"MiCId" refers to Microorganism Classification and Identification, a software tool used for identifying microorganisms and their antibiotic resistance (AMR) proteins. It utilizes mass spectrometry data (MS/MS spectra) and offers a graphical user interface (GUI) for ease of use. MiCId also provides biomass estimation and is computationally efficient.
MiCId modes and parameters: (click on to start)
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Pathogen Id New Job | Upload a spectra file and run a pathogen identification job. |
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Taxonomy | Check or exclude the organisms from consideration in the selected database. |
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Target DB | Create and edit a database of target organisms. |
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PTMs/TMT | Select the set of novel post-translational modifications (PTMs) and specify the tandem mass tag (TMT) parameters for the sample. |
References:
1. Alves G, Ogurtsov AY, Yu YK (2025) Biological Function Assignment Across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm. J Proteome Res, 24(8): 3818-3832.
Link to the paper
2. Alves G, Ogurtsov AY, Porterfield H, Maity T, Jenkins LM, Sacks D, and YKY (2024) Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm. J Am Soc Mass Spectrom, 35(6): 1138-1155.
DOI: 10.1021/jasms.3c00445
3. Ogurtsov A, Alves G, Rubio A, Joyce B, Andersson B, Karlsson R, Moore ERB, Yu YK (2024) MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall. J Comput Biol, 31: 175-178.
PMID: 38301204
DOI: 10.1089/cmb.2023.0149
4. Alves G, Ogurtsov A, Karlsson R, Jaén-Luchoro D, Piñeiro-Iglesias B, Salvà-Serra F, Andersson B, Moore ERB, Yu YK (2022) Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach. J Am Soc Mass Spectrom, 33: 917-931.
DOI: 10.1021/jasms.1c00347
5. Alves G, Yu YK (2020) Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 31: 85-102.
PMID: 32881514
DOI: 10.1021/jasms.9b00035
6. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Sacks DB, Yu YK (2018) Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 29: 1721-1737.
PMID: 29873019
DOI: 10.1007/s13361-018-1986-y
7. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Suffredini AF, Sacks DB, Yu YK (2016) Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. J Am Soc Mass Spectrom, 27: 194-210.
PMID: 26510657
DOI: 10.1007/s13361-015-1271-2
8. Alves G, Yu YK (2015) Mass spectrometry-based protein identification with accurate statistical significance assignment. Bioinformatics, 31: 699-706.
PMID: 25362092
DOI: 10.1093/bioinformatics/btu717
Link to the paper
2. Alves G, Ogurtsov AY, Porterfield H, Maity T, Jenkins LM, Sacks D, and YKY (2024) Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm. J Am Soc Mass Spectrom, 35(6): 1138-1155.
DOI: 10.1021/jasms.3c00445
3. Ogurtsov A, Alves G, Rubio A, Joyce B, Andersson B, Karlsson R, Moore ERB, Yu YK (2024) MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall. J Comput Biol, 31: 175-178.
PMID: 38301204
DOI: 10.1089/cmb.2023.0149
4. Alves G, Ogurtsov A, Karlsson R, Jaén-Luchoro D, Piñeiro-Iglesias B, Salvà-Serra F, Andersson B, Moore ERB, Yu YK (2022) Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach. J Am Soc Mass Spectrom, 33: 917-931.
DOI: 10.1021/jasms.1c00347
5. Alves G, Yu YK (2020) Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 31: 85-102.
PMID: 32881514
DOI: 10.1021/jasms.9b00035
6. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Sacks DB, Yu YK (2018) Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 29: 1721-1737.
PMID: 29873019
DOI: 10.1007/s13361-018-1986-y
7. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Suffredini AF, Sacks DB, Yu YK (2016) Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. J Am Soc Mass Spectrom, 27: 194-210.
PMID: 26510657
DOI: 10.1007/s13361-015-1271-2
8. Alves G, Yu YK (2015) Mass spectrometry-based protein identification with accurate statistical significance assignment. Bioinformatics, 31: 699-706.
PMID: 25362092
DOI: 10.1093/bioinformatics/btu717
Relevant group publications:
1. Jenson SC, Chu F, Alves G, Ogurtsov AY, Barente AS, Crockett DL, Lamar NC, Merkley ED, Yu YK, Jarman KH (2025) MARLOWE: Taxonomic Characterization of Unknown Samples for Forensics Using De Novo Peptide Identification. bioRxiv: the preprint server for biology, 20240930615220: 1-35.
DOI: 10.1101/2024.09.30.615220
2. Sénécaut N, Alves G, Weisser H, Lignières L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM (2021) Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. J Proteome Res, 20: 1476-1487.
PMID: 33573382
DOI: 10.1021/acs.jproteome.0c00478
3. Alves G, Yu YK (2020) Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 31: 85-102.
PMID: 32881514
DOI: 10.1021/jasms.9b00035
4. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Sacks DB, Yu YK (2018) Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 29: 1721-1737.
PMID: 29873019
DOI: 10.1007/s13361-018-1986-y
DOI: 10.1101/2024.09.30.615220
2. Sénécaut N, Alves G, Weisser H, Lignières L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM (2021) Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. J Proteome Res, 20: 1476-1487.
PMID: 33573382
DOI: 10.1021/acs.jproteome.0c00478
3. Alves G, Yu YK (2020) Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 31: 85-102.
PMID: 32881514
DOI: 10.1021/jasms.9b00035
4. Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Sacks DB, Yu YK (2018) Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry. J Am Soc Mass Spectrom, 29: 1721-1737.
PMID: 29873019
DOI: 10.1007/s13361-018-1986-y