DOI: 10.25345/c50z7172b
title: MassIVE MSV000093437 - Labeled Quantitative Proteomics of Optic Nerve Regeneration in Xenopus laevis
title: In this labeled quantitative proteomics dataset we profile the proteomic changes in a transgenic line of 1 year old Xenopus laevis Tg(islet2bgfp) frogs that were left untreated (naive) or had a monocular surgery of either a left optic crush injury (crush) or a sham surgery. Matching controls of uninjured optic nerves were also collected for a control factor. The Tg(islet2bgfp) frogs were allowed to recover for 12 and 27 days post optic nerve crush before euthanasia and optic nerve collection. A protein extraction was carried by homogenization of the tissue in extraction buffer (TEAB, NaCl, SDS) via Precellys. During extraction, three internal peptide standards, named as Regen III, were spiked to measure extraction efficiency. Protein amounts were estimated and normalized across experimental samples. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. TMT (Tandem Mass Tag) labelling was carried out using 3 sets of 13 tags from a 16plex TMT kit for quantification. The samples were fractionated into 8 fractions using Pierce High pH Reversed-Phase Peptide Fractionation Kit (Thermo Scientific). After fractionation and drying of all peptide samples, each TMT sample was spiked with two additional isobarically labelled human peptides to be used as an ionization control and cross-sample quantification standard (Regen II). The combination of Regen III and Regen II (Regen V) were used to compare and normalize against a future axon regeneration cohort. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LCMS/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10. After animals were euthanized, optic nerves were collected by dissection. There were six experimental conditions and six biological replicates for each condition for a total of 36 nerves. Protein extraction was carried out by homogenizing the optic nerve tissue in TEAB, NaCl and SDS. Three synthetic bacterial peptide standards (Regen III) were added to the samples during the extraction to measure extraction efficiency. Each standard was spiked into samples for a total concentration of 48uM per standard. After extraction was carried out, protein amounts were estimated using dot blot densitometry and ImageJ and normalized to 50ug/ul. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. Prior to labelling, three samples of mass spec grade pre-digested bovine serum albumin (BSA) were prepared at a concentration of 150pmol. These samples were included to account for differences in labelling efficiency between TMT batches. Three TMT batches were used to label the 36 experimental conditions, so three additional standards were prepared to be used for normalization. All samples, including the three BSA standards, were labelled using 3 sets of 13 tags from a 16plex TMT (Tandem Mass Tag) kit for quantification. Each BSA standard was labelled with a different tag. After combination and drying of all peptide samples, each combined TMT sample (including one BSA-labelled standard) was spiked with two additional human peptide standards containing isobaric labels (Regen II). The final concentration of Regen II was 54uM. These standards were spiked in directly before mass spectrometry analysis to be used as an ionization control. Additionally, all five standards, known as Regen V (Regen III + Regen II), serve as a normalization method that may be used to compare protein abundance data across multiple datasets. Raw mass spectrometry data files were analyzed using Proteome Discoverer 2.5. The mouse proteome was downloaded from UniProt and used as the target database for protein identification. Two additional local databases were created. One containing the Regen V internal standard peptide sequences, and the other containing BSA peptide sequences. The identification of the Regen V and BSA standards was run in a separate Proteome Discoverer workflow targeted to identify the internal standards separately from experimental proteins. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. Post translational modifications of the Regen II, (biotin, carbon13 and nitrogen15) were added during this step to ensure correct identification of the modified standards. The Normalization was set to total peptide amount and confidence to low.