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Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006.
Orchard S, Heck A, Uhlen M, Ping P. Orchard S, et al. Proteomics. 2007 Apr;7(7):1009-11. doi: 10.1002/pmic.200700015. Proteomics. 2007. PMID: 17340644
This meeting brought together delegates from industry, academia and the publishing houses to facilitate discussions on the level of support from the journals for the use of standardised data formats and their interest in the creation of a network of proteomics repositories …
This meeting brought together delegates from industry, academia and the publishing houses to facilitate discussions on the level of support …
The minimum information about a proteomics experiment (MIAPE).
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H. Taylor CF, et al. Nat Biotechnol. 2007 Aug;25(8):887-93. doi: 10.1038/nbt1329. Nat Biotechnol. 2007. PMID: 17687369 Review.
Assessment of SRM, MRM(3) , and DIA for the targeted analysis of phosphorylation dynamics in non-small cell lung cancer.
Schmidlin T, Garrigues L, Lane CS, Mulder TC, van Doorn S, Post H, de Graaf EL, Lemeer S, Heck AJ, Altelaar AF. Schmidlin T, et al. Proteomics. 2016 Aug;16(15-16):2193-205. doi: 10.1002/pmic.201500453. Epub 2016 Jun 27. Proteomics. 2016. PMID: 27219855
Hypothesis-driven MS-based targeted proteomics has gained great popularity in a relatively short timespan. Next to the widely established selected reaction monitoring (SRM) workflow, data-independent acquisition (DIA), also referred to as sequential window acquisition of a …
Hypothesis-driven MS-based targeted proteomics has gained great popularity in a relatively short timespan. Next to the widely establi …
Comparative proteome analysis to explore p53 pathway disruption in head and neck carcinogenesis.
Schaaij-Visser TB, Brakenhoff RH, Jansen JW, O'Flaherty MC, Smeets SJ, Heck AJ, Slijper M. Schaaij-Visser TB, et al. J Proteomics. 2009 Jul 21;72(5):803-14. doi: 10.1016/j.jprot.2009.05.001. Epub 2009 May 13. J Proteomics. 2009. PMID: 19446051
These proteins may serve as valuable biomarkers that can predict the presence of a precursor field. We used a squamous cell model for p53 inactivation, which was analyzed by 2D-DIGE and LC-MS/MS. This approach enabled us to identify a set of 74 proteins that …
These proteins may serve as valuable biomarkers that can predict the presence of a precursor field. We used a squamous cell mo …
A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells.
Dormeyer W, van Hoof D, Mummery CL, Krijgsveld J, Heck AJ. Dormeyer W, et al. Proteomics. 2008 Oct;8(19):4036-53. doi: 10.1002/pmic.200800143. Proteomics. 2008. PMID: 18763709 Review.
The comparison of their membrane proteomes will help unravel the biological principles of pluripotency, and the identification of biomarker proteins in their plasma membranes is considered a crucial step to fully exploit pluripotent cells for therapeutic purposes. ...Our o …
The comparison of their membrane proteomes will help unravel the biological principles of pluripotency, and the identification of biomarker …
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA. Côté RG, et al. Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 4. Mol Cell Proteomics. 2012. PMID: 22949509 Free PMC article.
All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for b …
All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare file …
Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID).
Kelstrup CD, Frese C, Heck AJ, Olsen JV, Nielsen ML. Kelstrup CD, et al. Mol Cell Proteomics. 2014 Aug;13(8):1914-24. doi: 10.1074/mcp.O113.035915. Epub 2014 Jun 3. Mol Cell Proteomics. 2014. PMID: 24895383 Free PMC article.
Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. ...Here, we present a systematic spectral-pattern-based ap …
Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally …
qcML: an exchange format for quality control metrics from mass spectrometry experiments.
Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L. Walzer M, et al. Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23. Mol Cell Proteomics. 2014. PMID: 24760958 Free PMC article.
Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. ...In addition to the XML f …
Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss r …
Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography.
Di Palma S, Zoumaro-Djayoon A, Peng M, Post H, Preisinger C, Munoz J, Heck AJ. Di Palma S, et al. J Proteomics. 2013 Oct 8;91:331-7. doi: 10.1016/j.jprot.2013.07.024. Epub 2013 Aug 3. J Proteomics. 2013. PMID: 23917254
This method typically leads to the detection of a few hundreds of phosphopeptides, albeit typically over 70% of those are Tyr phosphorylated. Here, we evaluated and compared phosphotyrosine peptides enriched by a phospho-Tyr immuno-affinity enrichment (employing pY9 …
This method typically leads to the detection of a few hundreds of phosphopeptides, albeit typically over 70% of those are Tyr phospho …
Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis.
Di Palma S, Hennrich ML, Heck AJ, Mohammed S. Di Palma S, et al. J Proteomics. 2012 Jul 16;75(13):3791-813. doi: 10.1016/j.jprot.2012.04.033. Epub 2012 May 4. J Proteomics. 2012. PMID: 22561838 Review.
In this review, we attempt to provide a historical perspective to separations in proteomics as well as indicate the principles of their operation and rationales for their implementation. Furthermore, we provide a guide on what are the possibilities for combining dif …
In this review, we attempt to provide a historical perspective to separations in proteomics as well as indicate the principles of the …
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