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PEAKS

Topic: Software

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PEAKS Studio
Developer(s)Bioinformatics Solutions Inc.
Stable release
13.5 / 13 June 2026; 2 months ago (2026-06-13)
Operating systemWindows 10+
TypeScientific software
LicenseProprietary commercial software
Websitewww.bioinfor.com/peaks-studio
PEAKS Online
Developer(s)Bioinformatics Solutions Inc.
Stable release
13.5 / 24 June 2026; 2 months ago (2026-06-24)
Operating systemWindows, Linux
TypeScientific software
LicenseProprietary commercial software
Websitewww.bioinfor.com/peaks-online

PEAKS is a suite of software programs designed for proteomic analysis of data obtained from mass spectrometers. Products within the suite include PEAKS Studio, PEAKS Online, PEAKS AB, and PEAKS GlycanFinder.

The PEAKS suit of proteomics software are commonly used for peptide identification (protein ID)[1][2] through de novo peptide sequencing assisted search engine database searching,[3] with protein quantification capabilities whilst also giving reproducible results.[4] PEAKS has also integrated PTM and mutation characterization through automatic peptide sequence tag based searching (SPIDER)[5] and PTM identification.[6] PEAKS supports analysis of DDA,[1] DIA,[2][7] hybrid-DIA, MRM, and PRM data with various workflows.

Overview

PEAKS Studio is a proteomics software program for bottom-up proteomics data collected by LC-MS and MS/MS designed for peptide sequencing, protein identification and quantification on desktop and workstation computers.[8]

PEAKS Online is a collaboration-based proteomics software designed for at-scale operation on servers and computer clusters.[9]

PEAKS is well-known for offering automated de novo sequencing[10] with two algorithms, the PEAKS de novo algorithm, and the DeepNovo algorithm. The PEAKS de novo algorithm uses the mass difference between two fragment ions to calculate the mass of an amino acid residue on the peptide backbone. The mass can usually uniquely determine the residue.[3] DeepNovo, under the current implementation GraphNovo,[11] is a deep learning based approach towards de novo sequencing. Decoy spectra are used in DeepNovo to estimate an FDR for de novo peptide sequencing. The decoy generation process ensures decoy spectra have the same fragment ion distribution as target spectra.[12] PEAKS provides a complete sequence for each peptide, with confidence scores on individual amino acid assignments, simple reporting for high-throughput analysis, amongst other information.[8][9]

To identify modifications and mutations, PEAKS uses two algorithms: SPIDER and PTM Search. SPIDER is a sequence tag based search tool within PEAKS, which deals with the possible overlaps between the de novo sequencing errors and the homology mutations. It reconstructs the real peptide sequence by combining both the de novo sequence tag and the homolog, automatically and efficiently.[5] PTM Search is a tool within PEAKS that provides PTM identification and profiling by de novo sequencing and database searching.[6]

Protein quantification can be done using the add-on tool PEAKS Q. It supports label (ICAT, iTRAQ, SILAC, TMT, 018, etc.) and label free techniques. Protein relative quantification is performed based on the extracted ion chromatograms of the whole isotopic envelope on MS1 level. Additionally, the LFQ algorithm extracts and uses the LC retention time and MS feature to align different runs, thus transferring IDs to matched features without IDs to retrieve quantification information.[13]

IMS-MS data analysis is supported with the PEAKS IMS add-on tool, which offers an additional dimension of separation when used with LC-MS/MS spectrometry.[14]

PEAKS QC is a tool within PEAKS that provides automated quality control of results obtained from analyses. QC allows for the assessment of statistical information of the raw data and results, which can provide more information on the attributes of the LC-MS acquisition.

Many algorithms and features of PEAKS Studio and PEAKS Online have been adapted and developed into multiple other software in the PEAKS suite. This list includes PEAKS AB, the first method for automatic monoclonal antibody sequencing;[15] PEAKS GlycanFinder, a project focused on glycan profiling and identification;[16] and ProteoformX, capable of intact and top-down proteomic mass analysis.[17]

Uses in Proteomics

The software is used in proteomics research for the analysis and interpretation of mass spectrometry data. Applications include protein identification,[18] peptide quantification,[19] post translation modifications (PTM) analysis,[20] and computer proteomics.[21]

The software has been used in biomarker discoveries,[22][23][24][25][26][27][28][29] clinical and pre-clinical proteomics,[30][31][32][33][34] cancer proteomics,[35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50] plant proteomics,[51][52][53][54] pharmaceutical research,[35][55][56][57][58][59] and systems biology.[60][61][62][63] The software can be used to interpret these data sets by feature extraction and identification from raw data.[64][65][66][67][68][69][49][70][71]

DIA data analysis, available in PEAKS software, supports the identification of peptides that are highly differentiated and are presented in low quantities.[72][73] DIA captures MS2 spectra of low abundance peptides, and the use of a spectral library and de novo peptide sequencing workflow is Incorporated to identify peptides from mass spectrometry data.[73][64]

Protein, peptide, etc. databases in .fasta format from sources such as Uniprot[74] and PRIDE[75] can be used with PEAKS. Mass spectrometry data and workflows generated by instruments and software from a multitude of vendors is possible as PEAKS is vendor neutral software. Examples include ThermoFisher Scientific (e.g XCalibur),[76][77] Sciex (e.g SCIEX MS Data Converter Software)[78][79] Bruker (e.g Bruker DataAnalysis)[80][81] and Agilent (e.g MassHunter or OpenLab).[82][83]

References

  1. ↑ 1.0 1.1 Chen, Yannic; Preikschat, Annica; Arnold, Annette; Pecori, Riccardo; Gomez-Zapeda, David; Tenzer, Stefan (2025-12-19). "Benchmarking Software for DDA-PASEF Immunopeptidomics". Molecular & Cellular Proteomics 25 (4). doi:10.1016/j.mcpro.2025.101492. PMID 41423049. 
  2. ↑ 2.0 2.1 Shahbazy, Mohammad; Ramarathinam, Sri H.; Illing, Patricia T.; Jappe, Emma C.; Faridi, Pouya; Croft, Nathan P.; Purcell, Anthony W. (2023-02-14). "Benchmarking Bioinformatics Pipelines in Data-Independent Acquisition Mass Spectrometry for Immunopeptidomics". Molecular & Cellular Proteomics 22 (4). doi:10.1016/j.mcpro.2023.100515. PMID 36796644. 
  3. ↑ 3.0 3.1 Zhang, J.; Xin, L.; Shan, B.; Chen, W.; Xie, M.; Yuen, D.; Zhang, W.; Zhang, Z. et al. (2011). "PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification". Molecular & Cellular Proteomics 11 (4). doi:10.1074/mcp.M111.010587. PMID 22186715. 
  4. ↑ Parker, Robert; Tailor, Arun; Peng, Xu; Nicastri, Annalisa; Zerwerk, Johannes; Reimer, Ulf; Wenschuh, Holger; Schnatbaum, Karsten et al. (2021-07-22). "The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires". Molecular & Cellular Proteomics 20. doi:10.1016/j.mcpro.2021.100124. PMID 34303857. 
  5. ↑ 5.0 5.1 Ma, Bin; Johnson, Richard (2012). "De novo sequencing and homology searching". Molecular & Cellular Proteomics 11 (2). doi:10.1074/mcp.O111.014902. PMID 22090170. 
  6. ↑ 6.0 6.1 Han, X.; He, L.; Xin, L.; Shan, B.; Ma, B. (2011). "PEAKS PTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications". Journal of Proteome Research 10 (7): 2930–2936. doi:10.1021/pr200153k. PMID 21609001. https://doi.org/10.1021/pr200153k. 
  7. ↑ Wang, Jianwei; Huang, Yi; Lu, Fanghua; Xu, Qinqin; Yang, Zhuo; Jiang, Yirong; Shi, Shaowen; Pan, Jianzhang et al. (2025-11-21). "Benchmarking informatics workflows for data-independent acquisition single-cell proteomics". Nature Communications 16 (1). doi:10.1038/s41467-025-65174-4. PMID 41271703. Bibcode: 2025NatCo..1610276W. 
  8. ↑ 8.0 8.1 Ma, Bin; Zhang, Kaizhong; Hendrie, Christopher; Liang, Chengzhi; Li, Ming; Dorerty-Kirby, Amanda; Lajoie, Gilles (2003). "PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry". Rapid Communications in Mass Spectrometry 17 (20): 2337–2342. doi:10.1002/rcm.1196. PMID 14558135. Bibcode: 2003RCMS...17.2337M. https://doi.org/10.1002/rcm.1196. Retrieved 19 June 2026. 
  9. ↑ 9.0 9.1 Xin, Lei; Qiao, Rui; Chen, Xin; Tran, Hieu; Pan, Shengying; Rabinoviz, Sahar; Bian, Haibo; He, Xianliang et al. (2022-06-07). "A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics". Nature Communications 13 (3108). doi:10.1038/s41467-022-30867-7. PMID 35672356. Bibcode: 2022NatCo..13.3108X. 
  10. ↑ Muth, Thilo; Renard, Bernhard Y (2018). "Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?". Briefings in Bioinformatics (Oxford Academic) 19 (5): 954–970. doi:10.1093/bib/bbx033. PMID 28369237. 
  11. ↑ Mao, Zeping; Zhang, Ruixue; Xin, Lei; Li, Ming (2023-10-19). "Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model". Nature Machine Intelligence 5 (11): 1250–1260. doi:10.1038/s42256-023-00738-x. https://doi.org/10.1038/s42256-023-00738-x. Retrieved 23 June 2026. 
  12. ↑ Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming (2017-07-18). "De novo peptide sequencing by deep learning". Proceedings of the National Academy of Sciences, USA 114 (31): 8247–8252. doi:10.1073/pnas.1705691114. PMID 28720701. Bibcode: 2017PNAS..114.8247T. 
  13. ↑ Chen, Weiwu; Shan, Baozhen; Zhang, Jing; Bonneil, Eric; Voyer, Janine; Lajoie, Gilles; Thibault, Pierre; Ma, Bin (2009-05-31). "ASMS. MPB 043. New Algorithm for Label-free Protein Quantification". Bioinformatics Solutions Inc, University of Montreal, University of Waterloo, Western University. https://www.bioinfor.com/wp-content/uploads/2017/02/peaks-newalgorithmforlabel-freeproteinquantification.pdf. 
  14. ↑ Baker, Erin Shammel; Livesay, Eric A.; Orton, Daniel J.; Moore, Ronald J.; Danielson, William F. III; Prior, David C.; Ibrahim, Yehia M.; LaMarche, Brian L. et al. (2009-12-09). "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies". Journal of Proteome Research 9 (2): 997–1006. doi:10.1021/pr900888b. PMID 20000344. PMC 2819092. https://doi.org/10.1021/pr900888b. Retrieved 24 June 2026. 
  15. ↑ Tran, Ngoc Hieu; Rahman, M. Ziaur; He, Lin; Xin, Lei; Shan, Baozhen; Li, Ming (2016-08-26). "Complete De Novo Assembly of Monoclonal Antibody Sequences" (in en). Scientific Reports 6. doi:10.1038/srep31730. ISSN 2045-2322. PMID 27562653. Bibcode: 2016NatSR...631730T. 
  16. ↑ Sun, Weiping; Zhang, Qianqiu; Zhang, Xiyue; Tran, Ngoc Hieu; Rahman, M. Ziaur; Chen, Zheng; Peng, Chao; Ma, Jun et al. (2023-07-08). "Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics". Nature Communications 14 (4046): 3108. doi:10.1038/s41467-022-30867-7. PMID 35672356. PMC 9174175. Bibcode: 2022NatCo..13.3108X. https://doi.org/10.1038/s41467-023-39699-5. Retrieved 18 June 2026. 
  17. ↑ Li, Kunyi; Shan, Baozhen; Xin, Lei; Li, Ming; Wang, Lusheng (2025-10-03). "Proteoform search from protein database with top-down mass spectra". Nature Computational Science 5 (11): 998–1009. doi:10.1038/s43588-025-00880-z. PMID 41044386. https://doi.org/10.1038/s43588-025-00880-z. Retrieved 18 June 2026. 
  18. ↑ Miroshnichenko, Yu.V.; Rybina, A.V.; Skvortsov, V.S. (2025). "Identification of proteins with variable levels of post-translational modifications in human temporal lobe epilepsy" (in ru). Biomeditsinskaya Khimiya 71 (5): 351–363. doi:10.18097/PBMCR1612. ISSN 2310-6905. PMID 41211733. http://pbmc.ibmc.msk.ru/en/article-en/PBMC-2025-71-5-351. 
  19. ↑ Zhang, Xinwen; Lv, Xiang; Qian, Dong; Li, Junxian; Qian, Yi; Wang, Jiaojiao; Zhu, Yuyu; Zhou, Jing et al. (2023). "Quantification of peptide components in cinobufacini injection and toad skin by ultra-high-performance liquid chromatography/triple quadrupole mass spectrometry" (in en). Journal of Separation Science 46 (16). doi:10.1002/jssc.202201048. ISSN 1615-9314. PMID 37155296. https://onlinelibrary.wiley.com/doi/abs/10.1002/jssc.202201048. 
  20. ↑ Ambli, Mouna; Deracinois, Barbara; Jenequin, Anne-Sophie; Ravallec, Rozenn; Cudennec, Benoit; Flahaut, Christophe (28 June 2023). "Impact of Bioinformatics Search Parameters for Peptides' Identification and Their Post-Translational Modifications: A Case Study of Proteolysed Gelatines from Beef, Pork, and Fish" (in en). Foods 12 (13): 2524. doi:10.3390/foods12132524. ISSN 2304-8158. PMID 37444262. 
  21. ↑ Halder, Ankit; Verma, Ayushi; Biswas, Deeptarup; Srivastava, Sanjeeva (2021). "Recent advances in mass-spectrometry based proteomics software, tools and databases" (in en). Drug Discovery Today: Technologies 39: 69–79. doi:10.1016/j.ddtec.2021.06.007. PMID 34906327. https://linkinghub.elsevier.com/retrieve/pii/S1740674921000160. 
  22. ↑ Nigro, Joseph T; Chatterjee, Sayantani; Freilich, Shira; Downs, Margeret; Candib, Alec; Berron, Erika; Stein, Thor D.; Zaia, Joseph et al. (2026). "Mass spectrometry analysis of young and aged mice and human Alzheimer's disease with Lewy body pathology using on-slide tissue digestion". Analytical and Bioanalytical Chemistry 418 (8). doi:10.1007/s00216-026-06385-6. PMID 41760936. 
  23. ↑ Sakaya, Gabriel R.; Parada, Carolina A.; Eichler, Rosangela A.; Yamaki, Vitor N; Navon, Ami; S. Heimann, Andrea; Figueiredo, Everval G.; Ferro, Emer S. (2021). "Peptidomic profiling of cerebrospinal fluid from patients with intracranial saccular aneurysms". Journal of Proteomics 240. doi:10.1016/j.jprot.2021.104188. PMID 33781962. 
  24. ↑ Nakashima, Ichiro; Fujinoki, Masakatsu; Fujihara, Kazuo; Kawamura, Takeshi; Nishimura, Toshihide (2007). "Alteration of cystatin C in the cerebrospinal fluid of multiple sclerosis". Annals of Neurology 62 (2). doi:10.1002/ana.20955. PMID 16958112. 
  25. ↑ Emami Khoonsari, Payam; Häggmark, Anna; Lönnberg, Maria; Mikus, Maria; Kilander, Lena; Lannfelt, Lars; Bergquist, Jonas; Ingelsson, Martin et al. (2016). "Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease". PLOS ONE 11 (3). doi:10.1371/journal.pone.0150672. PMID 26950848. Bibcode: 2016PLoSO..1150672K. 
  26. ↑ Muraoka, Satoshi; DeLeo, Annina M.; Sethi, Manveen K.; Yukawa-Takamatsu, Kayo; Yang, Zijian; Ko, Jina; Hogan, John D.; Ruan, Zhi et al. (2020). "Proteomic and biological profiling of extracellular vesicles from Alzheimer's disease human brain tissues". The Journal of the Alzheimer's Association 16 (6). doi:10.1002/alz.12089. PMID 32301581. 
  27. ↑ Santiago, Jessica.; Poceviciute, Dovile; Vogel, Jacob; Brinkmalm, Gunnar; Wennström, Malin; The Netherlands Brain Bank (2025). "Retinal tau phosphorylation in Alzheimer's disease: A mass spectrometry study". Neurobiology of Disease 215. doi:10.1016/j.nbd.2025.107057. PMID 40835172. 
  28. ↑ Smith, Stephan M.; Douaud, Gwenaelle; Chen, Winfield; Hanayik, Taylor; Alfaro-Almagro, Fidel; Sharp, Kevin; Elliot, Lloyd T. (2021). "An expanded set of genome-wide association studies of brain imaging phenotypes in UK Biobank". Nature Neuroscience 24 (5): 737–745. doi:10.1038/s41593-021-00826-4. PMID 33875891. 
  29. ↑ Binette, Alexa Pichet; Gaiteri, Chris; Wennstrom, Malin; Kumar, Atul; Hristovska, Ines; Spotorno, Nicola; Salvado, Gemma; Strandberg, Olof et al. (2024). "Proteomic changes in Alzheimer's disease associated with progressive Aβ plaque and tau tangle pathologies". Nat Neurosci 27 (10). doi:10.1038/s41593-024-01737-w. PMID 39187705. 
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  38. ↑ Samer Attalla, Sherif; Boucher, Jonathan; Proud, Hailey; Taifour, Tarek; Zuo, Dongmei; Sanguin-Gendreu, Virginie; Ling, Chen; Johnson, Gabriella et al. (2023). "HER2Δ16 Engages ENPP1 to Promote an Immune-Cold Microenvironment in Breast Cancer". Cancer Immunology Research 11 (9). doi:10.1158/2326-6066.CIR-22-0140. PMID 37311021. 
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  54. ↑ Sharma, Sonu; Pradhan, Ranjan; Manickavasagan, Annamalai; Thimmanagari, Mahendra; Dutta, Animesh (2022-09-15). "Exploration of corn distillers solubles from selective milling technology as a novel source of plant-based ACE inhibitory protein hydrolysates" (in en-US). Food Chemistry 388. doi:10.1016/j.foodchem.2022.133036. ISSN 0308-8146. PMID 35500330. https://www.sciencedirect.com/science/article/abs/pii/S0308814622009980. 
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