Quantification

Label-Free quantification

• LFQ is currently in a very early stage. It quantifies peptides based on MS1 intensity around an identifying MS2 spectrum.
• Quantification occurs after identification. All MS1 peaks around the identification MS2 spectrum within the retention time window are checked for an expected isotopic distribution. The most intense peak within the RT window that meets the isotopic distribution requirements is used as the intensity of the peptide.
• Peptides are quantified by apex intensity, meaning that the most intense peak that meets the quantification criteria will be reported as the Apex Intensity value in the PSMs output. Integration, etc is currently not enabled.
• Because modified peptides can ionize differently than unmodified peptides, and can thus affect the intensity of the detected ion, peptide intensity should only be compared to the same peptide with the same mods across runs. Make sure you're comparing apples to apples.

Tandem-Mass-Tag

TMT for HCD data is possible for up to 10-plex samples. Intensity is reported as a list of 10 intensities, one for each plex. The ion intensity is reported in order of each plex's diagnostic ion: 126.127725, 127.124760, 127.131079, 128.128114, 128.134433, 129.131468, 129.137787, 130.134822, 130.141141, 131.138176 with the "|" as the delimiter between each plex.

Proteins

• Quantification is not enabled for proteins yet. It is in the works and will arrive soon.