Mass spectra

PAMPA is designed to handle MS mass spectra, such as MALDI-TOF or MALDI-FT ICR spectra. Note that spectra must undergo mandatory deisotoping and calibration steps before being processed by PAMPA.

Mass spectra (-s)

The program processes a batch of mass spectra simultaneously. All mass spectra files should be placed in a same folder, and the folder path is provided as parameter to -s. There are three recognized formats: CSV, MGF and mzML.

CSV format : It consists of two columns. The first column is designated for mass (m/z), and the second column records intensity (I). Columns are separated by either a comma (',') or a semicolon (';'). Each file contains one spectrum. The initial row serves as the header. Name of the file : .csv or .CSV

MGF format : This is the Mascot Generic Format. Name of the file : .mgf or .MGF

mzML format : see https://www.psidev.info/mzML. With this format, a single file can contain several spectra. Name of the file: .mzML

Any other files present in the folder will be disregarded.

Error margin tolerance (-e)

The error margin is related to the resolution of the mass spectrometer and its ability to distinguish closely spaced peaks. This is the maximal deviation between a peak and the theoretical mass of the peptide marker. This option can be expressed in Dalton or in ppm (parts per million).

• If the value is smaller than 1, it is assumed to be in Da (Daltons). In this case, recommended values are 0.1 for MALDI-TOF, and 0.01 for MALDI-FTICR.
• If the value is larger than 1, it is assumed to be in ppm (parts per million). In this case, recommended values are 50 for MALDI-TOF, and 5 for MALDI-FTICR.