Dataset Information

Tyrosine kinase Ptk1 couples one carbon metabolism and virulence in an endogenous pathogen

ABSTRACT: Samples were analyzed by GelC MS using in-gel trypsinization. Digests were analyzed using an EASY nLC (ThermoFisher) UHPLC system and an Acclaim PepMap 100 trap coupled to an Acclaim PepMap RSLC 50 um separating column (ThermoFisher). The eluate was introduced into the LTQ-Orbitrap ELITE mass spectrometer using a Nanospray Flex source (ThermoElectron). A Nth Order Double Play method was created in Xcalibur v2.2. Scan event one of the method obtained an FTMS MS1 scan (normal mass range; 120,000 resolution, full scan type, positive polarity, profile data type) for the range 300 to 2000 m/z. Scan event two obtained ITMS MS2 scans (CID activation type, normal mass range, rapid scan rate, centroid data type) on up to twenty peaks that had a minimum signal threshold of 5000 counts from scan event one. The lock mass option was enabled using the 371.101236m/z polysiloxane peak as an internal calibrant. Peaks Studio Xpro (Bioinformatics Solutions) was used to analyze the data against the 9/30/2021 version of the P. gingivalis strain ATCC 33277 protein sequences from the UniProtKB (proteome identifier UP000008842) considering semi specific Trypsin (maximum two missed cleavages) with fragment tolerance (0.5 Da) from the ITMS and parent tolerance (15 ppm) from the FTMS. FDR estimation was enabled in the algorithms. A proteins.csv file was exported for curation in Microsoft Excel. Proteins and peptides were accepted at the 1% FDR threshold.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Porphyromonas Gingivalis (ncbitaxon:837)

SUBMITTER: Michael L. Merchant, PhD