Proteomic tools

General organization

We extracted 102 proteomics files (74 absolute value datasets and 28 relative expression datasets)

Proteomic database

Since no centralized database like ArrayExpress exists to browse proteomics data, we selected a list of 23 publications using the PubMed database (Table S5) in which a mass spectrometry experiment with a Listeria strain was performed. From core articles and supplementary files we extracted all available information on the biological conditions screened in each experiment. We extracted the information in the same format as for the transcriptomic datasets. In all the experiments a list of proteins detected was available, and in some cases we retrieved a list of proteins differently produced between two biological conditions.

ID	Pubmed Accession	Title	Day/Month/Year	Processed Data	Comment
1	15378702	Two-dimensional electrophoresis database of Listeria monocytogenes EGDe proteome and proteomic analysis of mid-log and stationary growth phase cells.	08/03/2004	http://onlinelibrary.wiley.com/doi/10.1002/pmic.200300841/abstract
2	15627966	Analysis of the Listeria cell wall proteome by two-dimensional nanoliquid chromatography coupled to mass spectrometry.	24/06/2004	http://onlinelibrary.wiley.com/doi/10.1002/pmic.200400936/abstract
3	15838904	Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species.	10/09/2004	http://onlinelibrary.wiley.com/doi/10.1002/pmic.200401024/abstract
4	15966022	"LaneSpector", a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography-tandem mass spectrometry analysis: application to Listeria monocytogenes membrane proteins.	10/06/2005	http://onlinelibrary.wiley.com/doi/10.1002/elps.200410348/abstract
5	16381897	LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.	08/10/2005	http://nar.oxfordjournals.org/content/34/suppl_1/D402.long
6	18065622	Proteomic analyses of a Listeria monocytogenes mutant lacking sigmaB identify new components of the sigmaB regulon and highlight a role for sigmaB in the utilization of glycerol.	10/02/2008	http://aem.asm.org/content/74/3/594.long	Cannot be added as it is a mix of strains
7	18836007	Comparative analysis of extracellular and intracellular proteomes of Listeria monocytogenes strains reveals a correlation between protein expression and serovar.	10/12/2008	http://aem.asm.org/content/74/23/7399.long
8	19028911	Comparative proteomic analysis of Listeria monocytogenes strains F2365 and EGD.	10/01/2009	http://aem.asm.org/content/75/2/366.long
9	19694553	Differential expression of proteins in Listeria monocytogenes under thermotolerance-inducing, heat shock, and prolonged heat shock conditions.	10/11/2009	http://online.liebertpub.com/doi/abs/10.1089/fpd.2009.0286?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed
10	19834917	Isolation and 2-D-DIGE proteomic analysis of intracellular and extracellular forms of Listeria monocytogenes.	10/12/2009	http://onlinelibrary.wiley.com/doi/10.1002/pmic.200900503/abstract
11	20620249	Proteomics for the elucidation of cold adaptation mechanisms in Listeria monocytogenes.	23/06/2010	http://www.sciencedirect.com/science/article/pii/S1874391910001892
12	20839850	Comprehensive appraisal of the extracellular proteins from a monoderm bacterium: theoretical and empirical exoproteomes of Listeria monocytogenes EGD-e by secretomics.	01/10/2010	http://pubs.acs.org/doi/abs/10.1021/pr1003642	No data available, and the strain used is not sequenced
13	21350852	Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms.	25/02/2011	http://link.springer.com/article/10.1007%2Fs00253-011-3172-z
14	21605710	Proteomic expression profiles of virulent and avirulent strains of Listeria monocytogenes isolated from macrophages.	11/05/2011	http://www.sciencedirect.com/science/article/pii/S1874391911001990
15	21846725	Association of ActA to peptidoglycan revealed by cell wall proteomics of intracellular Listeria monocytogenes.	16/12/2011	http://www.jbc.org/cgi/pmidlookup?view=long&pmid=21846725	Cannot be added as it is a mix of strains
16	22526570	Carbon catabolite control is important for Listeria monocytogenes biofilm formation in response to nutrient availability.	10/07/2012	http://link.springer.com/article/10.1007%2Fs00284-012-0125-4
17	22912771	Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses.	09/08/2012	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415414/
18	23558187	Listeria monocytogenes dairy isolates show a different proteome response to sequential exposure to gastric and intestinal fluids.	14/03/2013	http://www.sciencedirect.com/science/article/pii/S0168160513001219
19	23291529	Exoproteomic analysis of the SecA2-dependent secretion in Listeria monocytogenes EGD-e.	27/03/2013	http://www.sciencedirect.com/science/article/pii/S1874391912007968
20	23657685	Occurrence of mutations impairing sigma factor B (SigB) function upon inactivation of Listeria monocytogenes genes encoding surface proteins.	08/05/2013	http://mic.sgmjournals.org/cgi/pmidlookup?view=long&pmid=23657685
21	23970489	Proteomic identification of Listeria monocytogenes surface-associated proteins.	20/07/2013	http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200449/abstract
22	23977379	Transcription Factor sB Plays an Important Role in the Production of Extracellular Membrane-Derived Vesicles in Listeria monocytogenes	20/08/2013	http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073196
23	24564473	Proteomic analysis of cross protection provided between cold and osmotic stress in Listeria monocytogenes.	24/02/2014	http://pubs.acs.org/doi/abs/10.1021/pr401004a
24	25056936	A systematic proteomic analysis of Listeria monocytogenes house-keeping protein secretion systems.	13/11/2014	http://www.mcponline.org/content/13/11/3063.long
25	25516393	Attached and Planktonic Listeria monocytogenes Global Proteomic Responses and Associated Influence of Strain Genetics and Temperature.	09/01/2015	http://pubs.acs.org/doi/suppl/10.1021/pr501114e
26	25578509	Comparison of five methods for direct extraction of surface proteins from Listeria monocytogenes for proteomic analysis by orbitrap mass spectrometry	09/01/2015	http://www.sciencedirect.com/science/article/pii/S0167701215000056