter or via text or PSM list files. By default, peptides that are specified via PSM list files are only searched for in those spectra files which the peptides have been identified in.
Input files
- at least 1 spectra file (.mzdata | .mzdata.bz2 | .mzdata.gz | .mzdata.zip | .mzml | .mzml.bz2 | .mzml.gz | .mzml.zip | .mzxml | .mzxml.bz2 | .mzxml.gz | .mzxml.zip | .xml | .xml.bz2 | .xml.gz | .xml.zip)
- optional: PSM list files (.csv)
- optional: peptide files (.txt)
Output files
- Quantitation results (qtrace-results.csv)
- XHTML results (qtrace-results.xhtml)
Context
Parameters
- Label
- Describe the label here. Isotopes may be prepended with amino acids they correspond to, and probabilities may be specified in parantheses.
Examples: 15N, R 13C, K 13C, RP* 13C, RK 13C 15N, ^R 15N
- Amount estimation
-
Choices: isotope envelope fitting (default), fixed isotope peak count
- Scans to analyze
-
Choices: All MS1 scans (default), Full scans only, SIM scans only
- Peptides
- Multiple peptides can be separated by spaces or commas.
Default: empty
Peak picking
- Minimum charge
-
Default: 2
- Maximum charge
-
Default: 3
- Minimum SNR
-
Default: 2.0
- Mass accuracy
- Specify how accurately the Gauss fitted peaks must match to the target m/z values of the peptides. That is, enter the mass accuracy of your MS here.
Default: 5.0 ppm
- Check forbidden peak
-
Choices: yes (default), no
- Check overlapping peaks
-
Choices: yes, no (default)
- Absence mass accuracy factor
-
Default: 2.0
Isotope envelope fitting
- Require peaks down to
-
Default: 40.0 %
- Consider peaks down to
-
Default: 1.0 %
- Max fit error
-
Default: 20.0 %
Fixed isotope peak count
- Number of isotope peaks
-
Default: 3
Tweaks
- Search for all peptides in all spectra files
- Try to quantify all peptides in all spectra files, even if peptides have not been identified in some spectra files.
Default: false
- Exclude amino acids
- If you have reason to believe that certain amino acids will lead to problems during quantitation, please enter them here in single letter code. All peptides containing one of these amino acids will be ignored.
Default: empty
- XHTML report intensity axis
-
Choices: linear (default), logarithmic
Source code
qtrace.rb, qtrace.yaml (GitHub)