Table 1.
Commonly used software packages for peptide and protein identification.
| Category | Name | Description |
|---|---|---|
| Database search algorithms | Andromeda [18] | Probabilistic scoring-based peptide search engine integrated in MaxQuant. |
| Mascot [17] | Probability-based database searching algorithm. | |
| MSPLIT-DIA [19] | Sensitive Peptide Identification for Data Independent Acquisition. | |
| MudPIT [20] | Multidimensional protein identification. | |
| PepArML [21] | An Unsupervised, Model-Free, Machine-Learning Combiner for Peptide Identifications from Tandem Mass Spectra. | |
| PepHMM [22] | A hidden Markov model-based scoring function for mass spectrometry database search. | |
| Protein Prospector [23] | An integrated framework of about twenty proteomic analysis tools. | |
| SEQUEST [24] | An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database | |
| TopPIC [25] | A software tool for top-down mass spectrometry-based complex proteoforms identification. | |
| X!Tandem/X!!Tandem [12,26] | An open source software that search tandem mass spectra with peptide sequences in database. | |
| De novo peptide sequencing | DeepNovo-DIA [27] | De novo peptide sequencing by deep learning. |
| EigenMS [28] | De novo Analysis of Peptide Tandem Mass Spectra. | |
| NovoHMM [29] | A hidden Markov model for de novo peptide sequencing. | |
| PEAKS [30] | A fast de novo sequencing tool. | |
| PECAN [31] | Library Free Peptide Detection for Data-Independent Acquisition Tandem Mass Spectrometry Data. | |
| PepNovo [14] | De novo peptide sequencing via probabilistic network modeling. | |
| pNovo 3 [32] | A software for precise de novo peptide sequencing using a learning-to-rank framework. | |
| SHERENGA [13] | De novo peptide sequencing via tandem mass spectrometry. | |
| SWPepNovo [33] | An Efficient De Novo Peptide Sequencing Tool for Large-scale MS/MS Spectra Analysis. | |
| UniNovo [34] | A universal de novo peptide sequencing algorithm with a modified offset frequency function. | |
| Hybrid identification approach | ByOnic [35] | A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. |
| DirecTag [36] | Accurate sequence tags from peptide MS/MS with statistical scoring method. | |
| InsPecT [37] | A software for identification of peptides posttranslational modification (PTM) from tandem mass spectra. | |
| JUMP [38] | A tag-based database search tool for peptide identification. | |
| PEAKS DB [39] | A hybrid de novo sequencing tool run in parallel with database search. | |
| ProteomeGenerator [40] | A hybrid framework for based on de novo transcriptome assembly and database matching. | |
| Other software related to protein/PTM identification | DBParser [41] | Web-based software for shotgun proteomic data analyses. |
| DIA-Umpire [42] | Comprehensive computational framework for data independent acquisition proteomics. | |
| MassSieve [43] | Panning MS/MS peptide data for proteins. | |
| MAYU [44] | A novel strategy that reliably estimates false discovery rates for protein identifications in large-scale datasets. | |
| ModifiComb [45] | Mapping substoichiometric post-translational modifications. | |
| Nokoi [46] | A decoy-free approach for improved peptide identification accuracy | |
| Param-Medic [47] | A strategy for inferring optimal search parameters for shotgun proteomics analysis. | |
| Perseus [48] | Platform for comprehensive analysis of proteomics data. | |
| PROVALT [49] | A heuristic method for computing false discovery rate (FDR) for protein identifications. | |
| MetaMorpheus [50] | Enhanced Global Post-translational Modification Discovery. | |
| PTMselect [51] | Optimization of protein modifications discovery by mass spectrometry. |