Pressure Cycling Technology

Barocyclers are products of Pressure Biosciences Inc. The barocyclers NEP 2320 are optimized for productive biopsy tissue analysis.


Mass Spectrometry

We have several MS instruments of different vendors (Thermo Orbitrap HF, Sciex, Bruker Tims TOF Pro )


Proteomic Big Data

We analyze mass spectrometry-based proteomic big data with a variety of software tools.


Cloud Computing

We developed cloud based tool to analyze proteomic big data. e.g. BatchServer is a web server for batch effects evaluation, visualization, and correction. Check our github: BatchServer


01. Burman, K. D.; Wartofsky, L., CLINICAL PRACTICE. Thyroid Nodules. N Engl J Med 2015, 373 (24), 2347-56.

02. Singh Ospina, N.; Iniguez-Ariza, N. M.; Castro, M. R., Thyroid nodules: diagnostic evaluation based on thyroid cancer risk assessment. BMJ 2020, 368, l6670.

03. Jameson, J. L., Minimizing unnecessary surgery for thyroid nodules. N Engl J Med 2012, 367 (8), 765-7.


01 High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis Nature Methods ( IF 28.547 ) Pub Date : 2019-05-27 , DOI: 10.1038/s41592-019-0427-6

02 Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning Nature Methods ( IF 28.547 ) Pub Date : 2019-05-27 , DOI: 10.1038/s41592-019-0426-7

03 DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nature Methods ( IF 28.547 ) Pub Date : 2019-11-25 , DOI: 10.1038/s41592-019-0638-x

04 OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology ( IF 54.908 ) Pub Date : 2014 Mar , DOI: 10.1038/nbt.2841

05 Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses Nature Methods ( IF 28.547 ) Pub Date : 2017-08-21 00:00:00 , DOI: 10.1038/nmeth.4398

06 Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol (2018)14:e8126 doi:10.15252/msb.20178126

07 Data-Independent Acquisition Mass Spectrometry-Based Proteomics and Software Tools: A Glimpse in 2020. Proteomics Pub Date : 2020-04-10 , DOI: 10.1002/pmic.201900276

08Mass-spectrometric exploration of proteome structure and function. Nature 537, 347–355 (2016). DOI: 10.1038/nature19949

09SnapShot: Clinical proteomics. Cell Pub Date : 2021-09-02 , DOI: 10.1016/j.cell.2021.08.015

10 ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity.Journal of Proteomics Pub Date : 2015-07-15 , DOI: 10.1016/j.jprot.2015.07.001

11 A high-stringency blueprint of the human proteome.Nature Communications Pub Date : 2020-10-16 , DOI: 10.1038/s41467-020-19045-9

12 Mass spectrometry-based proteomics. Nature Pub Date : 2003-03-01 , DOI: 10.1038/nature01511

13 Next-generation proteomics: towards an integrative view of proteome dynamics. Nature Reviews Genetics Pub Date : 2012-12-04 , DOI: 10.1038/nrg3356

14 Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.Journal of the American Society for Mass Spectrometry Pub Date : 2019-01-22 , DOI: 10.1007/s13361-018-2122-8

15 Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries.Nature Communications Pub Date : 2020-02-07 , DOI: 10.1038/s41467-020-14609-1


01 Selected reaction monitoring for quantitative proteomics: a tutorial. Molecular Systems Biology Pub Date : 2008-10-16 , DOI: 10.1038/msb.2008.61

02 SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell Pub Date : 2008-Jul-25 , DOI: 10.1016/j.cell.2008.05.033

03 MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology Pub Date : 2008-Dec-01 , DOI: 10.1038/nbt.1511

04 Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics Pub Date : 2007-02-14 , DOI: 10.1002/pmic.200600625

05 In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nature Protocols Pub Date : 2006 , DOI: 10.1038/nprot.2006.468

06 Higher-energy C-trap dissociation for peptide modification analysis. Nature Methods Pub Date : 2007-08-26 , DOI: 10.1038/nmeth1060

07 A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nature Biotechnology Pub Date : 2006 Oct , DOI: 10.1038/nbt1240

08 PRIDE: the proteomics identifications database. Proteomics Pub Date : 2005-07-26 , DOI: 10.1002/pmic.200401303

09 Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Molecular & cellular proteomics : MCP Pub Date : 2004-09-24 , DOI: 10.1074/mcp.m400129-mcp200

10 A statistical model for identifying proteins by tandem mass spectrometry. Analytical Chemistry Pub Date : 2003-11-25 , DOI: 10.1021/ac0341261

11 Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nature Biotechnology Pub Date : 2003 Jun , DOI: 10.1038/nbt827

12 Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. Journal of Proteome Research Pub Date : 2003-03-20 , DOI: 10.1021/pr025556v

13 Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular & cellular proteomics : MCP Pub Date : 2002-07-16 , DOI: 10.1074/mcp.m200025-mcp200

14 Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Analytical Chemistry Pub Date : 2002-10-31 , DOI: 10.1021/ac025747h

15 Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnology Pub Date : 2001 Mar , DOI: 10.1038/85686

16 Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology Pub Date : 1999 Oct , DOI: 10.1038/13690

17 Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Analytical Chemistry Pub Date : 1996-03-01 , DOI: 10.1021/ac950914h

18 An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry Pub Date : 1994 Nov , DOI: 10.1016/1044-0305(94)80016-2

19 Complex-centric proteome profiling by SEC-SWATH-MS. Molecular Systems Biology Pub Date : 2019-01-14 , DOI: 10.15252/msb.20188438

20 Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions. Nature Methods Pub Date : 2012-05-30 , DOI: 10.1038/nmeth.2015

21 OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology Pub Date : 2014 Mar , DOI: 10.1038/nbt.2841

22 mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nature Methods Pub Date : 2011-03-20 , DOI: 10.1038/nmeth.1584

23 Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics Pub Date : 2010-02-09 , DOI: 10.1093/bioinformatics/btq054

24 Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Analytical Chemistry Pub Date : 2000-03-31 , DOI: 10.1021/ac9911600

25 Probability-based protein identification by searching sequence databases using mass spectrometry data.Electrophoresis Pub Date : 1999-12-28 , DOI: 10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>;2-2


01 Thyroid nodules, benign or malignant? AI-Empowered Proteomics(in Chinese) click here

02 Prolonged RNA shedding in COVID-19 patients: new molecular mechanisms allowing its prediction(in Chinese) click here

03 Precision Medicine: AI-assisted Proteomics with Limited Amount of Clinical Tissue Samples(in Chinese) click here

04 Introduction to Proteomics click here

05 Mass Spectrometry-Based Proteomics click here

06 DIA-tensor based proteomic big data analysis(in Chinese) click here

07 Applications of Proteomics to Understand Host Responses to SARS-CoV-2 click here

08 Computational Biology Talk – Westlake Omics x Qbit AI click here