1. Naming Conventions for Spectrum Matching Results Files

    (1) For the three standard scoring methods, namely cosine, projected cosine, and Jensen-Shannon divergence, use the following format:
        <standard_scoring_method>_<query_set_name>_<noise_level>_<library_name>_<preprocessing_scenario>_<number_of_minimum_matching_peaks>.tsv

    (2) For the two state-of-the-art search methods, Entropy score, and SpectraST, use this format:
        <search_method>_<query_set_name>_<noise_level>_<library_name>.tsv

    Please replace the placeholders in angled brackets (<>) with the appropriate values as per the following options:
        <standard_scoring_method>: cos, projcos, or jsd
        <search_method>: entropy or spectrast
        <query_set_name>: real or clean
        <noise_level>: 0, 1, 2, or 3
            "0": without additional noise
            "1": add  25% noise
            "2": add  50% noise
            "3": add 100% noise
        <library_name>: KB, KB-Anno or Prosit
        <preprocessing_scenario>: A, B, C, BC, D, E, F, G, or H
            "A": original spectrum
            "B": square root transformation (SQRT)
            "C": window filter (WF), 5, 50
            "BC": apply both "B" and "C"
            "D": signal-to-noise ratio filter (SNR), 3, 25%
            "E": signal-to-noise ratio filter (SNR), 5, 25%
            "F": top peak filter (TOP), 20
            "G": high-intensity filter (MAX), 1%
            "H": high-intensity filter (MAX), 5%
        <number_of_minimum_matching_peaks>: an integer between 0 and 24

2. Constructing USIs:

    Based on the information provided in "query_spectrum_provenance_info.tsv", you can construct the USIs for each query spectrum to visualize at https://massive.ucsd.edu/ProteoSAFe/usi.jsp#{%22usi%22:%22%22}:
    (1) Original spectrum
        USI: mzspec:MSV000079841:<original_file_name>:scan:<original_scan_number>:<original_MSGF+_identification>/<original_MSGF+_identification_charge>
    (2) Source noise spectrum
        USI: mzspec:MSV000083508:<noise_spectrum_filename>:scan:<noise_spectrum_scan_number>:<noise_spectrum_msgf+_identification>/<noise_spectrum_msgf+_identification_charge>
    (3) Shuffled noise spectrum
        USI: mzspec:<this_dataset>:29tissues69_annotated_shuffled.mgf:scan:<shuffled_noise_spectrum_scan_number>:<shuffled_noise_spectrum_identification>/<noise_spectrum_msgf+_identification_charge>

    Please replace the placeholders in angled brackets (<>) with the specific spectrum details from the corresponding column. <this_dataset> represents the MassIVE dataset index of this dataset.

    Example USI: mzspec:MSV000079841:b1906_293T_proteinID_01A_QE3_122212.mzXML:scan:1886:HAVSEGTK/2