Validation of MS/MS Identifications and Label-Free Quantification Using Proline

In the proteomics field, the production and publication of reliable mass spectrometry (MS)-based label-free quantitative results is a major concern. Due to the intrinsic complexity of bottom-up proteomics experiments (requiring aggregation of data relating to both precursor and fragment peptide ions into protein information, and matching this data across samples), inaccuracies and errors can occur throughout the data-processing pipeline. In a classical label-free quantification workflow, the validation of identification results is critical since errors made at this first stage of the workflow may have an impact on the following steps and therefore on the final result. Although false discovery rate (FDR) of the identification is usually controlled by using the popular target-decoy method, it has been demonstrated that this method can sometimes lead to inaccurate FDR estimates. This protocol shows how Proline can be used to validate identification results by using the method based on the Benjamini-Hochberg procedure and then quantify the identified ions and proteins in a single software environment providing data curation capabilities and computational efficiency.

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

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.