The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity
Open accessAbstract
ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and protein sequence databases has been developed. This algorithm uses a three tier scoring scheme. First, a binomial probability is used as a preliminary scoring scheme to select candidate peptides. The binomial probability scores generated by ProLuCID minimize molecular weight bias and are independent of database size. A modified cross-correlation score is calculated for each candidate peptide identified by the binomial probability. This cross-correlation scoring function models the isotopic distributions of fragment ions of candidate peptides which ultimately results in higher sensitivity and specificity than that obtained with the SEQUEST XCorr. Finally, ProLuCID uses the distribution of XCorr values for all of the selected candidate peptides to compute a Z score for the peptide hit with the highest XCorr. The ProLuCID Z score combines the discriminative power of XCorr and DeltaCN, the standard parameters for assessing the quality of the peptide identification using SEQUEST, and displays significant improvement in specificity over ProLuCID XCorr alone. ProLuCID is also able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data. A comparison of filtered data searched with SEQUEST and ProLuCID using the same false discovery rate as estimated by a target-decoy database strategy, shows that ProLuCID was able to identify as many as 25% more proteins than SEQUEST. ProLuCID is implemented in Java and can be easily installed on a single computer or a computer cluster. This article is part of a Special Issue entitled: Computational Proteomics.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Under serum-free survival conditions, we have previously observed that the cells do not proliferate, and thus we are measuring loss of viability in these cells under serum-free conditions with pharmacological treatment 49.”
From Manumycin polyketides act as molecular glues between UBR7 and P53 (2020) · cites this paper as [49]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Measuring the Accuracy of Diagnostic Systems
Swets, J. A. (1988) · Science · doi:10.1126/science.3287615 · Cited by 10,058
Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484
Self-citationKeller, A., Nesvizhskii, A., Kolker, E., & Aebersold, R. (2002) · Analytical Chemistry · doi:10.1021/ac025747h · Cited by 4,970
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
Washburn, M. P., Wolters, D. A., & Yates, J. R. (2001) · Nature Biotechnology · doi:10.1038/85686 · Cited by 4,768
Self-citationProcedures for Detecting Outlying Observations in Samples
Grubbs, F. E. (1969) · Technometrics · doi:10.1080/00401706.1969.10490657 · Cited by 4,105
TANDEM: matching proteins with tandem mass spectra
Craig, R., & Beavis, R. C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth092 · Cited by 2,546
Direct analysis of protein complexes using mass spectrometry
Link, A. J., Eng, J. K., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., & Yates, J. R. (1999) · Nature Biotechnology · doi:10.1038/10890 · Cited by 2,218
Self-citationOlsen, J. V., de Godoy, L. M. F., Li, G., Maček, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S. R., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500030-mcp200 · Cited by 1,539
Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
Self-citationError-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags
Mann, M., & Wilm, M. S. (1994) · Analytical Chemistry · doi:10.1021/ac00096a002 · Cited by 1,473
Open Mass Spectrometry Search Algorithm
Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M. Q., Maynard, D., Yang, X., Shi, W., & Bryant, S. H. (2004) · Journal of Proteome Research · doi:10.1021/pr0499491 · Cited by 1,420
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty‐Kirby, A., & Lajoie, G. (2003) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1196 · Cited by 1,382
Tabb, D. L., McDonald, W. H., & Yates, J. R. (2002) · Journal of Proteome Research · doi:10.1021/pr015504q · Cited by 1,369
Self-citationThe Orbitrap: a new mass spectrometer
Hu, Q., Noll, R. J., Li, H., Makarov, A., Hardman, M., & Cooks, R. G. (2005) · Journal of Mass Spectrometry · doi:10.1002/jms.856 · Cited by 1,338
Clauser, K. R., Baker, P. R., & Burlingame, A. L. (1999) · Analytical Chemistry · doi:10.1021/ac9810516 · Cited by 1,084
PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling
Frank, A. M., & Pevzner, P. A. (2005) · Analytical Chemistry · doi:10.1021/ac048788h · Cited by 691
InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra
Tanner, S. W., Shu, H., Frank, A. M., Wang, L.-C., Zandi, E., Mumby, M. C., Pevzner, P. A., & Bafna, V. (2005) · Analytical Chemistry · doi:10.1021/ac050102d · Cited by 568
A dual pressure linear ion trap orbitrap instrument with very high sequencing speed
Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., et al. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900375-mcp200 · Cited by 464
Kapp, E. A., Schütz, F., Connolly, L., Chakel, J. A., Meza, J. E., Miller, C. A., Fenyö, D., Eng, J. K., Adkins, J., Omenn, G. S., et al. (2005) · PROTEOMICS · doi:10.1002/pmic.200500126 · Cited by 344
A Correlation Algorithm for the Automated Quantitative Analysis of Shotgun Proteomics Data
MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R. G., & Yates, J. R. (2003) · Analytical Chemistry · doi:10.1021/ac034790h · Cited by 277
Self-citationGutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model
Tabb, D. L., Saraf, A., & Yates, J. R. (2003) · Analytical Chemistry · doi:10.1021/ac0347462 · Cited by 275
Self-citationA Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry
Chen, T., Kao, M., Tepel, M., Rush, A. J., & Church, G. M. (2001) · Journal of Computational Biology · doi:10.1089/10665270152530872 · Cited by 249
A Fast SEQUEST Cross Correlation Algorithm
Eng, J. K., Fischer, B., Grossmann, J., & MacCoss, M. J. (2008) · Journal of Proteome Research · doi:10.1021/pr800420s · Cited by 244
Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching
Nesvizhskii, A. I. (2006) · Humana Press eBooks · doi:10.1385/1-59745-275-0:87 · Cited by 234
Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect
Cociorva, D., Tabb, D. L., & Yates, J. R. (2006) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1304s16 · Cited by 228
Self-citationSadygov, R. G., & Yates, J. R. (2003) · Analytical Chemistry · doi:10.1021/ac034157w · Cited by 206
Self-citationFaster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra
Diament, B. J., & Noble, W. S. (2011) · Journal of Proteome Research · doi:10.1021/pr101196n · Cited by 191
Protein indentification using mass spectrometric information
Fenyö, D., Qin, J., & Chait, B. T. (1998) · Electrophoresis · doi:10.1002/elps.1150190615 · Cited by 188
PeaksPTM: Mass Spectrometry-Based Identification of Peptides with Unspecified Modifications
Xi, H., He, L., Xin, L., Shan, B., & Ma, B. (2011) · Journal of Proteome Research · doi:10.1021/pr200153k · Cited by 180
Performance of a Linear Ion Trap-Orbitrap Hybrid for Peptide Analysis
Yates, J. R., Cociorva, D., Liao, L., & Zabrouskov, V. (2005) · Analytical Chemistry · doi:10.1021/ac0514624 · Cited by 175
Self-citationpNovo: De novo Peptide Sequencing and Identification Using HCD Spectra
Chi, H., Sun, R.-X., Yang, B., Song, C., Wang, L., Liu, C., Fu, Y., Yuan, Z., Wang, H., He, S., et al. (2010) · Journal of Proteome Research · doi:10.1021/pr100182k · Cited by 169
Protein identification by spectral networks analysis
Bandeira, N., Tsur, D., Frank, A. M., & Pevzner, P. A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701130104 · Cited by 165
Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures
Second, T. P., Blethrow, J. D., Schwartz, J. C., Merrihew, G. E., MacCoss, M. J., Swaney, D. L., Russell, J. D., Coon, J. J., & Zabrouskov, V. (2009) · Analytical Chemistry · doi:10.1021/ac901278y · Cited by 160
Fast Multi-blind Modification Search through Tandem Mass Spectrometry
Na, S., Bandeira, N., & Paek, E. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.010199 · Cited by 157
Searle, B. C., Dasari, S., Turner, M., Reddy, A. P., Choi, D., Wilmarth, P. A., McCormack, A. L., David, L. L., & Nagalla, S. R. (2004) · Analytical Chemistry · doi:10.1021/ac035258x · Cited by 138
Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry
Frank, A. M., Tanner, S. W., Bafna, V., & Pevzner, P. A. (2005) · Journal of Proteome Research · doi:10.1021/pr050011x · Cited by 133
Searle, B. C., Dasari, S., Wilmarth, P. A., Turner, M., Reddy, A. P., David, L. L., & Nagalla, S. R. (2005) · Journal of Proteome Research · doi:10.1021/pr049781j · Cited by 123
Search engine processor: Filtering and organizing peptide spectrum matches
Carvalho, P. C., Fischer, J. D. S. D. G., Xu, T., Cociorva, D., Balbuena, T. S., Valente, R. H., Perales, J., Yates, J. R., & Barbosa, V. C. (2012) · PROTEOMICS · doi:10.1002/pmic.201100529 · Cited by 120
Self-citationSunyaev, S. R., Liska, A. J., Golod, A., Shevchenko, A., & Shevchenko, A. (2003) · Analytical Chemistry · doi:10.1021/ac026199a · Cited by 116
Shevchenko, A., Chernushevich, I. V., Wilm, M. S., & Mann, M. (2003) · Humana Press eBooks · doi:10.1385/1-59259-045-4:1 · Cited by 112
pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra
Chi, H., Chen, H., He, K., Wu, L., Yang, B., Sun, R.-X., Liu, J., Zeng, W., Song, C., He, S., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr3006843 · Cited by 104
Searching Sequence Databases via De Novo Peptide Sequencing by Tandem Mass Spectrometry
Johnson, R. S., & Taylor, J. A. (2002) · Molecular Biotechnology · doi:10.1385/mb:22:3:301 · Cited by 99
Rat brain proteins: Two-dimensional protein database and variations in the expression level
Fountoulakis, M., Schuller, E., Hardmeier, R., Berndt, P., & Lübec, G. (1999) · Electrophoresis · doi:10.1002/(sici)1522-2683(19991201)20:18 · Cited by 84
YADA: a tool for taking the most out of high-resolution spectra
Carvalho, P. C., Xu, T., Han, X., Cociorva, D., Barbosa, V. C., & Yates, J. R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp489 · Cited by 78
Self-citationDiscovering Known and Unanticipated Protein Modifications Using MS/MS Database Searching
Tang, W. H., Halpern, B. R., Shilov, I. V., Seymour, S. L., Keating, S. P., Loboda, A., Patel, A. A., Schaeffer, D. A., & Nuwaysir, L. M. (2005) · Analytical Chemistry · doi:10.1021/ac0481046 · Cited by 72
Venable, J. D., Wohlschlegel, J. A., McClatchy, D. B., Park, S. K., & Yates, J. R. (2007) · Analytical Chemistry · doi:10.1021/ac062054i · Cited by 63
Self-citationLu, B., & Chen, T. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1068 · Cited by 44
Self-citationCentral Limit Theorem as an Approximation for Intensity-Based Scoring Function
Sadygov, R. G., Wohlschlegel, J. A., Park, S. K., Xu, T., & Yates, J. R. (2005) · Analytical Chemistry · doi:10.1021/ac051206r · Cited by 31
Self-citationShotgun Protein Identification and Quantification by Mass Spectrometry
Lu, B., Xu, T., Park, S. K., & Yates, J. R. (2009) · Methods in molecular biology · doi:10.1007/978-1-60761-157-8_15 · Cited by 27
Self-citationNegative Ionization Micro Electrospray Mass Spectrometry of Oligonucleotides and their Complexes
Greig, M. J., Gaus, H. J., & Griffey, R. H. (1996) · Rapid Communications in Mass Spectrometry · doi:10.1002/(sici)1097-0231(19960115)10:1 · Cited by 27
Wirth, U., Müller, D., Schindler, P. A., Lange, J., & van Oostrum, J. (2002) · PROTEOMICS · doi:10.1002/1615-9861(200210)2:10 · Cited by 13
Flagged first, then by citations
Cited by
Sorted by citations
Li, X., Xiong, X., Zhang, M., Wang, K., Chen, Y., Zhou, J. L., Mao, Y., Lv, J., Yi, D., Chen, X., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.019 · Cited by 482
Harnessing the anti-cancer natural product nimbolide for targeted protein degradation
Spradlin, J. N., Hu, X., Ward, C. C., Brittain, S. M., Jones, M. D., Ou, L., To, M., Proudfoot, A., Ornelas, E., Woldegiorgis, M., et al. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0304-8 · Cited by 432
“…°C and the nanospray voltage was set to 2.75 kV. Data was extracted in the form of MS1 and MS2 files using Raw Extractor 1.9.9.2 (Scripps Research Institute) and searched against the Uniprot human database using ProLuCID search methodology in IP2 v.3 (Integrated Proteomics Applications, Inc) 36 .”
InfluentialHe, M., Chiang, H.-H., Luo, H., Zheng, Z., Qiao, Q., Wang, L., Tan, M., Ohkubo, R., Mu, W.-C., Zhao, S., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.01.009 · Cited by 425
“San Diego, CA) using ProLuCID/Sequest, DTASelect2 and Census (Cociorva et al., 2007; Park et al., 2008; Tabb et al., 2002; Xu et al., 2015).”
MethodDeubiquitinase-targeting chimeras for targeted protein stabilization
Henning, N. J., Boike, L., Spradlin, J. N., Ward, C. C., Liu, G., Zhang, E., Belcher, B. P., Brittain, S. M., Hesse, M. J., Dovala, D., et al. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-00971-2 · Cited by 344
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping
Sas‐Chen, A., Thomas, J. M., Matzov, D., Taoka, M., Nance, K. D., Nir, R., Bryson, K. M., Shachar, R., Liman, G. L. S., Burkhart, B. W., et al. (2020) · Nature · doi:10.1038/s41586-020-2418-2 · Cited by 336
Metadata
- Authors
- Xu, T., Park, S. K., Venable, J. D., Wohlschlegel, J. A., Diedrich, J. K., Cociorva, D., Lu, B., Liao, L., Hewel, J., Han, X., Wong, C. C. L., Fonslow, B., Delahunty, C., Gao, Y., Shah, H., & Yates, J. R.
- Affiliations
- Scripps Research Institute (US)
- Corresponding author
- Yates, J.R.
- ORCID
- Venue
- Journal of Proteomics
- Publisher
- Elsevier BV
- Published
- 2015-11
- Volume
- 129
- Pages
- 16-24
- ISSN
- 1874-3919 (ISSN-L)
- PMC
- PMC4630125
- OpenAlex
- W2182963873
- Cited by
- 511
- References
- 51
- Citations by year
- 2026: 23 · 2025: 41 · 2024: 65 · 2023: 45 · 2022: 51 · 2021: 56 · 2020: 56 · 2019: 60 · 2018: 43 · 2017: 46 · 2016: 22 · 2015: 3
- FWCI
- 16.92
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Proteomics (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- NIH (5U01 DE016267-04, 5R01 HL079442-04, R01 MH067880, P41 GM103533)
- NHLBI (HHSN268201000035C)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- peptide identification, tandem mass spectrometry, SEQUEST, Z-score
- MeSH terms
- Algorithms, Amino Acid Sequence, Molecular Sequence Data, Pattern Recognition, Automated, Peptide Mapping, Proteins, Sensitivity and Specificity, Software, Reproducibility of Results, Sequence Analysis, Protein, Databases, Protein, Tandem Mass Spectrometry, Data Mining
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
