The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics

Abstract

We present a mass spectral library-based method to identify tandem mass spectra of peptides that contain unanticipated modifications and amino acid variants. We describe this as a "hybrid" method because it combines matching both ion m/z and mass losses. The mass loss is the difference between the mass of an ion peak and the mass of its precursor. This difference, termed DeltaMass, is used to shift the product ions in the library spectrum that contain the modification, thereby allowing library product ions that contain the unexpected modification to match the query spectrum. Clustered unidentified spectra from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and Chinese hamster ovary cells were used to evaluate this method. The results demonstrate the ability of the hybrid method to identify unanticipated modifications, insertions, and deletions, which may include those due to an incomplete protein sequence database or to search settings that exclude the correct identification, in high-resolution tandem mass spectra without regard to their precursor mass. This has been made possible by indexing of the m/z value of each fragment ion and its difference in mass from its precursor ion.

Sensitive Method for the Confident Identification of Genetically Variant Peptides in Human Hair Keratin

“…Table compares the twenty most frequently identified DeltaMass values in three methods . For more information, Appendix S4 shows the histograms of all DeltaMass values obtained from hybrid search identifications in each method to give a broad view of the distribution of all DeltaMass values.…”

“…This “hair” library was used in combination with the “main” library for mass spectrum library searching. The 1% false discovery rate (FDR) level was determined by using the target‐decoy method described in the literature . The NIST‐formatted mass spectral libraries were built using the program Lib2NIST freely available online at chemdata.nist.gov.…”

“…Since this issue is important for every sample preparation method regarding GVP detection, below we examine the artifacts among the three methods: our direct method, modified NaOH + SDS method, and cleavable surfactant method. Table 5 compares the twenty most frequently identified Delta-Mass values in three methods (15). For more information, Appendix S4 shows the histograms of all DeltaMass values obtained from hybrid search identifications in each method to give a broad view of the distribution of all DeltaMass values.…”

Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

“…The mzCloud utilizes a proprietary similarity search algorithm that appears similar to the Hybrid search algorithm recently described by NIST. 15 By allowing similarity search according to the settings in Supplemental File 2 an additional 144 and 112 compounds were assigned as "similar to" compounds present in the mZCloud library compound when a delta mass shift is allowed, in positive and negative polarities, respectively. In ultra-high-resolution mass spectrometry, molecular formulas may be confidently assigned for relatively small compounds, based purely on mass alone.…”

Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units

“…As described previously, ANN-SoLo uses approximate nearest neighbor (ANN) indexing to speed up OMS by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This approach is combined with a cascade search strategy [12] to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate (FDR), as well as a shifted dot product score to sensitively match modified spectra to their unmodified counterparts [13,14].…”