Cited by 513Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsGenomics and Phylogenetic Studies

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ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

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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.·2015·Journal of Proteomics

DOI 10.1016/j.jprot.2015.07.001PMC PMC4630125

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Abstract

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.

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“A scoring evaluation (e.g., Xcorr and deltaCN in SEQUEST, Z-score in ProLuCID) is usually applied to describe the degree of matching between observed and in silico generated spectra.”
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Analysis of proteome-wide degradation dynamics in ALS SOD1 iPSC-derived patient neurons reveals disrupted VCP homeostasis
Tsioras, K., Smith, K. C., Edassery, S. L., Garjani, M., Li, Y., Williams, C., McKenna, E. D., Guo, W., Wilen, A. P., Hark, T. J., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113160 · Cited by 21
“…were searched against UniProt human protein database (downloaded on 01–01-2014 or 03–25-2014; UniProt Consortium, 2015) and matched to sequences using the ProLuCID/SEQUEST algorithm (ProLuCID version 3.1 91,92 with 50ppm peptide mass tolerance for precursor ions and 600 ppm for fragment ions.”
Influential
Thermal proteome profiling reveals fructose-1,6-bisphosphate as a phosphate donor to activate phosphoglycerate mutase 1
Zhang, Y., Cao, Y., Wu, X., Chen, Z., Chen, B., Wang, A., Guo, Y., Chen, W., Xue, R., Liu, Z., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53238-w · Cited by 19
Baculovirus AC102 Is a Nucleocapsid Protein That Is Crucial for Nuclear Actin Polymerization and Nucleocapsid Morphogenesis
Hepp, S. E., Borgo, G. M., Ticau, S., Ohkawa, T., & Welch, M. D. (2018) · Journal of Virology · doi:10.1128/jvi.00111-18 · Cited by 19
“Protein identification and quantification were done with Integrated Proteomics Pipeline IP2 software (Integrated Proteomics Applications) using ProLuCID/Sequest (46), DTASelect (47, 48), and Census (49).”
Method
Identification of 113 new histone marks by CHiMA, a tailored database search strategy
Gao, J., Sheng, X., Du, J., Zhang, D., Han, C., Chen, Y., Wang, C., & Zhao, Y. (2023) · Science Advances · doi:10.1126/sciadv.adf1416 · Cited by 20
“We next compared the distributions of the confidence scores, the major metric used by DTASelect to assess PSM confidence ( 18 ).”
Comparative Cross-Kingdom DDA- and DIA-PASEF Proteomic Profiling Reveals Novel Determinants of Fungal Virulence and a Putative Druggable Target
Ball, B., Sukumaran, A., Krieger, J. R., & Geddes‐McAlister, J. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00255 · Cited by 19
The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation
Bhattacharya, S., Lange, J. J., Levy, M. J., Florens, L. A., Washburn, M. P., & Workman, J. L. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101075 · Cited by 20
An apical protein, Pcr2, is required for persistent movement by the human parasite Toxoplasma gondii
Munera Lopez, J., Tengganu, I. F., Liu, J., Murray, J. M., Arias Padilla, L. F., Zhang, Y., Brown, P. T., Florens, L., & Hu, K. (2022) · PLOS Pathogens · doi:10.1371/journal.ppat.1010776 · Cited by 14
“3 [71] with a mass tolerance of 10 ppm for peptide and fragment ions.”
Background
Trans-Golgi protein TVP23B regulates host-microbe interactions via Paneth cell homeostasis and Goblet cell glycosylation
Song, R., McAlpine, W., Fond, A. M., Nair‐Gill, E., Choi, J. H., Nyström, E. E. L., Arike, L., Field, S., Li, X., SoRelle, J. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39398-1 · Cited by 17
Self-citation
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function
Lewis, B. M., Cho, C. Y., Her, H.-L., Mizrahi, O., Hunter, T. R., & Yeo, G. W.-M. (2022) · RNA · doi:10.1261/rna.079799.123 · Cited by 17
Phosphorylation and Proteasome Recognition of the mRNA-Binding Protein Cth2 Facilitates Yeast Adaptation to Iron Deficiency
Romero, A. M., Martínez-Pastor, M., Du, G., Solé, C., Carlos, M., Vergara, S. V., Sanvisens, N., Wohlschlegel, J. A., Toczyski, D. P., Posas, F., et al. (2018) · mBio · doi:10.1128/mbio.01694-18 · Cited by 17
“Phosphorylation sites were identiﬁed with the ProLuCID database search algorithm using a differential modiﬁcation search that considered a mass shift of 79.9663 on serines, threonines, and tyrosines (31).”
InfluentialSelf-citation
The mitochondrial lactate oxidation complex: endpoint for carbohydrate carbon disposal
Leija, R. G., Arevalo, J. A., Xing, D., Vázquez‐Medina, J. P., & Brooks, G. A. (2024) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00306.2024 · Cited by 17
Comparative reactivity profiling of cysteine-specific probes by chemoproteomics
Yang, F., Chen, N., Wang, F., Jia, G., & Wang, C. (2022) · Current Research in Chemical Biology · doi:10.1016/j.crchbi.2022.100024 · Cited by 16
The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform
Armony, G., Brehmer, S., Srikumar, T., Pfennig, L., Zijlstra, F., Trede, D., Kruppa, G. H., Lefeber, D. J., van Gool, A. J., & Wessels, H. J. C. T. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24097869 · Cited by 16
“To enable such real-time glycopeptide searches on PaSER, we set out to develop GlycoPaSER which takes advantage of the available real-time protein database search engine “ProLu-CID” [14].”
Method
Implicating the red body of Nannochloropsis in forming the recalcitrant cell wall polymer algaenan
Gee, C. W., Andersen‐Ranberg, J., Boynton, E., Rosen, R. Z., Jorgens, D. M., Grob, P., Holman, H. N., & Niyogi, K. (2024) · Nature Communications · doi:10.1038/s41467-024-49277-y · Cited by 17
Relapse-like behavior and nAChR sensitization following intermittent access nicotine self-administration
Tapia, M. A., Jin, X., Tucker, B. R., Thomas, L. N., Walker, N. B., Kim, V. J., Albertson, S. E., Damuka, N., Krizan, I. M., Edassery, S. L., et al. (2022) · Neuropharmacology · doi:10.1016/j.neuropharm.2022.109066 · Cited by 18
A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme
de Aquino, P. F., Carvalho, P. C., Nogueira, F. C. S., da Fonseca, C. O., Silva, J. C. T. D. S., Carvalho, M. D. G., Domont, G. B., Zanchin, N. I. T., & Fischer, J. D. S. D. G. (2016) · Frontiers in Oncology · doi:10.3389/fonc.2016.00183 · Cited by 17
Cleavage of the SUN-domain protein Mps3 at its N-terminus regulates centrosome disjunction in budding yeast meiosis
Li, P., Jin, H., Koch, B. A., Abblett, R. L., Han, X., Yates, J. R., & Yu, H.-G. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006830 · Cited by 16
Self-citation
The plasticity of the pyruvate dehydrogenase complex confers a labile structure that is associated with its catalytic activity
Lee, J., Oh, S., Bhattacharya, S., Zhang, Y., Florens, L. A., Washburn, M. P., & Workman, J. L. (2020) · PLoS ONE · doi:10.1371/journal.pone.0243489 · Cited by 15
“3) [36] against a database consisting of 5945 S.”
Background
Notch receptor-ligand binding facilitates extracellular vesicle-mediated neuron-to-neuron communication
Wang, Y., Castillon, C., Gebis, K. K., Bartom, E. T., d’Azzo, A., Contractor, A., & Savas, J. N. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113680 · Cited by 13
A tick saliva serpin, IxsS17 inhibits host innate immune system proteases and enhances host colonization by Lyme disease agent
Nguyen, T.-T., Kim, T. H., Bencosme-Cuevas, E., Berry, J., Gaithuma, A. K., Ansari, M. A., Kim, T. K., Tirloni, L., Radulović, Ž. M., Moresco, J. J., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012032 · Cited by 15
Self-citation
A kalihinol analog disrupts apicoplast function and vesicular trafficking in P. falciparum malaria
Chahine, Z. M., Abel, S., Hollin, T., Barnes, G. L., Chung, J. H., Daub, M. E., Renard, I., Choi, J., Vydyam, P., Pal, A. C., et al. (2024) · Science · doi:10.1126/science.adm7966 · Cited by 15
“MS/MS spectra were interpreted using ProluCID v.1.3.3 (94).”
Influential
Quantitative reactive cysteinome profiling reveals a functional link between ferroptosis and proteasome-mediated degradation
Wang, Y., & Wang, C. (2022) · Cell Death and Differentiation · doi:10.1038/s41418-022-01050-8 · Cited by 16
“Other important parameters: isolation window, 2.0 m/z units; default charge, 2+; normalized collision energy, 28%; maximum IT, 50 ms; and dynamic exclusion, 20.0 s. LC-MS/MS data were analyzed by ProLuCID [63] with static modification of cysteine carbamidomethylation (+57.0215 Da).”
MethodInfluential
Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins
Schiapparelli, L., Xie, Y., Sharma, P., McClatchy, D. B., Ma, Y., Yates, J. R., Maximov, A., & Cline, H. T. (2022) · Journal of Neuroscience · doi:10.1523/jneurosci.0707-22.2022 · Cited by 15
“Processing mass spectra and protein identification For ANL data, MS/MS spectra were searched with the ProLuCID algorithm (Xu et al., 2015) against the UniProt mouse database (release date, April 17, 2017) concatenated to a decoy database in which the sequence for each entry in the original database…”
MethodSelf-citation
Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila
Kachaev, Z. M., Lebedeva, L. A., Shaposhnikov, A. V., Moresco, J. J., Yates, J. R., Schedl, P. D., & Shidlovskii, Y. V. (2019) · FEBS Letters · doi:10.1002/1873-3468.13391 · Cited by 15
Self-citation
Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation
Chen, Y. S., Hou, W., Tracy, S., Harvey, A. T., Harjono, V., Xu, F., Moresco, J. J., Yates, J. R., & Zid, B. M. (2022) · eLife · doi:10.7554/elife.76965 · Cited by 14
Self-citation
Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope
Cheng, L.-C., Zhang, X., Baboo, S., Nguyen, J. A., Martínez‐Bartolomé, S., Loose, E., Diedrich, J. K., Yates, J. R., & Gerace, L. (2023) · Life Science Alliance · doi:10.26508/lsa.202301998 · Cited by 14
“Tandem mass spectra were extracted (mono-isotopic peaks) from raw ﬁ les using RawConverter (He et al, 2015) and were searched against the UniProt SwissProt Mus musculus database (release 2018_01) with reversed sequences using ProLuCID (Peng et al, 2003; Xu et al, 2015).”
InfluentialSelf-citation
Attenuation of ATM signaling by ROS delays replicative senescence at physiological oxygen
Stuart, A., Takai, K., Gabbasova, R. R., Sanford, H., Vinogradova, E. V., & de Lange, T. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.11.006 · Cited by 13
Proteomics Profiling of KAIMRC1 in Comparison to MDA-MB231 and MCF-7
Alghanem, B., Ali, R., Nehdi, A., Zahrani, H. A., Altolayyan, A., Shaibah, H., Baz, O., Alhallaj, A., Moresco, J. J., Diedrich, J. K., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21124328 · Cited by 14
“For protein identification, tandem mass spectra were searched against a database including the Uniprot human database, reversed sequences, and contaminate using ProLuCID [51].”
MethodSelf-citation
Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation
Chen, M., Kuhle, B., Diedrich, J. K., Liu, Z., Moresco, J. J., Yates, J. R., Pan, T., & Yang, X.-L. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa469 · Cited by 14
“Tandem mass spectra were extracted from raw files using RawConverter (19) and searched with ProLuCID (20) against human UniProt database.”
MethodSelf-citation
A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis
Páez-Moscoso, D. J., Ho, D. V., Pan, L., Hildebrand, K., Jensen, K. L., Levy, M. J., Florens, L., & Baumann, P. (2022) · Nature Communications · doi:10.1038/s41467-022-28545-9 · Cited by 10
Covalent Destabilizing Degrader of AR and AR-V7 in Androgen-Independent Prostate Cancer Cells
Zammit, C. M., Nadel, C. M., Lin, Y. Q., Koirala, S., Ahani, E., Potts, P. R., & Nomura, D. K. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.5c02801 · Cited by 15
Multiple-Cycle Polymeric Extracellular Vesicle Precipitation and Its Evaluation by Targeted Mass Spectrometry
Park, J., Go, E.-B., Oh, J. S., Lee, J. K., & Lee, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094311 · Cited by 13
“24 using the ProLuCID search algorithm [25] for peptide identification.”
Method
Increased proteomic complexity in Drosophila hybrids during development
Bamberger, C., Martínez-Bartolomé, S., Montgomery, M., Lavallée-Adam, M., & Yates, J. (2018) · Science Advances · doi:10.1126/sciadv.aao3424 · Cited by 13
Self-citation
Protein turnover models for LC–MS data of heavy water metabolic labeling
Sadygov, R. G. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab598 · Cited by 14
Vaccination elicits HIV broadly neutralizing antibodies in primates
Steichen, J. M., Madden, P. J., Flynn, C. T., Phulera, S., Shil, M., Kalyuzhniy, O., Liguori, A., Kifude, C., Sewall, L. M., Cottrell, C. A., et al. (2026) · Nature · doi:10.1038/s41586-026-10837-5 · Cited by 19
Self-citation
PARP1-SNAI2 transcription axis drives resistance to PARP inhibitor, Talazoparib
Ding, X., Zhu, Z., Lapek, J. D., McMillan, E. A., Zhang, A., Chung, C., Dubbury, S. J., Lapira, J., Firdaus, S. J., Kang, X., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-16623-3 · Cited by 13
mRNA lipid nanoparticles expressing cell-surface cleavage independent HIV Env trimers elicit autologous tier-2 neutralizing antibodies
Guenaga, J., Alirezaei, M., Feng, Y., Alameh, M., Lee, W.-H., Baboo, S., Cluff, J., Wilson, R., Bale, S., Ozorowski, G., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1426232 · Cited by 12
Self-citation
Proteomic analysis of bronchoalveolar lavage fluid in rat exposed to TiO2 nanostructured aerosol by inhalation
Chézeau, L., Kohlstaedt, L. A., Faou, A. L., Cosnier, F., Rihn, B. H., & Gaté, L. (2019) · Journal of Proteomics · doi:10.1016/j.jprot.2019.103451 · Cited by 12
Acrolein-conjugated proteomics in brains of adult C57BL/6 mice chronically exposed to acrolein and aged APP/PS1 transgenic AD mice
Chen, C., Chen, Y., Lu, J., Chen, Z., Wang, C., & Pi, R. (2021) · Toxicology Letters · doi:10.1016/j.toxlet.2021.03.001 · Cited by 12
Antipsychotics preserve telomere length in peripheral blood mononuclear cells after acute oxidative stress injury
Polho, G. B., Cardillo, G. M., Kerr, D. S., Chile, T., Gattaz, W. F., Forlenza, O. V., Brentani, H., & De-Paula, V. J. (2021) · Neural Regeneration Research · doi:10.4103/1673-5374.324852 · Cited by 12
“The aripiprazole has demonstrated neuroprotective effects through increasing transcripts and protein level of brainderived neurotrophic factor, phosphorylation and GSK-3β in SH-SY5Y cells (Gibson et al., 1999; Xu et al., 2015), and decreasing presynaptic-like glutamate release in synaptosomes (Yu et al, 2008).”
Background
SP3‐FAIMS‐Enabled High‐Throughput Quantitative Profiling of the Cysteinome
Desai, H. S., Yan, T., & Backus, K. M. (2022) · Current Protocols · doi:10.1002/cpz1.492 · Cited by 9
“For search, multiple algorithms including SEQUEST (Eng, McCormack, & Yates, 1994), ProLuCiD (Xu et al., 2015), MaxQuant (Tyanova, Temu, & Cox, 2016), Proteome Discoverer (Mnatsakanyan et al., 2019), and MSFragger (Kong, Leprevost, Avtonomov, Mellacheruvu, & Nesvizhskii, Desai et al. 3 of 31 Current Protocols 2017; Yu,…”
Method
Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics
Cheng, L.-C., Zhang, X., Abhinav, K., Nguyen, J. A., Baboo, S., Martínez‐Bartolomé, S., Branon, T. C., Ting, A. Y., Loose, E., Yates, J. R., et al. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00281 · Cited by 12
Self-citation
Identification of IMC43, a novel IMC protein that collaborates with IMC32 to form an essential daughter bud assembly complex in Toxoplasma gondii
Pasquarelli, R. R., Back, P., Sha, J., Wohlschlegel, J. A., & Bradley, P. J. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011707 · Cited by 12
“Data analysis was performed using ProLuCID and DTASelect2 implemented in Integrated Proteomics Pipeline IP2 (Integrated Proteomics Applications) [72–74].”
MethodSelf-citation
The protein kinase MBK-1 contributes to lifespan extension in daf-2 mutant and germline-deficient Caenorhabditis elegans
Mack, H. I. D., Zhang, P., Fonslow, B. R., & Yates, J. R. (2017) · Aging · doi:10.18632/aging.101244 · Cited by 12
“Tandem mass spectra were extracted to MS2 files from raw files using RawExtract 1.9.9 [57] and searched against a non-redundant UniProt human database with reversed sequences using ProLuCID [58].”
InfluentialSelf-citation
Function of the MYND Domain and C-Terminal Region in Regulating the Subcellular Localization and Catalytic Activity of the SMYD Family Lysine Methyltransferase Set5
Jaiswal, D., Turniansky, R., Moresco, J. J., Ikram, S., Ramaprasad, G., Akinwole, A., Wolf, J. B., Yates, J. R., & Green, E. M. (2019) · Molecular and Cellular Biology · doi:10.1128/mcb.00341-19 · Cited by 13
“Peptide matching was done against the UniProt Saccharomyces cerevisiae protein database with reversed sequences and recombinant proteins using ProLuCID (66, 67) Regulation of the SMYD Methyltransferase Set5 Molecular and Cellular Biology”
MethodInfluentialSelf-citation
Analysis of the Tropism of SARS-CoV-2 Based on the Host Interactome of the Spike Protein
Bamberger, C., Pankow, S., Martínez‐Bartolomé, S., Diedrich, J. K., Park, S. K. R., & Yates, J. R. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00387 · Cited by 12
Self-citation
Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins
Capitanchik, C., Dixon, C. R., Swanson, S. K., Florens, L. A., Kerr, A. R. W., & Schirmer, E. C. (2018) · Nucleus · doi:10.1080/19491034.2018.1469351 · Cited by 13
“3) [92] was used to search MS/MS datasets obtained from four NaOHextracted and three Salt-and-Detergent extracted liver NE samples and four NaOH-extracted and two Salt-and-Detergent extracted liver NE protein samples.”
Method

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: Xu, T.
Venable, J.D.
Wohlschlegel, J.A.
Diedrich, J.K.
Lu, B.
Liao, L.
Han, X.
Wong, C.C.L.
Delahunty, C.
Gao, Y.
Yates, J.R.
Venue: Journal of Proteomics
Publisher: Elsevier BV
Published: 2015-11
Volume: 129
Pages: 16-24
ISSN: 1874-3919 (ISSN-L)
DOI: 10.1016/j.jprot.2015.07.001
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
Licence: cc-by
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
creativecommons.org/licenses/by/4.0/ (vor)
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

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ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

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