MALDI-TOF/TOF Protein Identification

Mass spectra of trypsin digested proteins were obtained in Autoflex II MALDI TOF/TOF (Bruker Daltonics). Mass spectra were recorded in linear mode equipped with a pulsed N₂ laser (λ = 337nm, 50 Hz) at 54% power in positive ion mode. After MS spectra acquisition, the instrument was switched to LIFT mode. The MS/MS spectra of top ten peptides with highest intensity were recorded by fragmentation of these peptides using LID (laser induced dissociation). MS/MS spectra were acquired with a minimum of 4000 and a maximum of 8000 laser shots using the instrument calibration file. Spectra baseline subtraction, smoothing [26 (link)] and centroiding were performed in FlexAnalysis software v3.0 (Bruker Daltonics).

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Ghosh N., Sircar G., Saha B., Pandey N, & Gupta Bhattacharya S. (2015). Search for Allergens from the Pollen Proteome of Sunflower (Helianthus annuus L.): A Major Sensitizer for Respiratory Allergy Patients. PLoS ONE, 10(9), e0138992.

Publication 2015

Autoflex II MALDI TOF/TOF FlexAnalysis software v3.0

Maldi Mass proteins Mass spectra Ms ms Peptides Trypsin

Corresponding Organization : Bose Institute

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Variable analysis

independent variables

Mass spectrometer type (Autoflex II MALDI TOF/TOF)
Laser type (pulsed N2 laser)
Laser wavelength (λ = 337nm)
Laser pulse frequency (50 Hz)
Laser power (54%)

dependent variables

Mass spectra of trypsin digested proteins
MS/MS spectra of top ten peptides with highest intensity

control variables

Instrument mode (linear mode, LIFT mode)
Number of laser shots (minimum 4000, maximum 8000)
Instrument calibration file
Data processing (baseline subtraction, smoothing, centroiding)

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