Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

Thilo Muth, Dirk Benndorf, Udo Reichl, Erdmann Rapp and Lennart Martens

Mol. BioSyst., 2013, 9, 578
DOI: 10.1039/C2MB25415H

Dual use of peptide mass spectra: Protein atlas and genome annotation

Justin W. Walley and Steven P. Briggs

Current Plant Biology, 2015, 2, 21
DOI: 10.1016/j.cpb.2015.02.001

The proteomic future: where mass spectrometry should be taking us

Jay J. Thelen and Ján A. Miernyk

Biochemical Journal, 2012, 444, 169
DOI: 10.1042/BJ20110363

A proteogenomic approach to map the proteome of an unsequenced pathogen – Leishmania donovani

Harsh Pawar, Nandini A. Sahasrabuddhe, Santosh Renuse, Shivakumar Keerthikumar, Jyoti Sharma, Ghantasala. S. Sameer Kumar, Abhilash Venugopal, Nirujogi Raja Sekhar, Dhanashree S. Kelkar, Harshal Nemade, Sweta N. Khobragade, Babylakshmi Muthusamy, Kumaran Kandasamy, H. C. Harsha, Raghothama Chaerkady, Milind S. Patole and Akhilesh Pandey

Proteomics, 2012, 12, 832
DOI: 10.1002/pmic.201100505

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

Rui M M Branca, Lukas M Orre, Henrik J Johansson, Viktor Granholm, Mikael Huss, Åsa Pérez-Bercoff, Jenny Forshed, Lukas Käll and Janne Lehtiö

Nat Methods, 2014, 11, 59
DOI: 10.1038/nmeth.2732

New genes expressed in human brains: Implications for annotating evolving genomes

Yong E. Zhang, Patrick Landback, Maria Vibranovski and Manyuan Long

BioEssays, 2012, 34, 982
DOI: 10.1002/bies.201200008

Deep Coverage of the Escherichia coli Proteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments

Karsten Krug, Alejandro Carpy, Gesa Behrends, Katarina Matic, Nelson C. Soares and Boris Macek

Molecular & Cellular Proteomics, 2013, 12, 3420
DOI: 10.1074/mcp.M113.029165

Electron transfer dissociation mass spectrometry in proteomics

Min‐Sik Kim and Akhilesh Pandey

Proteomics, 2012, 12, 530
DOI: 10.1002/pmic.201100517

SMMRNA: a database of small molecule modulators of RNA

Ankita Mehta, Surabhi Sonam, Isha Gouri, Saurabh Loharch, Deepak K. Sharma and Raman Parkesh

Nucl. Acids Res., 2014, 42, D132
DOI: 10.1093/nar/gkt976

Dissecting Plasmodium yoelii Pathobiology: Proteomic Approaches for Decoding Novel Translational and Post-Translational Modifications

Devasahayam Arokia Balaya Rex, Arun H. Patil, Prashant Kumar Modi, Mrudula Kinarulla Kandiyil, Sandeep Kasaragod, Sneha M. Pinto, Nandita Tanneru, Puran Singh Sijwali and Thottethodi Subrahmanya Keshava Prasad

ACS Omega, 2022, 7, 8246
DOI: 10.1021/acsomega.1c03892

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

K. R. Rosenbloom, T. R. Dreszer, J. C. Long, V. S. Malladi, C. A. Sloan, B. J. Raney, M. S. Cline, D. Karolchik, G. P. Barber, H. Clawson, M. Diekhans, P. A. Fujita, M. Goldman, R. C. Gravell, R. A. Harte, A. S. Hinrichs, V. M. Kirkup, R. M. Kuhn, K. Learned, M. Maddren, L. R. Meyer, A. Pohl, B. Rhead, M. C. Wong, A. S. Zweig, D. Haussler and W. J. Kent

Nucleic Acids Research, 2012, 40, D912
DOI: 10.1093/nar/gkr1012

N-Terminal-oriented Proteogenomics of the Marine Bacterium Roseobacter Denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) Labeling and Diagonal Chromatography

Céline Bland, Erica M. Hartmann, Joseph A. Christie-Oleza, Bernard Fernandez and Jean Armengaud

Molecular & Cellular Proteomics, 2014, 13, 1369
DOI: 10.1074/mcp.O113.032854

Prebiotic Systems Chemistry: New Perspectives for the Origins of Life

Kepa Ruiz-Mirazo, Carlos Briones and Andrés de la Escosura

Chem. Rev., 2014, 114, 285
DOI: 10.1021/cr2004844

Fifteen years of physiological proteo(geno)mics with (marine) environmental bacteria

R. Rabus

Archives of Physiology and Biochemistry, 2014, 120, 173
DOI: 10.3109/13813455.2014.951658

Construction and assessment of individualized proteogenomic databases for large‐scale analysis of nonsynonymous single nucleotide variants

Karsten Krug, Sasa Popic, Alejandro Carpy, Christoph Taumer and Boris Macek

Proteomics, 2014, 14, 2699
DOI: 10.1002/pmic.201400219

“Matreshka” genes with alternative reading frames

E. V. Sheshukova, A. V. Shindyapina, T. V. Komarova and Yu. L. Dorokhov

Russ J Genet, 2016, 52, 125
DOI: 10.1134/S1022795416020149

Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project

Paula Díez, Conrad Droste, Rosa M. Dégano, María González-Muñoz, Nieves Ibarrola, Martín Pérez-Andrés, Alba Garin-Muga, Víctor Segura, Gyorgy Marko-Varga, Joshua LaBaer, Alberto Orfao, Fernando J. Corrales, Javier De Las Rivas and Manuel Fuentes

J. Proteome Res., 2015, 14, 3530
DOI: 10.1021/acs.jproteome.5b00474

Proteogenomic Analysis ofCandida glabratausing High Resolution Mass Spectrometry

T. S. Keshava Prasad, H. C. Harsha, Shivakumar Keerthikumar, Nirujogi Raja Sekhar, Lakshmi Dhevi N. Selvan, Praveen Kumar, Sneha M. Pinto, Babylakshmi Muthusamy, Yashwanth Subbannayya, Santosh Renuse, Raghothama Chaerkady, Premendu P. Mathur, Raju Ravikumar and Akhilesh Pandey

J. Proteome Res., 2012, 11, 247
DOI: 10.1021/pr200827k

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics

Stephan A. Müller, Sven Findeiß, Sandy R. Pernitzsch, Dirk K. Wissenbach, Peter F. Stadler, Ivo L. Hofacker, Martin von Bergen and Stefan Kalkhof

Journal of Proteomics, 2013, 86, 27
DOI: 10.1016/j.jprot.2013.04.036

Translational plant proteomics: A perspective

Ganesh Kumar Agrawal, Romina Pedreschi, Bronwyn J. Barkla, Laurence Veronique Bindschedler, Rainer Cramer, Abhijit Sarkar, Jenny Renaut, Dominique Job and Randeep Rakwal

Journal of Proteomics, 2012, 75, 4588
DOI: 10.1016/j.jprot.2012.03.055

Viral Short ORFs and Their Possible Functions

Yaara Finkel, Noam Stern‐Ginossar and Michal Schwartz

Proteomics, 2018, 18
DOI: 10.1002/pmic.201700255

Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry

Matthys G. Potgieter, Kehilwe C. Nakedi, Jon M. Ambler, Andrew J. M. Nel, Shaun Garnett, Nelson C. Soares, Nicola Mulder and Jonathan M. Blackburn

Front. Microbiol., 2016, 7
DOI: 10.3389/fmicb.2016.00427

Brain Proteomics of Anopheles gambiae

Sutopa B. Dwivedi, Babylakshmi Muthusamy, Praveen Kumar, Min-Sik Kim, Raja Sekhar Nirujogi, Derese Getnet, Priscilla Ahiakonu, Gourav De, Bipin Nair, Harsha Gowda, T.S. Keshava Prasad, Nirbhay Kumar, Akhilesh Pandey and Mobolaji Okulate

OMICS: A Journal of Integrative Biology, 2014, 18, 421
DOI: 10.1089/omi.2014.0007

Protein and Peptide Biomarkers in Organ Transplantation

Tara K Sigdel, Xiaoxiao Gao and Minnie M Sarwal

Biomarkers Med., 2012, 6, 259
DOI: 10.2217/bmm.12.29

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

M. Wang, M. Weiss, M. Simonovic, G. Haertinger, S.P. Schrimpf, M.O. Hengartner and C. von Mering

Molecular & Cellular Proteomics, 2012, 11, 492
DOI: 10.1074/mcp.O111.014704

Hiding in plain sight: advances in discovery and functional description of plant sORF-encoded peptides

Alyssa Kearly, Andrew D L Nelson and Robert Hancock

Journal of Experimental Botany, 2025
DOI: 10.1093/jxb/eraf240

Methods, Tools and Current Perspectives in Proteogenomics

Kelly V. Ruggles, Karsten Krug, Xiaojing Wang, Karl R. Clauser, Jing Wang, Samuel H. Payne, David Fenyö, Bing Zhang and D.R. Mani

Molecular & Cellular Proteomics, 2017, 16, 959
DOI: 10.1074/mcp.MR117.000024

Editorial: Proteomics of Microbial Human Pathogens

Nelson C. Soares, German Bou and Jonathan M. Blackburn

Front. Microbiol., 2016, 7
DOI: 10.3389/fmicb.2016.01742

Computational Identification of Novel Genes: Current and Future Perspectives

Steffen Klasberg, Tristan Bitard-Feildel and Ludovic Mallet

Bioinform Biol Insights, 2016, 10, BBI.S39950
DOI: 10.4137/BBI.S39950

Cancer proteogenomics: current impact and future prospects

D. R. Mani, Karsten Krug, Bing Zhang, Shankha Satpathy, Karl R. Clauser, Li Ding, Matthew Ellis, Michael A. Gillette and Steven A. Carr

Nat Rev Cancer, 2022, 22, 298
DOI: 10.1038/s41568-022-00446-5

Emerging evidence for functional peptides encoded by short open reading frames

Shea J. Andrews and Joseph A. Rothnagel

Nat Rev Genet, 2014, 15, 193
DOI: 10.1038/nrg3520

Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot, Ludovic Delage, Alain Viari, Yves Vandenbrouck, Emmanuelle Com, Andrés Ritter, Régis Lavigne, Dominique Marie, Pierre Peterlongo, Philippe Potin and Charles Pineau

BMC Genomics, 2019, 20
DOI: 10.1186/s12864-019-5431-9

Genomic Evaluation of Thermoanaerobacter spp. for the Construction of Designer Co-Cultures to Improve Lignocellulosic Biofuel Production

Tobin J. Verbeke, Xiangli Zhang, Bernard Henrissat, Vic Spicer, Thomas Rydzak, Oleg V. Krokhin, Brian Fristensky, David B. Levin, Richard Sparling and Mickaël Desvaux

PLoS ONE, 2013, 8, e59362
DOI: 10.1371/journal.pone.0059362