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)