Plasma Proteome Database as a resource for proteomics research: 2014 update

Vishalakshi Nanjappa, Joji Kurian Thomas, Arivusudar Marimuthu, Babylakshmi Muthusamy, Aneesha Radhakrishnan, Rakesh Sharma, Aafaque Ahmad Khan, Lavanya Balakrishnan, Nandini A. Sahasrabuddhe, Satwant Kumar, Binit Nitinbhai Jhaveri, Kaushal Vinaykumar Sheth, Ramesh Kumar Khatana, Patrick G. Shaw, Srinivas Manda Srikanth, Premendu P. Mathur, Subramanian Shankar, Dindagur Nagaraja, Rita Christopher, Suresh MathivananRajesh Raju, Ravi Sirdeshmukh, Aditi Chatterjee, Richard J. Simpson, H. C. Harsha, Akhilesh Pandey, T. S.Keshava Prasad

Research output: Contribution to journalArticle

148 Citations (Scopus)

Abstract

Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/) was initially described in the year 2005 as a part of Human Proteome Organization's (HUPO's) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10 546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set. We believe that PPD will facilitate both clinical and basic research by serving as a comprehensive reference of plasma proteins in humans and accelerate biomarker discovery and translation efforts.

Original languageEnglish (US)
JournalNucleic acids research
Volume42
Issue numberD1
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

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Proteome
Proteomics
Databases
Blood Proteins
Tuberculin
Research
Proteins
Biomarkers
Peptides
Serum
Mass Spectrometry
Technology

ASJC Scopus subject areas

  • Genetics

Cite this

Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., ... Prasad, T. S. K. (2014). Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic acids research, 42(D1). https://doi.org/10.1093/nar/gkt1251

Plasma Proteome Database as a resource for proteomics research : 2014 update. / Nanjappa, Vishalakshi; Thomas, Joji Kurian; Marimuthu, Arivusudar; Muthusamy, Babylakshmi; Radhakrishnan, Aneesha; Sharma, Rakesh; Ahmad Khan, Aafaque; Balakrishnan, Lavanya; Sahasrabuddhe, Nandini A.; Kumar, Satwant; Jhaveri, Binit Nitinbhai; Sheth, Kaushal Vinaykumar; Kumar Khatana, Ramesh; Shaw, Patrick G.; Srikanth, Srinivas Manda; Mathur, Premendu P.; Shankar, Subramanian; Nagaraja, Dindagur; Christopher, Rita; Mathivanan, Suresh; Raju, Rajesh; Sirdeshmukh, Ravi; Chatterjee, Aditi; Simpson, Richard J.; Harsha, H. C.; Pandey, Akhilesh; Prasad, T. S.Keshava.

In: Nucleic acids research, Vol. 42, No. D1, 01.01.2014.

Research output: Contribution to journalArticle

Nanjappa, V, Thomas, JK, Marimuthu, A, Muthusamy, B, Radhakrishnan, A, Sharma, R, Ahmad Khan, A, Balakrishnan, L, Sahasrabuddhe, NA, Kumar, S, Jhaveri, BN, Sheth, KV, Kumar Khatana, R, Shaw, PG, Srikanth, SM, Mathur, PP, Shankar, S, Nagaraja, D, Christopher, R, Mathivanan, S, Raju, R, Sirdeshmukh, R, Chatterjee, A, Simpson, RJ, Harsha, HC, Pandey, A & Prasad, TSK 2014, 'Plasma Proteome Database as a resource for proteomics research: 2014 update', Nucleic acids research, vol. 42, no. D1. https://doi.org/10.1093/nar/gkt1251
Nanjappa V, Thomas JK, Marimuthu A, Muthusamy B, Radhakrishnan A, Sharma R et al. Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic acids research. 2014 Jan 1;42(D1). https://doi.org/10.1093/nar/gkt1251
Nanjappa, Vishalakshi ; Thomas, Joji Kurian ; Marimuthu, Arivusudar ; Muthusamy, Babylakshmi ; Radhakrishnan, Aneesha ; Sharma, Rakesh ; Ahmad Khan, Aafaque ; Balakrishnan, Lavanya ; Sahasrabuddhe, Nandini A. ; Kumar, Satwant ; Jhaveri, Binit Nitinbhai ; Sheth, Kaushal Vinaykumar ; Kumar Khatana, Ramesh ; Shaw, Patrick G. ; Srikanth, Srinivas Manda ; Mathur, Premendu P. ; Shankar, Subramanian ; Nagaraja, Dindagur ; Christopher, Rita ; Mathivanan, Suresh ; Raju, Rajesh ; Sirdeshmukh, Ravi ; Chatterjee, Aditi ; Simpson, Richard J. ; Harsha, H. C. ; Pandey, Akhilesh ; Prasad, T. S.Keshava. / Plasma Proteome Database as a resource for proteomics research : 2014 update. In: Nucleic acids research. 2014 ; Vol. 42, No. D1.
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