{'fraction_non_alphanumeric': 0.029916410030796304, 'fraction_numerical': 0.008798944126704795, 'mean_word_length': 5.23013698630137, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
MS-based Immunopeptidomics Analysis with PEAKS Studio X

Workflows for immunopeptidomics are different from ones for more established shotgun proteomics. There are inherent challenges with the abundance and natural complexity when doing mass spectrometry analysis for the exploration of human immunopeptidome (e.g. HLA class-I and class-II peptides). A new approach harnessed by PEAKS Studio X was integrated with PEAKS’ de novo sequencing and database searching workflow for HLA peptide identifications, which increased peptide sequencing coverage and confidence. In addition, by introducing a feature-based identification method, PEAKS Studio X can also resolve the identification challenge of co-eluting peptides. Comparing with PEAKS Studio 8.5 and MaxQuant, PEAKS Studio X results show an increase of 13% and 73% more peptides identified, respectively. Introduction Identification of tumor antigens is needed for development of effective cancer immunotherapy. Ideal sources for such antigens are the pools of peptides presented by human leukocyte antigen (HLA) molecules on the tumor cells exclusively. Some of these tumor-specific antigens can induce strong and prolonged anti-cancer immune reaction to eradicate the tumors and thus serve as good candidates for cancer immunotherapeutics. Mass spectrometry (MS)-based methodology has been demonstrated to have great potential to identify such peptides directly. Methods HLA peptidomes of glioblastoma multiforme (GBM), the most aggressive brain tumor with poor prognosis, was analyzed by high resolution LC-MS/MS previously [1]. Briefly, HLA-presenting peptides were extracted from GBM patient peripheral blood by using the immunoaffinity purification method. Then, bound peptides were eluted, purified and analyzed using a Q-Exactive-Plus mass spectrometer in a data-dependent manner. The dataset was re-analyzed with PEAKS Studio 8.5 and PEAKS Studio X and the results were compared. A MS2 isolation window of ± 0.9 Da was used. Thermo .RAW files were analyzed with PEAKS Studio 8.5 and PEAKS Studio X. Associating feature with chimera scan was enabled on PEAKS X. 1% FDR was applied at peptide-spectrum match (PSM) level. Analysis parameters Settings Precursor mass tolerance 10 ppm Fragment mass tolerance 0.03 Da