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ProteinPilot specifications


Unique identifier OMICS_30176
Name ProteinPilot
Software type Application/Script
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Windows
Computer skills Medium
Version 5.0.1
Stability Stable
Free trial Yes
Registration required Yes
Maintained Yes


  • Paragon
  • Pro Group


No version available



  • person_outline Sean Seymour

Publication for ProteinPilot

ProteinPilot citations


A new inhibitor of glucose 6 phosphate dehydrogenase blocks pentose phosphate pathway and suppresses malignant proliferation and metastasis in vivo

PMCID: 5951921
PMID: 29760380
DOI: 10.1038/s41419-018-0635-5

[…] ws (optimized on an IDA datafile of the same samples) of 25 ms between 100 and 1500 m/z giving a cycle time of 2.6 s.A spectral library for SWATH data extraction was constructed using the output from ProteinPilot 5.0 (Sciex) searching against the Swissprot Human database (January 2015) with the addition of iRT peptides to the. fasta file, combining eight IDA runs (pooled samples) and filtered and […]


Region of Interest analysis using mass spectrometry imaging of mitochondrial and sarcomeric proteins in acute cardiac infarction tissue

Sci Rep
PMCID: 5945593
PMID: 29748547
DOI: 10.1038/s41598-018-25817-7
call_split See protocol

[…] arch parameters: taxonomy = Homo sapiens; database = SwissProt; MS tolerance = 0.2 Da; MS/MS tolerance = 0.3 Da; enzyme = trypsin; missed cleavage = 1. Peptides and proteins were identified using the Paragon algorithm provided with ProteinPilot 4.5 Beta (AB SCIEX, Danaher Corporation, Washington, D.C.) combined with the UniProt-Swiss-Prot database (version 2010-6, Homo sapiens) and sequences of th […]


Exosome markers associated with immune activation and oxidative stress in HIV patients on antiretroviral therapy

Sci Rep
PMCID: 5940833
PMID: 29740045
DOI: 10.1038/s41598-018-25515-4

[…] kings/Dionex nanoflow LC, and mass spectrometry was done on an ABSciex 4800Plus MALDI-TOF/TOF mass spectrometer. For peptide mapping and protein identification, database searches were performed using ProteinPilot 4.5b (ABSciex, Framingham, MA). Protein identifications with at least 95% confidence as determined by ProteinPilot were considered significant. In experiments using the second mass spectr […]


Two independent proteomic approaches provide a comprehensive analysis of the synovial fluid proteome response to Autologous Chondrocyte Implantation

PMCID: 5932832
PMID: 29720234
DOI: 10.1186/s13075-018-1573-4

[…] d in the quantitative analysis if they were identified with two or more unique peptides with 95% confidence or above. p Values and false discovery rates for the iTRAQ ratios were calculated using the ProteinPilot software. Proteins with iTRAQ ratios with p values ≤ 0.05 and with differential abundance of greater than or equal to ± 2.0-fold change (FC) were used in further analysis. […]


A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing

Nat Commun
PMCID: 5923290
PMID: 29703894
DOI: 10.1038/s41467-018-04132-9

[…] p809 KO MEFs (Fig. ). In the PBS-pro VL30 group, both Setdb1 and Zfp809 KO MEFs showed derepression of VL30 (Fig. ); however, derepression in the Setdb1 KO was less prominent than that in the non-PBS-pro group, as shown in Fig. . These results indicate that ERVs possessing non-PBS-pro escape repression by Zfp809, but are targeted by other silencing factors that can recruit Setdb1. Zfp809 is requir […]


Influence of Major Coping Strategies on Treatment Non adherence and Severity of Comorbid Conditions in Hemodialysis Patients

PMCID: 5944213
PMID: 29760606
DOI: 10.3346/jkms.2018.33.e148

[…] the CKD etiology. The mean duration of CKD was 104.3 ± 11.0 months, and the mean duration of hemodialysis was 73.3 ± 9.8 months. Based on the major SC reported, seven participants (14.3%) were in the PRO group, 12 (24.5%) were in the SUP group, and 30 (61.2%) were in the HOP group. No participants reported mainly using emotion-focused CSs. […]

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ProteinPilot institution(s)
Applied Biosystems/MDS Sciex, Foster City, CA, USA

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