Spectral Library Searching To Identify Cross-Linked Peptides

Schweppe, Devin K.; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Ruiz, Bianca Y.; Eng, Jimmy K.; Lam, Henry H N; Bruce, James E.

doi:10.1021/acs.jproteome.6b00014

Cited by 12 publications

(8 citation statements)

References 23 publications

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“…A spectral library was generated using the cross-linked identifications observed in this study, as described previously (29). This spectral library is available in Dataset S3.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry

Schweppe

Chavez

Lee

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

173

206

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Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex. Cross-linked sites showed excellent agreement with empirical protein structures and delivered complementary constraints for in silico protein docking. These data established direct physical evidence of the assembly of the complex I-III respirasome and enabled prediction of in situ interfacial regions of the complexes. Finally, we established a database and tools to harness the cross-linked interactions we observed as molecular probes, allowing quantification of conformation-dependent protein interfaces and dynamic protein complex assembly. mitochondria | mass spectrometry | interactome | cross-linking | protein interaction reporter M itochondrial proteins play a diverse role in cellular biology and disease. Mitochondrial dysfunction directly causes multiple inherited diseases (1) and is implicated in common diseases, including neurological developmental disorders (2, 3), neurodegenerative and cardiovascular diseases (4-6), diabetes (7), asthma (8), cancer (9), and age-related disease (10). In mammals, these organelles have evolved to retain more than 1,000 proteins that interact within a complex, i.e., dual membrane architecture (11,12). Within the mitochondrial proteome, the "powerhouse" functions are carried out by the core constituents of the oxidative phosphorylation (OXPHOS) system [complexes I-IV of the electron transport chain (ETC) and ATP synthase (complex V)]. These proteins are necessary for creation of the mitochondrial electrochemical gradient that powers synthesis of ATP. This system includes critical protein-protein interactions within individual OXPHOS complexes as well as "supercomplex" interactions between ETC complexes I, III, and IV in the respirasome (13). Deficient supercomplex formation has been proposed as a critical mitochondrial defect in failing hearts (5,6,14,15), and dynamic rearrangement of supercomplexes has been implicated in noncanonical mitochondrial functions such as antibacterial innate immune responses (16). Assessing these interactions is further complicated by regulatory posttranslational modification and conformational changes of mitochondrial proteins (17)(18)(19)(20). Advances in this area have been impeded, in part, by the lack of large-scale detection of dynamic, sometimes transient, interactions between membrane proteins. Thus, large-scale determination of the protein interactome within mitochondria would provide a valuable tool to adv...

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“…A spectral library was generated using the cross-linked identifications observed in this study, as described previously (29). This spectral library is available in Dataset S3.…”

Section: Methodsmentioning

confidence: 99%

“…Work by many groups has led to improvements in instrumentation (24), cross-linker chemistry (25,26), database searching (23,24,27,28), spectral match filtering (29), and structural analysis based on sites of cross-linking (30)(31)(32). Large-scale XL-MS offers two key benefits.…”

mentioning

confidence: 99%

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry

Schweppe

Chavez

Lee

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

173

206

View full text Add to dashboard Cite

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“…Later numerous spectral library tools have been developed, including Bibliospec 2 , X!Hunter 3 , SpectraST 4 , Pepitome 5 , Peptide Atlas 6 , spec2spec 7 , MSPLIT-DIA 8 , and Tremolo 9 . In addition, several spectral library tools were also developed for identification with peptide modifications, such as QuickMod 10 and pMatch 11 for post-translational modification, Hybrid for unanticipated modifications 12 , cross-linked peptide identification 13 , and GPQuest 14 for N-linked glycopeptides. Owing to improved sensitivity and turnaround time, several sample-specific libraries have been built, such as the neuropeptide database 15 , and a database for cancer cell lines 16 .…”

Section: Introductionmentioning

confidence: 99%

Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra

et al. 2018

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Tandem mass tag (TMT)-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a proven approach for large-scale multiplexed protein quantification. However, the identification of TMT-labeled peptides is compromised by the labeling during traditional sequence database searches. In this study, we aim to use a spectral library search to increase the sensitivity and specificity of peptide identification for TMT-based MS data. Compared to MS/MS spectra of unlabeled peptides, the spectra of TMT-labeled counterparts usually display intensified b ions, suggesting that TMT labeling can alter product ion patterns during MS/MS fragementation. We compiled a human TMT spectral library of 401,168 unique peptides of high quality from millions of peptide-spectrum matches in tens of profiling projects, matching to 14,048 nonredundant proteins (13,953 genes). A mouse TMT spectral library of similar size was also constructed. The libraries were subsequently appended with decoy spectra to evaluate the false discovery rate, which was validated by a simulated null TMT data set. The performance of the library search was further optimized by removing TMT reporter ions and selecting an appropriate library construction method. Finally, we searched a human TMT data set against the spectral library to demonstrate that the spectral library outperformed the sequence database. Both human and mouse TMT libraries were made publicly available to the research community.

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“…As opposed to comparing each query MS2 spectrum against theoretical fragment ions of putative peptides, it compares the query spectrum against a library of experimental reference spectra for which the identifications are known, resulting in more sensitive and more rapid identification 4 – 8 . To date, spectral library searching has been successfully applied to a number of important research topics regarding phosphopeptides 9 , 10 , intact glycopeptides 11 , 12 , cross-linked peptides 13 , and missing proteins 14 .…”

Section: Introductionmentioning

confidence: 99%

Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics

Wang

Choong

Chen

et al. 2022

Sci Rep

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Identifying peptides and proteins from mass spectrometry (MS) data, spectral library searching has emerged as a complementary approach to the conventional database searching. However, for the spectrum-centric analysis of data-independent acquisition (DIA) data, spectral library searching has not been widely exploited because existing spectral library search tools are mainly designed and optimized for the analysis of data-dependent acquisition (DDA) data. We present Calibr, a spectral library search tool for spectrum-centric DIA data analysis. Calibr optimizes spectrum preprocessing for pseudo MS2 spectra, generating an 8.11% increase in spectrum–spectrum match (SSM) number and a 7.49% increase in peptide number over the traditional preprocessing approach. When searching against the DDA-based spectral library, Calibr improves SSM number by 17.6–26.65% and peptide number by 18.45–37.31% over two state-of-the-art tools on three different data sets. Searching against the public spectral library from MassIVE, Calibr improves state-of-the-art tools in SSM and peptide numbers by more than 31.49% and 25.24%, respectively, for two data sets. Our analyses indicate higher sensitivity of Calibr results from the use of various spectral similarity measures and statistical scores, coupled with machine learning-based statistical validation for FDR control. Calibr executable files including a graphical user-interface application are available at https://ms.iis.sinica.edu.tw/COmics/Software_CalibrWizard.html and https://sourceforge.net/projects/comics-calibr.

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Spectral Library Searching To Identify Cross-Linked Peptides

Cited by 12 publications

References 23 publications

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry

Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra

Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics

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