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MassSieve specifications


Unique identifier OMICS_09162
Name MassSieve
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Douglas J. Slotta

Publication for MassSieve

MassSieve citations


Proteomic analysis of the human retina reveals region specific susceptibilities to metabolic and oxidative stress related diseases

PLoS One
PMCID: 5821407
PMID: 29466423
DOI: 10.1371/journal.pone.0193250

[…] s were searched using OMSSA with precursor mass tolerance settings of +/- 20 ppm, product ions mass tolerance of +/- 1.5 Da, and fragment settings of +/- 0.5 Da []. XML output files were parsed using MassSieve (NIH). A minimum peptide length of 6 amino acids was used for protein matches. Proteins were required to have 2 or more unique peptides with E-value scores of 0.01 or less. Relative quantita […]


Myocilin Regulates Metalloprotease 2 Activity Through Interaction With TIMP3

PMCID: 5644706
PMID: 29049729
DOI: 10.1167/iovs.16-20336

[…] sed cluster compute instances using the Proteome Cluster interface (, in the public domain). XML output files were parsed and nonredundant protein sets determined using MassSieve (, in the public domain). Proteins were required to have two or more unique peptides across the analyzed samples with E value scores of 0. […]


The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling

J Extracell Vesicles
PMCID: 4169610
PMID: 25317274
DOI: 10.3402/jev.v3.24858
call_split See protocol

[…] 5). Peptides with ion scores below their identity scores were rejected. MASS SIEVE was used to calculate percentage coverage for each protein identification ( Peptide identifications from 1 representative experiment are shown. […]


Integrating Genomic, Transcriptomic, and Interactome Data to Improve Peptide and Protein Identification in Shotgun Proteomics

J Proteome Res
PMCID: 4059263
PMID: 24792918
DOI: 10.1021/pr500194t

[…] oduces a statistically significant peptide-spectrum match (PSM) score. Finally, identified peptides are transformed into a list of identified proteins through protein assembly tools such as IDPicker, MassSieve, or ProteinProphet, among others.Although this strategy has been successful, there are several critical challenges that cannot be fully addressed by simply improving database searching and p […]


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MassSieve institution(s)
Laboratory of Neurotoxicology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA

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