Proline: an efficient and user-friendly software suite for large-scale proteomics

Abstract

Motivation The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data management system to process and curate hundreds of datasets associated with a single proteomics study. Results Here, we present Proline, a robust software suite for analysis of MS-based proteomics data, which collects, processes and allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency. The DDA label-free quantification workflow efficiency was assessed by comparing results obtained with Proline to those obtained with a widely used software using a spiked-in sample. This assessment demonstrated Proline’s ability to provide high quantification accuracy in a user-friendly interface for datasets of any size. Availability and implementation Proline is available for Windows and Linux under CECILL open-source license. It can be deployed in client–server mode or in standalone mode at http://proline.profiproteomics.fr/#downloads. Supplementary information Supplementary data are available at Bioinformatics online.

Mass Spectrometry-Based Characterization of the Virion Proteome, Phosphoproteome, and Associated Kinase Activity of Human Cytomegalovirus

“…Peptide modifications allowed during the search were: carbamidomethyl (C, fixed), acetyl (protein N-term, variable), oxidation (M, variable), and phosphoration (STY, variable). The Proline software [37] was used to filter the results according to conservation of rank 1 peptides, peptide-spectrum-match score ≥25, peptide length ≥6 amino acids, false discovery rate of peptide-spectrum-match identifications <1% as calculated on peptide-spectrum-match scores by employing the reverse database strategy, and minimum of 1 specific peptide per identified protein group. Proline was then used to perform compilation, grouping, and comparison of the protein groups and phosphosites identified in the different samples.…”

“…Extracted peptides were submitted to reversed-phase nanoLC coupled to tandem MS using a high-resolution hybrid quadrupole orbitrap. Data were processed using Mascot [36] and Proline [37], allowing identification of 73 viral proteins (67 in the three replicates, and three each in two and one replicates), representing the highest number of viral proteins identified in purified HCMV virions. In total, 82 different viral proteins were identified in purified HCMV virions by these four studies using MS-based proteomics (Figure 2, Supplementary Table S1).…”

Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy

“…Protein modifications were fixed carbamidomethylation of cysteines, variable phosphorylation of serine and threonine, variable oxidation of methionine and variable acetylation of protein N-terminus. Proline software was used for the validation and the label-free quantification of identified proteins in each sample (http://proline.profiproteomics.fr/) [47]. Mascot identification results were imported into Proline.…”

Proteomic Analysis of Two Weight Classes of Mule Duck “foie gras” at the End of an Overfeeding Period

“…It was set to 0.8 Da for fragment ions in CID mode (detection in the ions trap). Validation of identifications was performed through a false-discovery rate set to 1% at protein and peptide-sequence match level determined by target-decoy search using the in-house-developed software Prolinesoftware version 1.6 3 (Bouyssié et al, 2020). Raw MS signal extraction of identified peptides was performed with Proline across different samples.…”