News and Updates

New publication: "Prosit"05/27/2019

Prosit: Proteome-wide prediction of peptide tandem mass spectra by deep learning

We are very excited to present the latest progress in the ProteomeTools project termed "Prosit".

Prosit (https://www.proteomicsdb.org/prosit/) is a deep learning framework that offers free and easy generation of custom spectral libraries using  very high quality predicted HCD MS2 spectra for any organism and protease as well as iRT prediction. Prosit is part of the ProteomeTools project and was trained on the project's high quality synthetic datasets.

Abstract: In mass spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily relies on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we extended the ProteomeTools synthetic peptide library to 550k tryptic peptides and 21M high quality tandem mass spectra. We trained a deep neural network, termed Prosit, resulting in chromatographic retention time and fragment ion intensity predictions that exceed the quality of the experimental data. Integrating Prosit into database search pipelines led to more identifications at >10x lower false discovery rates. We show the general applicability of Prosit by predicting spectra for other proteases, generating spectral libraries for data independent acquisition, and improving the analysis of metaproteomes. Integration into ProteomicsDB allows search result re-scoring and custom spectral library generation for any organism based on peptide sequence alone.

Read the article at publisher's

Read the TUM press release

Access Prosit via ProteomicsDB.org/prosit

ProteomeTools @ ASMS 2019 Conference
05/02/2019
Annual meeting of the American Society for Mass Spectrometry

The ProteomeTools team will be present at the ASMS 2019 Conference in Atlanta  (GA, USA), June 2nd to 6th. We are looking forward to presenting new developments and to discussing the project.

Join us for the following presentations:

Oral:

“Library-Free” DIA Analysis: Using Proteome-Wide in-silico Generated Spectral Libraries byProsit for DIA Data Analysis

T. Schmidt, Tuesday TOA pm 02:50, INFORMATICS: DATA-INDEPENDENT ACQUISITION Session

ProteomeTools: Exploiting the Largest Collection of Synthetic Peptides Carrying Biologically Relevant Post-Translational Modifications for Proteome Research

D. P. Zolg, ThOC am 09:10, POST-TRANSLATIONALMODIFICATIONS:QUALITATIVE&
QUANTITATIVE ANALYSIS Session

 

Poster:

Prosit: Investigating Vast and Complex Peptide Spaces by Boosting Identification Confidence through Highly-Accurate Fragment Intensity Predictions

S. Gessulat, Monday Poster MP 383

Extending the Scope of Prosit: Accurate Fragment Ion Intensity and Retention Time Prediction for (Un)Modified (Non-)Tryptic Peptides

M. Wilhelm, Wednesday Poster WP 398

 

Usermeetings and Workshops:

PROSIT for Deep Learning-based Prediction of Mass Spectra

S. Gessulat, Thermo Scientific Proteome Discoverer Software Workshop, Saturday June 1st (link)

Using Prosit for PRM assay development and optimization

T. Schmidt, Skyline User Meeting at ASMS 2019, Sunday 2nd June (link)

For abstracts and additional information, please refer to the ASMS 2019 Final Program.

ProteomeTools content presented on ASMS 2018
07/09/2018

Reprints of ProteomeTools content:

We are happy to provide access to posters presented on ASMS 2018 in San Diego:

  • "Prosit: Deep learning enables proteome wide prediction of peptide tandem mass spectra with high accuracy" - download
  • "ProteomeTools: Systematic characterization of 21 post-translational protein modifications by LC-MS/MS using synthetic peptides" - download -  PMID 2984878
  • "ProteomicsDB: A source for high quality spectral libraries and an auxiliary tool for the development of targeted assays" - download

In case you have been attending ASMS, you can watch the webcast of the two oral contributions on the ASMS webcast website:

 
New Research Article
05/30/2018
ProteomeTools: Systematic characterization of 21 post-translational protein modifications by LC-MS/MS using synthetic peptides

We are happy to present our newest study on modified peptides:

"To more broadly understand the LC-MS/MS characteristics of PTMs, we synthesized and analyzed ~5,000 peptides representing 21 different naturally occurring modifications of lysine, arginine, proline and tyrosine side chains and their unmodified counterparts. The analysis identified changes in retention times, shifts of precursor charge states and differences in search engine scores between modifications. PTM-dependent changes in the fragmentation behavior were evaluated using eleven different fragmentation modes or collision energies. We also systematically investigated the formation of diagnostic ions or neutral losses for all PTMs, confirming 10 known and identifying 5 novel diagnostic ions for lysine modifications."

Read article at publishers.

ProteomeTools @ ASMS 2018 Conference
04/30/2018
Annual meeting of the American Society for Mass Spectrometry

The ProteomeTools team will be present at the ASMS 2018 Conference in San Diego (CA, USA), June 3rd to 7th. We are looking forward to presenting new developments and to discussing the project.

Join us for the following presentations:

Talks:

  • Using Synthetic Peptides from the ProteomeTools Project to Estimate FDR in HLA-Datasets
    M. Wilhelm et al,, Monday MOG 09:30 a.m. in the INFORMATICS: INNOVATIONS session.

  • ProteomeTools: Progress on the Generation of Reference Peptides and Spectra for the Human Proteome
    D. P. Zolg et al., Wednesday WOG 10:10 a.m. in the INFORMATICS: PEPTIDE AND PROTEIN DENTIFICATION, PROTEOMICS session

Poster:

  • PROSIT: Deep Learning Enables Proteome WidePredicti on of Peptide Tandem Mass Spectra with High Accuracy
    S. Gessulat et al., Tuesday TP354

  • ProteomicsDB: A Source for High-Quality Spectral Libraries and an Auxiliary Tool for the Development of Targeted Assays
    T. Schmidt et al., Monday MP356

  • Systematic Characterization of the Chromatographic and Mass Spectrometric Properties of 21 Post-Translational Modifications Using Synthetic Peptides
    D.P. Zolg et al., Wednesday WP619

     

For abstracts and additional information, please refer to the ASMS 2018 Final Program.

New Research Article
02/04/2018

Mining the human tissue proteome for protein citrullination.

We are happy to present a research paper the ProteomeTools project contributed to:

" Citrullination is a post-translational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss of a positive charge may cause structural or functional alterations and while the modification has been linked to several diseases including rheumatoid arthritis and cancer, its physiological or pathophysiological roles remain largely unclear. In part this is owing to limitations in available methodology able to robustly enrich, detect and localize the modification. In this study, we mined data from mass spectrometry-based deep proteomic profiling of 30 human tissues to identify citrullination sites on endogenous proteins. Because citrullination is easily confused with deamidation, we synthesized ~2,200 citrullinated and 1,300 deamidated peptides to build a library of reference spectra. This led to the validation of 375 citrullination sites on 209 human proteins. Further analysis showed that >80% of the identified modifications sites were new and for 56% of the proteins, citrullination was detected for the first time."

Read the article at publishers

DOI:10.1074/mcp.RA118.000696
New Research Article
09/09/2017

PROCAL: A set of 40 peptide standards for retention time indexing, column performance monitoring and collision energy calibration.

We are happy to present PROCAL, a peptide standard developed withing the ProteomeTools project:

"We describe PROCAL (ProteomeTools Calibration Standard), a set of 40 synthetic peptides that span the entire hydrophobicity range of tryptic digests, enabling not only accurate determination of retention time indices but also monitoring of chromatographic separation performance over time. The fragmentation characteristics of the peptides can also be used to calibrate and compare collision energies between mass spectrometers."

Read article at publishers.

DOI: 10.1002/pmic.201700263

PROCAL peptides can be obtained at jpt.com

ProteomeTools @ HUPO 2017, Dublin, Ireland
09/01/2017
HUPO 2017 | 16th Human Proteome Organisation World Congress

The ProteomeTools team will be present at the 16th Human Proteome Organisation World Congress (HUPO), Sept 17th to 21st. We are looking forwards to discussing the project. 

Poster ID: 465
Abstract Title: Building ProteomeTools based on a complete synthetic human proteome
Date: TBA
Conference Website
ProteomeTools ASMS 2017 Conference
04/25/2017
Annual meeting of the American Society for Mass Spectrometry

The ProteomeTools team will be present at the ASMS 2017 Conference in Indianapolis (IN, USA), June 4nd to 8th. We are looking forwards presenting new developments and to discussing the project.

ProteomeTools @ Proteomic Forum 2017 Conference
03/13/2017
Annual meeting of the German Society for Proteome Research

The ProteomeTools team will be present at the Proteomic Forum 2017 Conference in Potsdam (Germany), April 2nd to 5th. We are looking forwards to discussing the project. 

Poster ID: P050
 Abstract Title: Building ProteomeTools based on a complete synthetic human proteome
 Poster Category: Mass Spectrometry Technologies
 Poster Session: Poster Session B
 Poster Session date: Monday, 3 April 2017
 Poster Session time: 15:00-16:30
Conference Website
News and Views about ProteomeTools
02/28/2017
Synthetic human proteomes for accelerating protein research

The ProteomeTools project and other efforts to cover the human proteome with synthetic peptides standards are featured in a News and Views article in Nature Methods.

Read article in Nature Methods

ProteomeTools' first paper published in Nature Methods01/30/2017

Building ProteomeTools based on a complete synthetic human proteome.

"We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquid chromatography–tandem mass spectrometry analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products, and we exemplify the utility of these data in several applications. The resource (available at www.proteometools.org) will be extended to >1 million peptides, and all data will be shared with the community via ProteomicsDB and ProteomeXchange."

Read article for free at Nature Methods

DOI 10.1038/nmeth.4153