Supplementary MaterialsSupporting Information PMIC-18-na-s001. and sensitive NSCLC cells is usually carried out. Altogether, changes in expression of 3773 proteins are quantified, and changes in ubiquitylation of 2893 lysine sites in 1415 proteins are measured in both cells. Interestingly, lysosomal and endocytic pathways, which are involved in autophagy regulation, are enriched with upregulated proteins or ubiquitylated proteins in gefitinib\resistant cells. In addition, HMGA2 overexpression or ALOX5 knockdown suppresses gefitinib resistance in NSCLC cells by inhibiting autophagy. Overall, these results reveal the previously unknown global ubiquitylome and proteomic features associated with gefitinib resistance, uncover the opposing functions of HMGA2 or ALOX5 in regulating gefitinib resistance and autophagy, and will help to identify KU-0063794 new therapeutic targets in overcoming gefitinib resistance. scan range was 350 to 1800. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE13 partner repository (http://www.ebi.ac.uk/pride/archive/) with the dataset identifier PXD004941. 2.8. Protein Quantification LC\MS/MS analysis data are further analyzed using the MaxQuant software. Based on the MS/MS spectra, the peptides are recognized Rabbit polyclonal to ZNF561 while the ratios of the according SILAC pairs are used for relative quantification. In each LC\MS run, we normalize peptide ratios so that the median of their logarithms is usually zero, which corrects for unequal protein loading, assuming that the majority of proteins show no differential regulation. Protein ratios are calculated as the median of all SILAC peptide ratios, minimizing the effect of outliers. We normalize the protein ratios to correct for unequal protein amounts. Whenever the set of recognized peptides in one protein is equal to or completely contained in the set of recognized peptides of another protein these two proteins are joined in a protein group. Shared peptides are most parsimoniously associated with the group with the highest number of KU-0063794 recognized peptides (razor peptides) but remain in all groups where they occur. Peptide identification information from your proteomic study is usually provided (Table S1, Supporting Information). 2.9. Database Search The producing MS/MS data was processed using MaxQuant with integrated Andromeda search engine (v.188.8.131.52). Tandem mass spectra were searched against Swissprot_human (20?274 sequences) database concatenated with reverse decoy database. Trypsin/P was specified as cleavage enzyme allowing up to four missing cleavages, four modifications per peptide, and five charges. Mass error was set to 10 ppm for precursor ions and 0.02 Da for fragment ions. Carbamidomethylation on Cys was specified as fixed modification and oxidation on Met, ubiquitylation on Lys and acetylation on protein N\terminal were specified as variable modifications. False discovery rate (FDR) thresholds for protein, peptide and modification site were specified at 1%. Minimum peptide length was set at 7. All the other parameters in MaxQuant were set to default values. The site localization probability was set as 0.75. 2.10. Gene Ontology Annotation Gene Ontology (GO) annotation proteome was derived from the UniProt\GOA database (http://www.ebi.ac.uk/GOA/). Firstly, transforming recognized protein ID to UniProt ID and then mapping to GO IDs by protein ID. If some recognized proteins were not annotated by UniProt\GOA database, the InterProScan soft would KU-0063794 be used to annotate protein’s GO functional based on protein sequence alignment method. Then proteins were classified by Gene Ontology annotation based on three groups: biological process, cellular component, and molecular function. 2.11. Domain name Annotation Identified proteins domain name functional description were annotated by InterProScan (a sequence analysis application) based on protein sequence alignment method, and the InterPro domain name database was used. InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains, and functional sites, and makes it freely available to the public via Web\based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has power in the large\level analysis of whole genomes and meta\genomes, as well as in characterizing individual protein sequences. 2.12. KEGG Pathway Annotation First, KEGG online service tool, KAAS, was used to annotate protein’s KEGG database description. Then, the annotation results were mapped around the KEGG pathway database using KEGG online service tools KEGG mapper. 2.13. Subcellular Localization Wolf psort, a subcellular localization predication software, was used to predict subcellular localization of proteins. Wolf psort is an updated version of PSORT/PSORT II for the prediction of protein subcellular localization based on their sequences.14 2.14. Motif Analysis The motif\X software was used to analyze the motif of sequences constituted with amino acids in specific positions of modifier\21\mers (ten amino acids upstream and downstream of the site).