Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides

ProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics

(2021) Rachel M. Miller et al.   JOURNAL OF PROTEOME RESEARCH

Comparative proteomic profiling of unannotated microproteins and alternative proteins in human cell lines

(2020) Xiongwen Cao et al.   JOURNAL OF PROTEOME RESEARCH

Multi-protease analysis of Pleistocene bone proteomes

(2020) Liam T. Lanigan et al.   Journal of Proteomics

Complementarity of Different SDS‐PAGE Gel Staining Methods for the Identification of Short Open Reading Frame‐encoded Peptides

(2020) Philipp T. Kaulich et al.   PROTEOMICS

Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii

(2020) Sebastian Zahn et al.   FEBS Journal

Optimized Proteomics Workflow for the Detection of Small Proteins

(2020) Jürgen Bartel et al.   JOURNAL OF PROTEOME RESEARCH

Multidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame-encoded peptides in top-down proteomics

(2020) Liam Cassidy et al.   Journal of Proteomics

PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations

(2019) Bo Wen et al.   GENOME RESEARCH

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Depletion of High-Molecular-Mass Proteins for the Identification of Small Proteins and Short Open Reading Frame Encoded Peptides in Cellular Proteomes

(2019) Liam Cassidy et al.   JOURNAL OF PROTEOME RESEARCH

Small-protein enrichment assay enables the rapid, unbiased analysis of over 100 low abundance factors from human plasma

(2019) Dylan Harney et al.   MOLECULAR & CELLULAR PROTEOMICS

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

(2019) Hila Sberro et al.   CELL

Alternative ORFs and small ORFs: shedding light on the dark proteome

(2019) Mona Wu Orr et al.   NUCLEIC ACIDS RESEARCH

Top-Down Proteomic Characterization of Truncated Proteoforms

(2019) Dapeng Chen et al.   JOURNAL OF PROTEOME RESEARCH

Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins

(2019) Tristan Cardon et al.   ANALYTICAL CHEMISTRY

Enrichment and identification of small proteins in a simplified human gut microbiome

(2019) Hannes Petruschke et al.   Journal of Proteomics

An Approach to Incorporate Multi-Enzyme Digestion into C-TAILS for C-Terminomics Studies

(2017) Yang Zhang et al.   PROTEOMICS

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

(2017) Sondos Samandi et al.   eLife

Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei

(2016) Liam Cassidy et al.   JOURNAL OF PROTEOME RESEARCH

Six alternative proteases for mass spectrometry–based proteomics beyond trypsin

(2016) Piero Giansanti et al.   Nature Protocols

Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea

(2016) Daniel Dar et al.   Nature Microbiology

First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1

(2015) Daniela Prasse et al.   BIOCHIMIE

Identification and relative quantification of phosphopeptides by a combination of multi-protease digestion and isobaric labeling

(2015) Dennis Linke et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   Annual Review of Biochemistry

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification

(2014) Pitter F Huesgen et al.   NATURE METHODS

Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography

(2012) Alexander Leitner et al.   MOLECULAR & CELLULAR PROTEOMICS

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

Protease bias in absolute protein quantitation

(2012) Mao Peng et al.   NATURE METHODS

Optimization of parameters for coverage of low molecular weight proteins

(2010) Stephan A. Müller et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

S-layer, Surface-Accessible, and Concanavalin A Binding Proteins ofMethanosarcina acetivoransandMethanosarcina mazei

(2009) Deborah R. Francoleon et al.   JOURNAL OF PROTEOME RESEARCH

A centrifugal ultrafiltration strategy for isolating the low-molecular weight (≤25K) component of human plasma proteome

(2009) David W. Greening et al.   Journal of Proteomics

Top-down proteomics reveals novel protein forms expressed in methanosarcina acetivorans

(2009) Jonathan T. Ferguson et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability

(2009) D. Jager et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Analysis of Gel Mobility of Proteins and Its Use in Target Identification

(2008) Atsuko Shirai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY