Example MS-Viewer Datasets

Trnka M. J., Baker P. R., Robinson P. J. J., Burlingame A. L. and Chalkley R. J., Matching cross-linked peptide spectra: only as good as the worse identification. Molecular and Cellular Proteomics, doi:10.1074/mcp.M113.034009 (pdf)


Trinidad J.C., Barkan D.T., Gulledge B.F., Thalhammer A., Sali A., Schoepfer R., Burlingame A.L., Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Molecular and Cellular Proteomics, Vol. 11, No. 8, Pp. 215-229 (2012) (pdf)


Song Z., Chen L., Wang J., Lu Y., Jiang W., Zhang W., A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803. Molecular and Cellular Proteomics, pii: mcp.M113.035675 (2014) (pdf)


Spectrum Mill Results

Shah A. K., Le Cao K-A., Choi E., Chen D., Gautier B., Nancarrow D, Whiteman D. C., Saunders N. A., Barbour A. P., Josho V., Hill M. M., Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarker candidates for esophageal adenocarcinoma. Molecular and Cellular Proteomics, doi:10.1074/mcp.M115.050922 (2015) (pdf)


MaxQuant Results

Ti4+-IMAC label-free quantification (Pride Dataset ID: PXD000293)

de Graaf E.L., Giansanti P., Altelaar A.F., Heck A.J., Single-step Enrichment by Ti4+-IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution. Molecular and Cellular Proteomics, Vol. 13, No. 9, Pp. 2426-2434 (2014) (pdf)


Scheltema R.A., Hauschild J-P., Lange O., Hornburg D., Denisov E., Damoc E., Kuehn A., Makarov A., Mann M. The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High Performance Quadrupole and an Ultra-High Field Orbitrap Analyzer. Molecular and Cellular Proteomics, pii: mcp.M114.043489 (2014) (pdf)


Ramond E, Gesbert G, Guerrera IC, Chhuon C, Dupuis M, Rigard M, Henry T, Barel M, Charbit A. Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts. Molecular and Cellular Proteomics, pii: mcp.M114.044552 (2015) (pdf)


BiblioSpec libraries

Geiger T, Wehner A, Schaab C, Cox J, Mann M. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Molecular and Cellular Proteomics, 2012 Mar;11(3) (pdf)


3 replicate runs of mouse bone marrow lysate run on the Q Exactive Plus using 8 hr gradients on monolithic column.


NIST libraries


SpectraST libraries


Pride Dataset ID: PXD000001 (PRIDE XML Files)

TMT spikes. Species=Erwinia carotovora (Unpublished)


Pride Dataset ID: PXD000008 (PRIDE XML Files)

Ene I.V., Heilmann C.J., Sorgo A.G., Walker L.A., de Koster C.G., Munro C.A., Klis F.M., Brown A.J., Carbon source-induced reprogramming of the cell wall proteome and secretome modulates the adherence and drug resistance of the fungal pathogen Candida albicans. Proteomics, Vol. 12, No. 21, Pp. 3164-79 (2012) (pdf)


Pride Dataset ID: PXD000012 (PRIDE XML Files)

Rosenow A., Noben J.P., Jocken J., Kallendrusch S., Fischer-Posovszky P., Mariman E.C., Renes J. Resveratrol-induced changes of the human adipocyte secretion profile. J. Proteome Res., Vol. 11, No. 9, Pp. 4733-4743 (2012) (pdf)


Pride Dataset ID: PXD000021 (PRIDE XML Files)

Vaudel M., Breiter D., Beck F., Rahnenfuhrer J., Martens L., Zahedi R.P. D-score: a search engine independent MD-score. Proteomics, Vol. 13, No. 6, Pp. 1036-1041 (2013) (pdf)


Pride Dataset ID: PXD000056 (Thermo MSF Database)


Pride Dataset ID: PXD000111 (Thermo MSF Viewer)

Albrethsen J., Agner J., Piersma S.R., Hojrup P., Pham T.V., Weldingh K., Jimenez C.R., Andersen P., Rosenkrands I., o-score: a search engine independent MD-score. mic Profiling of Mycobacterium tuberculosis Identifies Nutrient-starvation-responsive Toxin-antitoxin Systems. Mol Cell Proteomics, Vol. 12, No. 15, Pp. 1180-1191 (2013) (pdf)


Pride Dataset ID: PXD000158 (multiple pepXML Files and ms2 Peaklists)

Kooij V, Holewinski RJ, Murphy AM, Van Eyk JE, Characterization of the cardiac myosin binding protein-C phosphoproteome in healthy and failing human hearts. J Mol Cell Cardiol, 60():116-20(2013) J Mol Cell Cardiol, Vol. 60, Pp. 116-120 (2013) (pdf)


Pride Dataset ID: PXD000442 (PRIDE XML Files)

Chr16-HPP. Shotgun Analysis improvement. JPR HPP Special issue 2013. MCF7 Cell line.


MassIVE Dataset ID: MSV000079123 (pepXML files from Morpheus search engine)

Global Identification of Protein PTMs in a Single-pass Database Search.

Jurkat Fractions


B6 Mouse Fractions


CAST Mouse Fractions